Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites

31 32 Interactions between b acteria, bacteriophages , and their satellites are shaped by a 33 myriad of defence and counter-defence mechanisms. Here, we identified and 34 characterized the defence hotspots of thousands of P2-like phages and P4-like satellites 35 to elucidate the origins and evolutionary dynamics of defence systems. Both P4 and P2 36 encode a broad diversity of recognizable defence systems. Defences are a substantial, 37 yet likely underestimated, share of the elements’ pangenomes, as shown by novel 38 antiviral functions discovered in P4 loci lacking known defence genes. Defence loci are 39 very rapidly swapped , without pseudogenization, suggesting defences are replaced 40 before becoming non-adaptive. This intense local recombination melds components of 41 distinct systems into novel functional chimeras. Systems swap so rapidly that many 42 elements with identical core genes have completely diYerent defences. Surprisingly, 43 despite P4 and P2’s concomitant replication and packaging, they almost never exchange 44 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint defence genes. In contrast, near identical defence systems can be found in distinct types 45 of MGEs and in cryptic chromosomal locations. Our findings highlight P4 and P2 as 46 mobile platforms driving the modular diversification of bacterial antiviral repertoires. 47 Hence, bacterial defences change quickly by phage and satellite turnover , and by the 48 quick swap of defences within these elements. 49 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint

50 51 Microbial ecosystems are shaped by complex interactions between bacteria and 52 bacteriophages (phages). These interactions range from the direct antagonism between 53 virulent phages and bacteria1 to the more nuanced continuum between antagonism and 54 commensalism of temperate phages and their hosts, where the interests of both bacteria 55 and phage can be aligned 2,3. One key example of the latter is the presence of antiviral 56 defences in prophages, which protect their host bacteria from predation by other phages, 57 thus ensuring the survival of both4,5. Prophages are not the only mobile genetic elements 58 (MGEs) that provide antiviral functions to their hosts. Anti-MGE defence systems are 59 frequently encoded by MGEs present in bacterial genomes6, possibly because of 60 competition, and/or cooperation, between MGEs7. This is exemplified by phage satellites, 61 non-autonomous mobile elements (hitchers) that hijack (helper) phages to mobilize 62 between bacteria 8,9. S ome P4-like satellites encode antiviral defences against 63 competitors of P2-like helper phages, protecting both helper and bacterial host10. Hence, 64 the associations between satellites, phages and bacteria evolve in a mutualism -65 parasitism continuum, where partners incur in costs and benefits associated with the 66 presence of the other elements8. 67 68 The diversity of known defence systems is rapidly increasing. Defence genes have one of 69 the highest rates of gain/loss across bacterial genomes 11, and i n bacteria, the ir 70 acquisition is typically associated with the mobility of the MGEs carrying them12. But little 71 is known about the evolutionary dynamics of defence genes in MGEs themselves. Where 72 do these genes come from, and how stable are they? What is the fate of these genes, and 73 that of the MGEs carrying them, once defences are no longer useful? These questions are 74 intricately linked not only with the ecology of MGEs (who is defending whom, when and 75 against what), but also with the ir genomic organization, which for some elements like 76 phages and satellites, can be tightly conserved9,13,14. The accumulation of accessory 77 genes in phages is constrained by the size of their genomes , which must fit within their 78 capsids15, and the very modular genomic organization of both satellites and phages 9,14. 79 Although prophages often have accessory genes useful to their bacterial hosts, their high 80 gene density suggests they rarely have pseudogenes and is thought to explain the low 81 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint frequency of transposable elements in their genomes , in contrast with plasmids 16. 82 Hence, the systematic detection of defence genes in prophages and satellites reflects 83 the selective importance of these functions for their ecology and evolution. At a broader 84 level, understanding the prevalence, localization and evolutionary dynamics of antiviral 85 genes can highlight the rules that govern the genomic plasticity and genomic organization 86 of MGEs, as well as their ecological associations and interactions with bacterial hosts 87 and with other MGEs. 88 89 Several defence systems were previously detected in P2-like phages and P4-like 90 satellites, in a single hotspot near the cos site of each element 10. Here, we delimit 91 satellite and phage genomes to identify additional hotspots and to account for MGE 92 similarity when studying the evolutionary dynamics of antiviral genes within and across 93 P4 satellites and P2 helpers. To extend the diversity of our dataset, w e coupled the 94 detection and precise delimitation of thousands of P4 -like satellites 17 and P2-like 95 prophages in complete bacterial genomes with thousands of additional P4-like satellites 96 detected in metagenomes to generate the most abundant and diverse genomic 97 collection of satellites and helper phages to date. The extensive dataset of P4 and P2 98 genomes allowed to uncover the quick turnover of defence genes encoded by P4 and P2, 99 the genetic exchanges that underly this turnover , and how they shape defen ce 100 repertoires. 101 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint

102 103 Defence systems’ loci are pervasive in a few hotspots of P2 and P4 104 105 We identified the P2 -like prophages (P2 for short) and P4-like satellites (P4 for short) in 106 the complete genomes of Escherichia coli, Klebsiella pneumoniae, Salmonella enterica. 107 We also used the P4-like contigs detected in Logan, a repository of assembled sequence 108 data from tens of millions of public sequencing experiments 18, which greatly expanded 109 the number and genomic diversity of known P4 satellites (Fig S1, see Methods). The 3085 110 P4 (from complete bacterial genomes and metagenomes) and 1511 P2 (from complete 111 bacterial genomes) elements in our dataset were dereplicated and genetically delimited 112 at the nucleotide level by identification of their att sites (see Methods). We then identified 113 the defence system s in P4 and P2 using DefenseFinder19 and PADLOC20. We also 114 searched for anti-defence systems, for which we only find two types (Anti_RM and 115 Anti_CRISPR) distributed in 28 P2. Most of these P2 have a single anti-antiviral system, 116 but one has five distinct systems. We detected no anti-defence systems in P4. Given the 117 low numbers of these anti-defence systems, we decided to exclude them from the main 118 analysis. 119 120 We found a very broad diversity of known types of defence systems, which occurred in 121 57% of P4 and in 49% of P2 (Fig 1A and B, Fig S2A for PADLOC classification). Some types 122 of systems were detected in both satellites and phages (e.g., AbiU or PD-T7-2), whereas 123 others were found in only one of them (e.g., AbiP2 in P2 and Hachiman in P4 ). We also 124 identified individual genes that are usually associated with defence systems, but that do 125 not form a complete known system (see the two rightmost columns in Fig 1A for systems 126 that were partially detected by DefenseFinder). We will refer to these as putative defence 127 systems and will explore them in more detail in a subsequent section. If we include both 128 complete and putative systems, the proportion of elements that encode defence -129 associated genes increases to 73% (P4) and 81% (P2) (Fig 1B). Hence, a large majority of 130 these two types of MGEs encode genes associated with antiviral activity. 131 132 Even if this is by far the largest known dataset of P4 and P2, the pangenome saturation 133 curves show that we are far from having uncovered the full genetic diversity of these 134 elements (Fig 1C ). Known defence genes correspond to a sizeable fraction of the se 135 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint pangenomes (orange lines): 34% for P4 and 17% for P2. P4 and P2 account for 11-16% of 136 the genetic diversity of the defence systems in their hosts’ species (Fig S3). Moreover, up 137 to 50% of the total defence systems of some genomes are encoded in their P4 or P2 138 elements (Fig 1D, Fig S4). This suggests that P4 and P2 are important contributors to the 139 defence repertoire of bacteria. 140 141 Most defence systems in P4 are in a hotspot between the integrase and Psu -Delta-Sid, 142 whilst many of the defence systems in P2 are in a hotspot between the primase (GpA) and 143 the portal (GpQ) (Fig 1E). These are the two previously described hotspots 10. However, 144 other less populated defence hotspots exist between the primase and one of the att sites 145 of P4 ( 7% of the systems in P4), between the integrase and the att site of P2 ( 3% of the 146 systems in P2), between the integrase and the primase in P2 ( 8% of the systems in P2) 147 and within the late genes of P2. Although it is atypical for integrated elements to mobilize 148 genes between att sites and the integrase, this was previously observed for defence 149 systems of PICI21. An additional P2 defence hotspot was found downstream of GpL (16% 150 of the systems in P2) , consistent with previous descriptions of a hotspot of accessory 151 genes within the tail genes in the classical P2 phage 22. Moreover, some of these P2 152 defence hotspots correspond to known integration sites of horizontally transferred genes 153 in P223, and to the hotspots of accessory genes described recently in more than 1000 P2-154 like phages24. In either P4 or P2, some defence systems were consistently found in a 155 single hotspot, whilst others were found across genomic locations of the elements (Fig 156 S5A). Of the P2 with complete defence systems, 10% have multiple defence systems 157 across diYerent hotspots (Fig S2C, see also genomes in Fig 1E for examples). This fraction 158 is much lower for P4 (1%), suggesting that the accumulation of multiple defence systems 159 occurs more often in the larger genomes of P2. These results confirm that whilst defence 160 systems are very abundant and diverse in P4 and P2, representing a large fraction of their 161 accessory genes, they are encoded in a small number of genomic locations. 162 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 163 164 Figure 1. Abundance, distribution and localization of defence systems in P4-like satellites and in P2-165 like prophages. A. Number of the di_erent types of complete (two leftmost columns) and putative (two 166 rightmost columns) defence systems detected by DefenseFinder in P4 (1st and 3rd column) and P2 (2nd and 167 4th column). Darker colours in the heatmap correspond to higher numbers of systems. B. The proportion of 168 P4 and P2 elements with defence systems deemed complete (orange, as detected by DefenseFinder or 169 Lit 343128169521721172732381161517124421431431126443019221123423996111437312172934247322151142061241538111114351322111578672078202625121816571933591382313541135217111554111141276512268349898611140605213835284510357128136392714161910112028172212434104100412112 AbiGAbiHAbiJAbiP2AbiUAll_UGAvsBelisamaButters_gp30_gp31CBASSCoCoNutCRISPRDarTGDazbogdCTPdeaminaseDndDpdDRTDRT_3Druantia_IIDS-12BDS-13DS-14DS-15DS-16DS-18DS-20DS-21DS-22DS-23DS-25DS-27DS-29DS-32DS-34DS-37DS-39DS-4DS-40DS-43DS-44DS-5DS-7DS-9DsrEleosFS_GIY_YIGFS_HPFS_HsdR_likeGabijaGao_ApeGao_HerGao_IetGao_PplGAPS1GAPS4GAPS6gcu142gcu24HachimanHEC-01HEC-03HEC-04HEC-07HnaKiwaLamassu-FamMenshenNLROgmiosOld_exonucleasepAgoParisParis_IParis_IIPD-Lambda-1PD-Lambda-2PD-Lambda-4PD-Lambda-5PD-T4-10PD-T4-2PD-T4-8PD-T4-9PD-T7-1PD-T7-2PD-T7-3PD-T7-5PifPycsarRetronRetron_VII_2RexABRloCRMRM_Type_IIRM_Type_IIIRM_Type_IVRosmerTARst_2TM_1TM_TIRRst_3HPRst_DUF4238Rst_gop_beta_cllRst_HelicaseDUF2290Rst_Hydrolase-3TmRst_RT-nitrilase-TmRst_TIR-NLRSEFIRSeptuSheduShosTASironaSspBCDESucellosThoerisThoeris_IThoeris_IVTIR-IVToutatisWadjet # of systems Defence system % of elementsTotal defence systems in host >200 A B D E P4 P2 C 1 P4 with system P2 with system P4 with putative P2 with putative P4 P2 0 20 40 60 80 100 27% 19% 16% 32% 57% 49% No Detected Defence Systems With Putative Defence Systems With Defence Systems 0 1000 2000 3000 # of P4 elements Total gene families Defence-associated gene families P4 core gene families 0 200 400 600 800# of new gene families 0 500 1000 1500 # of P2 elements 0 500 1000 1500# of new gene families 0.0 0.2 0.4 0.6 0.8 1.0 10 20 30 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 Hosts with P4 Hosts with P2 Hosts with P4 or P2 Int Int Psu Delta Sid AlpA Ash Alpha 93% 62% 16% 7% 8% 3% 3%8% gpQ gpP gpO gpN gpM gpLgpA Att Att Att Att 2.5kb 2.5kb Proportion in P4 Proportion in P2 Proportion in P4 or P2 Total gene families Defence-associated gene families P2 core gene families .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint PADLOC) or putative (light orange, detected by DefenseFinder). C. The pangenome (black) of P4-like 170 satellites (top) and P2-like phages (bottom) with the relative contributions of the core (blue for P4, red for 171 P2) and the defence-associated genes (orange). D. Fraction of systems (detected by DefenseFinder) of the 172 host encoded in its P4 and P2 elements. The proportions of complete defence systems encoded by P4 in 173 hosts that have at least one P4 (leftmost panel), encoded by P2 in hosts that have at least one P2 (middle 174 panel), or encoded either by P4 or P2 in hosts that have at least one of either element (rightmost panel) are 175 shown in the x-axis. The size of the circles corresponds to the frequency of each (x,y) pair. E. Distribution 176 of defence systems in hotspots of P4-like satellites (top) and P2-like prophages (bottom). Hotspots are 177 defined as locations among successive core gene families and are indicated by the edges in the graphs (% 178 indicates the proportion of defence systems at these locations). When the core genes are not successive, 179 it reflects cases where either one of the core genes is missing, or the cores genes are arranged di_erently 180 from the prototypical organization of their respective element . Colour codes in genetic loci and graphs 181 coincide; orange indicating complete and light orange indicating putative defence systems. Grey indicates 182 genes that are neither core nor defence-associated. 183 184 Rapid turnover of defence systems 185 186 We then enquired on the turnover of the defence systems , i.e. how frequently closely 187 related elements diYer in the system s they encode. The phylogen ies of P4 and P2 188 elements, based on their core genes (see Methods), show highly similar elements often 189 carrying unrelated defences (Fig 2A and D). This can best be appreciated by focusing on 190 the parts of the trees with many very similar elements and inspecting the diversity of 191 systems they contain. To quantify this eYect, w e compared the gene repertoire 192 relatedness (with wGRR, see Methods) of core genes and of defence genes between pairs 193 of elements with defence systems. Consistent with the phylogenies, w e observed an 194 overwhelmingly large proportion of pairs of the same type of elements with non-195 homologous defence systems (99% in P4 and 99% in P2 pairs have wGRR defence<0.05). 196 Since this includes pairs of very similar elements (i.e., with highly similar core genes) (Fig 197 2B and E, right panels), it shows that defence genes change very rapidly in both P4 and 198 P2. We observed only a few pairs of dissimilar elements with similar defence systems 199 suggesting that convergent acquisition of defences is rare (Fig 2 B and E, left panels). 200 These patterns remain qualitatively unchanged when comparing full genomes instead of 201 core genes and when including the putative defence systems (Fig S6). If defence systems 202 evolved in linkage with the core genomes of P4 and P2, we would expect a linear 203 relationship between core and defence similarity, with deviations corresponding to 204 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint potential events of horizontal transfer of antiviral genes. Instead, the association 205 between the evolution of defence systems and the core genes is almost null. 206 207 We then quantified the genetic linkage between defence genes and each individual core 208 gene (Fig 1E). The Spearman correlations between the wGRR of defence genes and the 209 sequence similarity of each core gene in pairs of P4 ( Fig 2C and Fig S7A) and P2 ( Fig 2F 210 and Fig S7B) were all very low (≤0.2), in contrast to the correlations between core genes 211 themselves. In summary, similar elements rarely encode similar defence genes and the 212 latter show little genetic linkage with core genes. Both indicate very rapid turnover of 213 defence systems in the genomes of P4 and P2. 214 215 216 Figure 2. Relationship between antiviral repertoires and the core genomes of P4 and P2. A. Phylogeny 217 of core genes of P4. Bootstraps of at least 90 are indicated with a circle (the larger the circle, the higher the 218 bootstrap value). Colours in the innermost circle indicate the bacterial host of each P4 (white spaces 219 0.160.200.310.170.190.450.170.210.460.950.160.200.380.930.940.190.180.510.930.910.880.180.240.390.900.910.910.900.180.160.440.960.940.930.940.91 0.190.090.010.070.030.700.080.000.660.530.080.020.820.630.660.100.030.650.580.690.690.090.020.850.630.620.800.67 0.190.090.010.070.030.700.080.000.660.530.080.020.820.630.660.100.030.650.580.690.690.090.020.850.630.620.800.67 0.190.090.010.070.030.700.080.000.660.530.080.020.820.630.660.100.030.650.580.690.690.090.020.850.630.620.800.67 0.190.090.010.070.030.700.080.000.660.530.080.020.820.630.660.100.030.650.580.690.690.090.020.850.630.620.800.67 0.190.090.010.070.030.700.080.000.660.530.080.020.820.630.660.100.030.650.580.690.690.090.020.850.630.620.800.67 Other Other E. coli Bacterial hosts (Inner circle) K. pneumoniae RM Spearman correlation Spearman correlation SheduRloCRst_3HPRetronDS-34Lamassu-FamHEC-04AbiUAbiP2 Rst-Hydrolase-3TmRst-gop-beta-cllRst-Helicase-DUF2290PD-T7-2RMRetronParisLamassu-FamKiwaAll_UG Bacterial Host Bootstraps >=90 Bootstraps >=90 Bacterial Host P4 Core A B C D E F 2.5kb Identity (%) 0 100 Identity (%) 0 100 2.5kb 2.5kb 2.5kb P2 Core Defense Defense Defense Defense Integrase Integrase Integrase gpA gpA gpL gpL gpM gpM gpN gpN gpO gpO gpP gpP gpQ gpQ Integrase Psu Psu Delta Delta Sid Sid AlpA AlpA Ash Ash Alpha Alpha 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 S. enterica Metagenome Contig.141475.P4.TypeB.variant000002.Set1Contig.146503.P4.TypeB.variant000002.Set1 Contig.41786.P4.TypeB.variant000002.Set1Contig.150144.P4.TypeB.variant000002.Set1 Contig.60724.P4.TypeB.variant000002.Set1Contig.45755.P4.TypeB.variant000002.Set1Contig.20624.P4.TypeB.variant000002.Set1Contig.49739.P4.TypeB.variant000002.Set1Contig.82334.P4.TypeB.variant000002.Set1ESCO001.0523.02109.001C.P4.TypeA.Set1 Contig.157939.P4.TypeA.Set1Contig.141617.P4.TypeA.Set1 Contig.148152.P4.TypeB.variant000002.Set1 Contig.92702.P4.TypeA.Set1Contig.131481.P4.TypeA.Set1 Contig.08394.P4.TypeA.Set1Contig.00754.P4.TypeA.Set1Contig.60164.P4.TypeA.Set1 Contig.01459.P4.TypeB.variant000002.Set1Contig.17644.P4.TypeB.variant000002.Set1Contig.08497.P4.TypeB.variant000002.Set1 Contig.113621.P4.TypeA.Set1Contig.179839.P4.TypeA.Set1 ESCO001.0523.01506.001C.P4.TypeA.Set1 Contig.23539.P4.TypeA.Set1Contig.186936.P4.TypeA.Set1 Contig.62093.P4.TypeA.Set1Contig.194601.P4.TypeA.Set1Contig.146985.P4.TypeA.Set1Contig.205588.P4.TypeA.Set1 Contig.12098.P4.TypeB.variant000002.Set1 Contig.42903.P4.TypeA.Set1Contig.185692.P4.TypeA.Set1 Contig.13504.P4.TypeA.Set1Contig.11234.P4.TypeA.Set1Contig.118256.P4.TypeA.Set1 Contig.28516.P4.TypeA.Set1Contig.196279.P4.TypeA.Set1Contig.131376.P4.TypeA.Set1Contig.147904.P4.TypeA.Set1 ESCO001.0523.00722.001C.P4.TypeA.Set1ESCO001.0523.00471.001C.P4.TypeA.Set2 Contig.93816.P4.TypeA.Set1Contig.87955.P4.TypeA.Set1 ESCO001.0523.01813.001C.P4.TypeA.Set1 Contig.44761.P4.TypeA.Set1 ESCO001.0523.00282.001C.P4.TypeA.Set1 Contig.43199.P4.TypeA.Set1 ESCO001.0523.01721.001C.P4.TypeA.Set2 Contig.135377.P4.TypeA.Set1 Contig.03113.P4.TypeA.Set1Contig.50179.P4.TypeA.Set1 ESCO001.0523.01040.001C.P4.TypeA.Set1ESCO001.0523.01770.001C.P4.TypeA.Set2ESCO001.0523.01502.001C.P4.TypeA.Set1 Contig.181816.P4.TypeA.Set1 Contig.90263.P4.TypeA.Set1Contig.19012.P4.TypeA.Set1Contig.170177.P4.TypeA.Set1 ESCO001.0523.00963.001C.P4.TypeA.Set1 Contig.153110.P4.TypeA.Set1 Contig.60081.P4.TypeA.Set1Contig.132990.P4.TypeA.Set1 Contig.109726.P4.TypeB.variant000001.Set1 Contig.146934.P4.TypeA.Set1 Contig.28547.P4.TypeA.Set1Contig.27693.P4.TypeA.Set1Contig.78500.P4.TypeA.Set1Contig.186373.P4.TypeA.Set1 Contig.112133.P4.TypeA.Set1Contig.187736.P4.TypeA.Set1 Contig.11824.P4.TypeA.Set1Contig.210670.P4.TypeA.Set1 SAEN001.0523.00415.001C.P4.TypeA.Set1 Contig.34562.P4.TypeA.Set1Contig.205411.P4.TypeA.Set1 ESCO001.0523.02547.001C.P4.TypeA.Set1 Contig.22388.P4.TypeB.variant000002.Set1 Contig.41781.P4.TypeA.Set1Contig.137120.P4.TypeA.Set1 Contig.44297.P4.TypeA.Set1Contig.107289.P4.TypeA.Set1 Contig.09205.P4.TypeA.Set1 Contig.80850.P4.TypeA.Set1 Contig.00752.P4.TypeA.Set1 Contig.78637.P4.TypeA.Set1 Contig.85794.P4.TypeA.Set1 Contig.78166.P4.TypeA.Set1 Contig.66443.P4.TypeA.Set1 ESCO001.0523.02285.001C.P4.TypeA.Set1 Contig.07038.P4.TypeA.Set1 ESCO001.0523.00507.001C.P4.TypeA.Set1 Contig.175054.P4.TypeA.Set1 Contig.27196.P4.TypeA.Set1 Contig.91678.P4.TypeA.Set1Contig.128444.P4.TypeA.Set1 Contig.06713.P4.TypeA.Set1 Contig.41885.P4.TypeA.Set1Contig.204649.P4.TypeA.Set1 Contig.150827.P4.TypeA.Set1 Contig.23568.P4.TypeA.Set1 Contig.14062.P4.TypeA.Set1Contig.164442.P4.TypeA.Set1 ESCO001.0523.00461.001C.P4.TypeA.Set1 Contig.159532.P4.TypeA.Set1 ESCO001.0523.02063.001C.P4.TypeA.Set1 Contig.148350.P4.TypeA.Set1 Contig.03142.P4.TypeA.Set1 Contig.80130.P4.TypeA.Set1Contig.111593.P4.TypeA.Set1Contig.195769.P4.TypeA.Set1 Contig.05237.P4.TypeA.Set1 Contig.66440.P4.TypeA.Set1 Contig.72549.P4.TypeA.Set1 Contig.38489.P4.TypeA.Set1 ESCO001.0523.00179.001C.P4.TypeA.Set1 Contig.03560.P4.TypeA.Set1Contig.130100.P4.TypeA.Set1 Contig.124698.P4.TypeA.Set1 SAEN001.0523.00585.001C.P4.TypeA.Set1 Contig.22923.P4.TypeA.Set1 Contig.93442.P4.TypeA.Set1Contig.191584.P4.TypeA.Set1 ESCO001.0523.00617.001C.P4.TypeA.Set1 Contig.91333.P4.TypeA.Set1 Contig.91332.P4.TypeA.Set1 Contig.34786.P4.TypeA.Set1 ESCO001.0523.01301.001C.P4.TypeA.Set2 Contig.101773.P4.TypeA.Set1 Contig.39380.P4.TypeA.Set1 Contig.02999.P4.TypeA.Set1Contig.161326.P4.TypeA.Set1 Contig.187364.P4.TypeA.Set1 Contig.28602.P4.TypeA.Set1Contig.107042.P4.TypeA.Set1 Contig.80604.P4.TypeA.Set1 Contig.09302.P4.TypeA.Set1Contig.112585.P4.TypeA.Set1 Contig.167607.P4.TypeA.Set1 Contig.05160.P4.TypeA.Set1 Contig.53082.P4.TypeA.Set1 Contig.39464.P4.TypeA.Set1 Contig.55803.P4.TypeA.Set1Contig.129405.P4.TypeA.Set1 Contig.151405.P4.TypeA.Set1 Contig.110410.P4.TypeA.Set1 Contig.88541.P4.TypeA.Set1Contig.115815.P4.TypeA.Set1 Contig.07847.P4.TypeA.Set1Contig.164445.P4.TypeA.Set1 Contig.191453.P4.TypeA.Set1 Contig.79335.P4.TypeA.Set1 Contig.09799.P4.TypeA.Set1 Contig.02638.P4.TypeA.Set1 Contig.63585.P4.TypeA.Set1 Contig.99251.P4.TypeA.Set1 Contig.25939.P4.TypeA.Set1Contig.143224.P4.TypeA.Set1 Contig.142386.P4.TypeA.Set1 ESCO001.0523.01960.001C.P4.TypeA.Set1 ESCO001.0523.01486.001C.P4.TypeB.variant0001.Set2 Contig.142823.P4.TypeA.Set1 Contig.33450.P4.TypeA.Set1 Contig.41600.P4.TypeA.Set1 Contig.13167.P4.TypeA.Set1 Contig.01364.P4.TypeA.Set1 Contig.71241.P4.TypeA.Set1 Contig.42401.P4.TypeA.Set1 ESCO001.0523.01312.001C.P4.TypeA.Set1 ESCO001.0523.00660.001C.P4.TypeA.Set3 ESCO001.0523.02449.001C.P4.TypeA.Set1 Contig.164668.P4.TypeA.Set1 Contig.100981.P4.TypeA.Set1 ESCO001.0523.02047.001C.P4.TypeA.Set1 ESCO001.0523.00723.001C.P4.TypeA.Set1 ESCO001.0523.01175.001C.P4.TypeA.Set3 Contig.108042.P4.TypeA.Set1 Contig.36818.P4.TypeA.Set1 Contig.34543.P4.TypeA.Set1Contig.110395.P4.TypeA.Set1 Contig.91906.P4.TypeA.Set1 Contig.58704.P4.TypeA.Set1Contig.164024.P4.TypeA.Set1 Contig.100801.P4.TypeA.Set1 ESCO001.0523.01007.001C.P4.TypeA.Set1 Contig.158151.P4.TypeA.Set1 Contig.163518.P4.TypeB.variant000002.Set1 Contig.71843.P4.TypeA.Set1 Contig.04236.P4.TypeB.variant000002.Set1 Contig.179585.P4.TypeA.Set1 Contig.179595.P4.TypeA.Set1 Contig.176407.P4.TypeB.variant000002.Set1 Contig.01729.P4.TypeA.Set1 Contig.87827.P4.TypeA.Set1 Contig.111746.P4.TypeA.Set1 Contig.80780.P4.TypeA.Set1 Contig.90583.P4.TypeA.Set1Contig.165182.P4.TypeA.Set1 Contig.94875.P4.TypeA.Set1 Contig.09889.P4.TypeA.Set1Contig.109352.P4.TypeA.Set1 Contig.63618.P4.TypeA.Set1 Contig.53883.P4.TypeA.Set1 Contig.63624.P4.TypeA.Set1 Contig.81468.P4.TypeA.Set1 Contig.80539.P4.TypeA.Set1Contig.199381.P4.TypeA.Set1 Contig.29582.P4.TypeA.Set1 Contig.71805.P4.TypeA.Set1 Contig.77329.P4.TypeA.Set1Contig.193441.P4.TypeA.Set1 Contig.08100.P4.TypeA.Set1 Contig.07644.P4.TypeA.Set1Contig.164028.P4.TypeA.Set1 Contig.06382.P4.TypeA.Set1Contig.155079.P4.TypeA.Set1 Contig.57838.P4.TypeA.Set1 Contig.27128.P4.TypeA.Set1 Contig.26263.P4.TypeA.Set1Contig.177451.P4.TypeA.Set1 Contig.116392.P4.TypeA.Set1 Contig.109344.P4.TypeA.Set1 Contig.20659.P4.TypeA.Set1Contig.136955.P4.TypeA.Set1 Contig.81591.P4.TypeA.Set1 Contig.45877.P4.TypeA.Set1 Contig.104405.P4.TypeA.Set1 Contig.65218.P4.TypeA.Set1 Contig.107119.P4.TypeA.Set1 Contig.20601.P4.TypeA.Set1 Contig.59708.P4.TypeA.Set1 Contig.205124.P4.TypeA.Set1 Contig.205806.P4.TypeA.Set1 Contig.148767.P4.TypeA.Set1 Contig.109405.P4.TypeA.Set1 ESCO001.0523.01029.001C.P4.TypeA.Set1 ESCO001.0523.02059.001C.P4.TypeA.Set2 ESCO001.0523.01912.001C.P4.TypeA.Set2 Contig.131374.P4.TypeA.Set1 Contig.148564.P4.TypeA.Set1 Contig.110129.P4.TypeA.Set1 Contig.44987.P4.TypeA.Set1 Contig.56559.P4.TypeA.Set1 ESCO001.0523.02230.001C.P4.TypeA.Set2 Contig.32847.P4.TypeA.Set1 Contig.77288.P4.TypeA.Set1 Contig.71242.P4.TypeA.Set1 Contig.179862.P4.TypeA.Set1 ESCO001.0523.02475.001C.P4.TypeA.Set1 Contig.01216.P4.TypeA.Set1 Contig.119751.P4.TypeA.Set1 Contig.142911.P4.TypeA.Set1 Contig.46474.P4.TypeA.Set1 ESCO001.0523.02176.001C.P4.TypeA.Set2 Contig.40043.P4.TypeA.Set1 Contig.40797.P4.TypeA.Set1 Contig.43785.P4.TypeA.Set1 Contig.81614.P4.TypeA.Set1 Contig.28689.P4.TypeA.Set1 ESCO001.0523.02547.001C.P4.TypeA.Set2 Contig.139841.P4.TypeA.Set1 Contig.33099.P4.TypeB.variant000002.Set1 Contig.45008.P4.TypeB.variant000002.Set1 SAEN001.0523.00530.001C.P4.TypeA.Set2 Contig.123070.P4.TypeA.Set1 Contig.42926.P4.TypeA.Set1 Contig.48951.P4.TypeA.Set1 Contig.147436.P4.TypeA.Set1 ESCO001.0523.00619.001C.P4.TypeA.Set1 Contig.141803.P4.TypeA.Set1 Contig.14547.P4.TypeA.Set1 Contig.40665.P4.TypeA.Set1 Contig.11991.P4.TypeA.Set1 Contig.41793.P4.TypeA.Set1 Contig.82355.P4.TypeA.Set1 Contig.00838.P4.TypeA.Set1 Contig.15165.P4.TypeA.Set1 Contig.99366.P4.TypeA.Set1 Contig.93663.P4.TypeA.Set1 Contig.09009.P4.TypeA.Set1 Contig.57833.P4.TypeA.Set1 Contig.117280.P4.TypeA.Set1 Contig.204058.P4.TypeA.Set1 Contig.153755.P4.TypeA.Set1 Contig.199191.P4.TypeA.Set1 Contig.64656.P4.TypeA.Set1 Contig.130063.P4.TypeA.Set1 Contig.01928.P4.TypeA.Set1 Contig.108158.P4.TypeA.Set1 Contig.91271.P4.TypeA.Set1 Contig.07914.P4.TypeA.Set1 Contig.59295.P4.TypeA.Set1 Contig.30555.P4.TypeA.Set1 Contig.111586.P4.TypeA.Set1 Contig.09903.P4.TypeA.Set1 Contig.28753.P4.TypeA.Set1 ESCO001.0523.01740.001C.P4.TypeA.Set1 Contig.28621.P4.TypeA.Set1 Contig.00009.P4.TypeA.Set1 ESCO001.0523.02078.001C.P4.TypeA.Set1 Contig.140910.P4.TypeA.Set1 ESCO001.0523.00084.001C.P4.TypeA.Set2 Contig.152794.P4.TypeA.Set1 Contig.73477.P4.TypeA.Set1 Contig.205622.P4.TypeA.Set1 Contig.24377.P4.TypeA.Set1 Contig.67338.P4.TypeA.Set1 Contig.06570.P4.TypeA.Set1 Contig.42973.P4.TypeA.Set1 Contig.41880.P4.TypeA.Set1 Contig.63978.P4.TypeA.Set1 Contig.155136.P4.TypeA.Set1 Contig.120760.P4.TypeA.Set1 Contig.80540.P4.TypeA.Set1 Contig.190479.P4.TypeA.Set1 Contig.165093.P4.TypeA.Set1 Contig.206687.P4.TypeA.Set1 Contig.167120.P4.TypeA.Set1 Contig.31662.P4.TypeA.Set1 Contig.121200.P4.TypeA.Set1 Contig.148347.P4.TypeA.Set1 Contig.185764.P4.TypeA.Set1 Contig.21305.P4.TypeA.Set1 Contig.81822.P4.TypeA.Set1 Contig.34100.P4.TypeA.Set1 Contig.05425.P4.TypeA.Set1 Contig.88304.P4.TypeA.Set1 Contig.39337.P4.TypeA.Set1 Contig.209712.P4.TypeA.Set1 Contig.140839.P4.TypeA.Set1 Contig.84513.P4.TypeA.Set1 Contig.26628.P4.TypeA.Set1 Contig.57932.P4.TypeB.variant000002.Set1 Contig.94080.P4.TypeA.Set1 Contig.110200.P4.TypeA.Set1 Contig.25941.P4.TypeA.Set1 ESCO001.0523.00470.001C.P4.TypeA.Set2 Contig.49732.P4.TypeB.variant000002.Set1 Contig.17863.P4.TypeB.variant000002.Set1 ESCO001.0523.01390.001C.P4.TypeB.variant0002.Set1 Contig.195150.P4.TypeB.variant000002.Set1 Contig.140159.P4.TypeB.variant000002.Set1 Contig.105779.P4.TypeB.variant000002.Set1 Contig.66517.P4.TypeB.variant000002.Set1 Contig.72299.P4.TypeA.Set1 Contig.20813.P4.TypeA.Set1 Contig.15292.P4.TypeA.Set1 Contig.207868.P4.TypeA.Set1 Contig.78167.P4.TypeA.Set1 Contig.51177.P4.TypeA.Set1 Contig.202235.P4.TypeA.Set1 Contig.140793.P4.TypeA.Set1 Contig.180254.P4.TypeA.Set1 Contig.96771.P4.TypeA.Set1 Contig.08427.P4.TypeA.Set1 Contig.150694.P4.TypeA.Set1 Contig.54832.P4.TypeA.Set1 Contig.179627.P4.TypeA.Set1 Contig.153617.P4.TypeA.Set1 Contig.106384.P4.TypeA.Set1 Contig.160148.P4.TypeA.Set1 Contig.204623.P4.TypeA.Set1 ESCO001.0523.00211.001C.P4.TypeB.variant0002.Set1 ESCO001.0523.00891.001C.P4.TypeB.variant0002.Set1 Contig.106849.P4.TypeB.variant000002.Set1 ESCO001.0523.00006.001C.P4.TypeB.variant0002.Set2 ESCO001.0523.00005.001C.P4.TypeB.variant0002.Set2 Contig.49574.P4.TypeA.Set1 Contig.10186.P4.TypeA.Set1 Contig.197922.P4.TypeB.variant000002.Set1 Contig.00076.P4.TypeB.variant000002.Set1 Contig.203240.P4.TypeA.Set1 Contig.149132.P4.TypeA.Set1 Contig.89631.P4.TypeA.Set1 Contig.09301.P4.TypeA.Set1 Contig.39049.P4.TypeA.Set1 Contig.01980.P4.TypeA.Set1 ESCO001.0523.01034.001C.P4.TypeA.Set2 Contig.08395.P4.TypeA.Set1 Contig.125684.P4.TypeB.variant000002.Set1 Contig.171329.P4.TypeA.Set1 Contig.42709.P4.TypeA.Set1 Contig.01858.P4.TypeA.Set1 Contig.210644.P4.TypeB.variant000002.Set1 Contig.197987.P4.TypeA.Set1 Contig.37142.P4.TypeA.Set1 Contig.21972.P4.TypeB.variant000002.Set1 Contig.51591.P4.TypeA.Set1 Contig.150153.P4.TypeA.Set1 ESCO001.0523.01493.001C.P4.TypeA.Set1 ESCO001.0523.01261.001C.P4.TypeA.Set1 ESCO001.0523.02341.001C.P4.TypeA.Set2 ESCO001.0523.01952.001C.P4.TypeB.variant0001.Set2 SAEN001.0523.00861.001C.P4.TypeA.Set2 ESCO001.0523.00369.001C.P4.TypeB.variant0006.Set1 Contig.02077.P4.TypeA.Set1 ESCO001.0523.00571.001C.P4.TypeA.Set1 Contig.71210.P4.TypeA.Set1 Contig.04266.P4.TypeB.variant000002.Set1 Contig.87905.P4.TypeA.Set1 Contig.132932.P4.TypeA.Set1 Contig.94090.P4.TypeA.Set1 Contig.11248.P4.TypeA.Set1 Contig.133185.P4.TypeA.Set1 Contig.44296.P4.TypeA.Set1 ESCO001.0523.00107.001C.P4.TypeA.Set1 Contig.53017.P4.TypeA.Set1 Contig.103086.P4.TypeA.Set1 Contig.128264.P4.TypeA.Set1 Contig.150140.P4.TypeA.Set1 Contig.164027.P4.TypeA.Set1 Contig.88498.P4.TypeA.Set1 Contig.165509.P4.TypeB.variant000002.Set1 Contig.32955.P4.TypeA.Set1 Contig.144498.P4.TypeA.Set1 Contig.114460.P4.TypeA.Set1 Contig.83342.P4.TypeA.Set1 Contig.14321.P4.TypeA.Set1 ESCO001.0523.02102.001C.P4.TypeA.Set4 Contig.176777.P4.TypeA.Set1 Contig.141205.P4.TypeA.Set1 Contig.111366.P4.TypeA.Set1 Contig.100068.P4.TypeA.Set1 ESCO001.0523.01473.001C.P4.TypeA.Set2 ESCO001.0523.00108.001C.P4.TypeA.Set1 Contig.104656.P4.TypeA.Set1 ESCO001.0523.00318.001C.P4.TypeA.Set1 Contig.85002.P4.TypeB.variant000002.Set1 Contig.33798.P4.TypeA.Set1 Contig.11895.P4.TypeA.Set1 Contig.55348.P4.TypeA.Set1 Contig.204284.P4.TypeA.Set1 Contig.71237.P4.TypeA.Set1 Contig.135120.P4.TypeA.Set1 Contig.101898.P4.TypeA.Set1 Contig.159007.P4.TypeA.Set1 Contig.09273.P4.TypeA.Set1 Contig.31170.P4.TypeA.Set1 Contig.105734.P4.TypeA.Set1 Contig.14426.P4.TypeA.Set1 ESCO001.0523.02063.001C.P4.TypeA.Set3 Contig.146352.P4.TypeA.Set1 Contig.90615.P4.TypeA.Set1 Contig.13391.P4.TypeA.Set1 Contig.60722.P4.TypeA.Set1 Contig.23522.P4.TypeA.Set1 Contig.33879.P4.TypeB.variant000002.Set1 Contig.130880.P4.TypeB.variant000002.Set1 Contig.01817.P4.TypeA.Set1 Contig.107251.P4.TypeA.Set1 Contig.03105.P4.TypeA.Set1 Contig.39035.P4.TypeA.Set1 ESCO001.0523.00381.001C.P4.TypeA.Set2 Contig.109579.P4.TypeA.Set1 Contig.197065.P4.TypeA.Set1 Contig.115089.P4.TypeA.Set1 ESCO001.0523.00669.001C.P4.TypeA.Set1 SAEN001.0523.00301.001C.P4.TypeA.Set3 Contig.163954.P4.TypeA.Set1 Contig.201344.P4.TypeA.Set1 Contig.99242.P4.TypeA.Set1 Contig.08500.P4.TypeB.variant000002.Set1 Contig.41872.P4.TypeA.Set1 Contig.08146.P4.TypeA.Set1 Contig.74036.P4.TypeA.Set1 Contig.106823.P4.TypeA.Set1 Contig.23567.P4.TypeA.Set1 ESCO001.0523.00739.001C.P4.TypeA.Set1 Contig.00758.P4.TypeB.variant000002.Set1 Contig.87909.P4.TypeA.Set1 Contig.143742.P4.TypeA.Set1 Contig.180960.P4.TypeA.Set1 Contig.94644.P4.TypeA.Set1 Contig.05090.P4.TypeA.Set1 Contig.47192.P4.TypeA.Set1 Contig.146976.P4.TypeA.Set1 Contig.160146.P4.TypeA.Set1 Contig.181556.P4.TypeA.Set1 Contig.152397.P4.TypeA.Set1 Contig.61390.P4.TypeA.Set1 ESCO001.0523.00354.001C.P4.TypeA.Set1 ESCO001.0523.00738.001C.P4.TypeA.Set1ESCO001.0523.00859.001C.P4.TypeB.variant0006.Set1 Contig.162607.P4.TypeA.Set1 ESCO001.0523.00125.001C.P4.TypeB.variant0001.Set2 Contig.88386.P4.TypeB.variant000002.Set1 Contig.22970.P4.TypeA.Set1 Contig.49413.P4.TypeA.Set1 Contig.32379.P4.TypeA.Set1 Contig.06781.P4.TypeA.Set1 Contig.83546.P4.TypeA.Set1 Contig.93662.P4.TypeA.Set1 Contig.43661.P4.TypeA.Set1 Contig.209571.P4.TypeA.Set1 Contig.12833.P4.TypeA.Set1 Contig.169283.P4.TypeA.Set1 Contig.40502.P4.TypeA.Set1 Contig.191136.P4.TypeA.Set1 Contig.78974.P4.TypeA.Set1 Contig.161482.P4.TypeA.Set1ESCO001.0523.01812.001C.P4.TypeA.Set1 Contig.49997.P4.TypeA.Set1 Contig.29643.P4.TypeA.Set1 Contig.145516.P4.TypeA.Set1Contig.32865.P4.TypeB.variant000002.Set1 Contig.78786.P4.TypeA.Set1 Contig.195203.P4.TypeA.Set1 Contig.110587.P4.TypeA.Set1 Contig.55085.P4.TypeA.Set1ESCO001.0523.00617.001C.P4.TypeA.Set2 ESCO001.0523.00618.001C.P4.TypeA.Set1 Contig.84131.P4.TypeA.Set1 Contig.80652.P4.TypeA.Set1 Contig.63460.P4.TypeA.Set1 Contig.72360.P4.TypeA.Set1 Contig.176716.P4.TypeA.Set1Contig.181691.P4.TypeB.variant000002.Set1 Contig.150050.P4.TypeA.Set1 Contig.21412.P4.TypeA.Set1 Contig.181127.P4.TypeA.Set1 Contig.61470.P4.TypeA.Set1 Contig.162943.P4.TypeA.Set1ESCO001.0523.01035.001C.P4.TypeA.Set1 Contig.19347.P4.TypeA.Set1 Contig.167092.P4.TypeA.Set1 Contig.95567.P4.TypeA.Set1ESCO001.0523.00506.001C.P4.TypeA.Set2 Contig.63385.P4.TypeA.Set1 Contig.44988.P4.TypeA.Set1 Contig.60120.P4.TypeA.Set1 Contig.10532.P4.TypeA.Set1 Contig.44284.P4.TypeA.Set1ESCO001.0523.02177.001C.P4.TypeA.Set3 Contig.110646.P4.TypeA.Set1 Contig.00300.P4.TypeA.Set1ESCO001.0523.02135.001C.P4.TypeA.Set1 Contig.110705.P4.TypeB.variant000002.Set1 Contig.97266.P4.TypeB.variant000002.Set1 Contig.42352.P4.TypeB.variant000002.Set1 Contig.109317.P4.TypeB.variant000002.Set1 Contig.29702.P4.TypeB.variant000002.Set1 Contig.79417.P4.TypeB.variant000002.Set1 Contig.27182.P4.TypeB.variant000002.Set1 Contig.27317.P4.TypeB.variant000002.Set1 Contig.42979.P4.TypeA.Set1 Contig.55075.P4.TypeA.Set1ESCO001.0523.00466.001C.P4.TypeA.Set1 Contig.32995.P4.TypeA.Set1ESCO001.0523.01250.001C.P4.TypeA.Set1ESCO001.0523.00497.001C.P4.TypeB.variant0004.Set1 ESCO001.0523.00346.001C.P4.TypeA.Set1 ESCO001.0523.01250.001C.P4.TypeA.Set2 ESCO001.0523.01039.001C.P4.TypeA.Set1 ESCO001.0523.01102.001C.P4.TypeA.Set1 Contig.104408.P4.TypeA.Set1 Contig.29727.P4.TypeA.Set1 Contig.84442.P4.TypeA.Set1 Contig.20805.P4.TypeA.Set1 Contig.122110.P4.TypeA.Set1 Contig.09306.P4.TypeA.Set1 Contig.83913.P4.TypeA.Set1 Contig.28738.P4.TypeA.Set1 Contig.84384.P4.TypeA.Set1ESCO001.0523.01451.001C.P4.TypeA.Set2 Contig.00856.P4.TypeA.Set1 Contig.132699.P4.TypeA.Set1 Contig.33751.P4.TypeA.Set1 Contig.126905.P4.TypeA.Set1 Contig.205130.P4.TypeA.Set1SAEN001.0523.00935.001C.P4.TypeA.Set1 ESCO001.0523.01678.001C.P4.TypeA.Set1 ESCO001.0523.02435.001C.P4.TypeA.Set1 ESCO001.0523.02440.001C.P4.TypeA.Set1 Contig.149391.P4.TypeA.Set1Contig.91589.P4.TypeB.variant000002.Set1 Contig.81814.P4.TypeA.Set1 Contig.127781.P4.TypeA.Set1 Contig.03501.P4.TypeA.Set1 Contig.04227.P4.TypeA.Set1 Contig.57650.P4.TypeA.Set1 Contig.169213.P4.TypeA.Set1 Contig.88051.P4.TypeA.Set1 Contig.13452.P4.TypeA.Set1 Contig.19296.P4.TypeA.Set1 Contig.23526.P4.TypeA.Set1 Contig.131474.P4.TypeA.Set1 Contig.17821.P4.TypeA.Set1 Contig.204573.P4.TypeA.Set1 Contig.48812.P4.TypeA.Set1 Contig.11617.P4.TypeA.Set1 Contig.20583.P4.TypeA.Set1 Contig.13102.P4.TypeA.Set1 Contig.44054.P4.TypeA.Set1 Contig.108348.P4.TypeA.Set1ESCO001.0523.02093.001C.P4.TypeA.Set2 Contig.137229.P4.TypeA.Set1 Contig.14212.P4.TypeA.Set1ESCO001.0523.00289.001C.P4.TypeA.Set1 Contig.107055.P4.TypeA.Set1ESCO001.0523.01657.001C.P4.TypeA.Set1 Contig.41624.P4.TypeA.Set1 Contig.185609.P4.TypeA.Set1 Contig.40721.P4.TypeA.Set1 Contig.62850.P4.TypeA.Set1 Contig.27111.P4.TypeA.Set1 Contig.46564.P4.TypeA.Set1 Contig.132504.P4.TypeA.Set1 ESCO001.0523.00845.001C.P4.TypeA.Set1 Contig.140592.P4.TypeA.Set1 Contig.118519.P4.TypeA.Set1 Contig.203764.P4.TypeA.Set1 Contig.107840.P4.TypeA.Set1 Contig.11367.P4.TypeA.Set1 Contig.27199.P4.TypeA.Set1 ESCO001.0523.01842.001C.P4.TypeA.Set1 Contig.89342.P4.TypeA.Set1 Contig.26111.P4.TypeA.Set1 Contig.101767.P4.TypeA.Set1 Contig.09845.P4.TypeA.Set1 Contig.60818.P4.TypeA.Set1 Contig.162484.P4.TypeA.Set1 Contig.198492.P4.TypeA.Set1 Contig.07656.P4.TypeA.Set1 Contig.140661.P4.TypeA.Set1 Contig.21440.P4.TypeA.Set1 Contig.139948.P4.TypeA.Set1 Contig.209851.P4.TypeA.Set1 Contig.110474.P4.TypeA.Set1 Contig.102902.P4.TypeA.Set1 Contig.72437.P4.TypeA.Set1 Contig.146942.P4.TypeA.Set1 Contig.20670.P4.TypeB.variant000002.Set1 Contig.20589.P4.TypeB.variant000002.Set1 Contig.07910.P4.TypeA.Set1 Contig.14200.P4.TypeA.Set1 Contig.31213.P4.TypeA.Set1 Contig.53948.P4.TypeA.Set1 Contig.126897.P4.TypeA.Set1 Contig.12014.P4.TypeA.Set1 Contig.00111.P4.TypeA.Set1 Contig.176362.P4.TypeA.Set1 Contig.13070.P4.TypeA.Set1 Contig.61782.P4.TypeA.Set1 Contig.10268.P4.TypeA.Set1 Contig.142433.P4.TypeA.Set1 Contig.203443.P4.TypeA.Set1 Contig.04570.P4.TypeA.Set1 Contig.84102.P4.TypeA.Set1 Contig.157221.P4.TypeA.Set1 ESCO001.0523.01560.001C.P4.TypeA.Set2 ESCO001.0523.01645.001C.P4.TypeA.Set1 Contig.01785.P4.TypeA.Set1 ESCO001.0523.00470.001C.P4.TypeA.Set1 ESCO001.0523.00470.001C.P4.TypeA.Set3 Contig.143533.P4.TypeA.Set1 Contig.21522.P4.TypeA.Set1 Contig.21531.P4.TypeA.Set1 Contig.52830.P4.TypeA.Set1 Contig.204634.P4.TypeA.Set1 Contig.43777.P4.TypeA.Set1 Contig.111518.P4.TypeA.Set1 ESCO001.0523.01219.001C.P4.TypeB.variant0001.Set1 Contig.89528.P4.TypeA.Set1 Contig.20667.P4.TypeA.Set1 Contig.135126.P4.TypeA.Set1 Contig.74090.P4.TypeA.Set1 Contig.28446.P4.TypeA.Set1 Contig.27459.P4.TypeA.Set1 ESCO001.0523.00006.001C.P4.TypeB.variant0001.Set1 Contig.127678.P4.TypeA.Set1 Contig.44280.P4.TypeA.Set1 ESCO001.0523.00480.001C.P4.TypeA.Set1 Contig.150569.P4.TypeA.Set1 Contig.184889.P4.TypeA.Set1 Contig.50485.P4.TypeA.Set1 ESCO001.0523.01033.001C.P4.TypeA.Set1 ESCO001.0523.01038.001C.P4.TypeA.Set1 Contig.89159.P4.TypeB.variant000001.Set1 Contig.80865.P4.TypeA.Set1 Contig.43266.P4.TypeB.variant000002.Set1 Contig.170509.P4.TypeA.Set1 Contig.79575.P4.TypeA.Set1 Contig.135145.P4.TypeA.Set1 Contig.112051.P4.TypeA.Set1 Contig.179565.P4.TypeA.Set1 Contig.20736.P4.TypeB.variant000002.Set1 Contig.135533.P4.TypeB.variant000002.Set1 ESCO001.0523.02528.001C.P4.TypeA.Set1 Contig.96116.P4.TypeB.variant000002.Set1 ESCO001.0523.01960.001C.P4.TypeA.Set2 Contig.39975.P4.TypeB.variant000002.Set1 ESCO001.0523.01201.001C.P4.TypeA.Set1 Contig.44574.P4.TypeB.variant000002.Set1 ESCO001.0523.02491.001C.P4.TypeA.Set1 Contig.157441.P4.TypeB.variant000002.Set1 ESCO001.0523.01975.001C.P4.TypeA.Set1 ESCO001.0523.00423.001C.P4.TypeA.Set2 Contig.63193.P4.TypeB.variant000002.Set1 ESCO001.0523.00753.001C.P4.TypeA.Set1 Contig.31180.P4.TypeB.variant000002.Set1 Contig.58871.P4.TypeB.variant000002.Set1 Contig.14210.P4.TypeB.variant000002.Set1 Contig.185563.P4.TypeB.variant000002.Set1 Contig.12829.P4.TypeB.variant000002.Set1 Contig.199345.P4.TypeB.variant000002.Set1 Contig.01442.P4.TypeB.variant000002.Set1 Contig.01451.P4.TypeB.variant000002.Set1 ESCO001.0523.00004.001C.P4.TypeA.Set2 ESCO001.0523.02144.001C.P4.TypeA.Set2 ESCO001.0523.01793.001C.P4.TypeA.Set2 ESCO001.0523.00252.001C.P4.TypeA.Set1 ESCO001.0523.00506.001C.P4.TypeA.Set4 ESCO001.0523.00229.001C.P4.TypeA.Set1 Contig.33769.P4.TypeB.variant000002.Set1 SAEN001.0523.00301.001C.P4.TypeA.Set1 ESCO001.0523.01007.001C.P4.TypeA.Set2 ESCO001.0523.00618.001C.P4.TypeA.Set2 ESCO001.0523.00617.001C.P4.TypeA.Set3 ESCO001.0523.02061.001C.P4.TypeA.Set1 Contig.133862.P4.TypeB.variant000002.Set1 Contig.139896.P4.TypeB.variant000002.Set1 Contig.164019.P4.TypeB.variant000002.Set1 ESCO001.0523.01936.001C.P4.TypeA.Set1 Contig.65198.P4.TypeB.variant000002.Set1 Contig.23519.P4.TypeB.variant000002.Set1 ESCO001.0523.01679.001C.P4.TypeA.Set1 Contig.21302.P4.TypeA.Set1 Contig.20804.P4.TypeA.Set1 Contig.179994.P4.TypeA.Set1 Contig.104657.P4.TypeA.Set1 Contig.21333.P4.TypeB.variant000002.Set1 Contig.56479.P4.TypeA.Set1 Contig.78996.P4.TypeA.Set1 Contig.70412.P4.TypeA.Set1 Contig.105113.P4.TypeA.Set1 Contig.83382.P4.TypeA.Set1 Contig.36257.P4.TypeA.Set1 Contig.66424.P4.TypeA.Set1 Contig.147825.P4.TypeA.Set1 Contig.162127.P4.TypeA.Set1 Contig.59808.P4.TypeA.Set1 ESCO001.0523.00040.001C.P4.TypeA.Set1 ESCO001.0523.00943.001C.P4.TypeA.Set2 Contig.192215.P4.TypeA.Set1 Contig.94015.P4.TypeA.Set1 ESCO001.0523.01639.001C.P4.TypeA.Set1 Contig.87917.P4.TypeB.variant000002.Set1 Contig.150149.P4.TypeB.variant000002.Set1 Contig.101892.P4.TypeB.variant000002.Set1 Contig.02610.P4.TypeA.Set1 ESCO001.0523.01928.001C.P4.TypeA.Set1 ESCO001.0523.01925.001C.P4.TypeA.Set1 ESCO001.0523.01912.001C.P4.TypeA.Set1 Contig.28392.P4.TypeA.Set1 Contig.06138.P4.TypeA.Set1 Contig.11369.P4.TypeA.Set1 Contig.10269.P4.TypeA.Set1 Contig.163197.P4.TypeA.Set1 Contig.171593.P4.TypeA.Set1 ESCO001.0523.00778.001C.P4.TypeA.Set1 ESCO001.0523.00661.001C.P4.TypeB.variant0002.Set1Contig.15439.P4.TypeA.Set1 Contig.195617.P4.TypeA.Set1 Contig.20609.P4.TypeA.Set1 Contig.204128.P4.TypeA.Set1 Contig.179616.P4.TypeB.variant000002.Set1 ESCO001.0523.01712.001C.P4.TypeB.variant0006.Set1Contig.62809.P4.TypeA.Set1 Contig.26404.P4.TypeA.Set1 Contig.62908.P4.TypeA.Set1 Contig.04286.P4.TypeA.Set1 Contig.150141.P4.TypeA.Set1 Contig.146243.P4.TypeA.Set1 Contig.157035.P4.TypeA.Set1 Contig.96920.P4.TypeA.Set1 Contig.62072.P4.TypeA.Set1 Contig.132611.P4.TypeA.Set1 Contig.77512.P4.TypeA.Set1 Contig.67723.P4.TypeA.Set1 Contig.131380.P4.TypeA.Set1 ESCO001.0523.00515.001C.P4.TypeA.Set1Contig.86324.P4.TypeA.Set1 ESCO001.0523.01495.001C.P4.TypeA.Set1 Contig.206705.P4.TypeA.Set1 Contig.195829.P4.TypeA.Set1 Contig.20798.P4.TypeA.Set1 Contig.130896.P4.TypeA.Set1 Contig.126851.P4.TypeA.Set1 Contig.157442.P4.TypeA.Set1 Contig.142787.P4.TypeA.Set1 Contig.04203.P4.TypeA.Set1 Contig.71412.P4.TypeA.Set1 Contig.195806.P4.TypeA.Set1 Contig.129399.P4.TypeA.Set1 Contig.174520.P4.TypeA.Set1 Contig.118271.P4.TypeA.Set1 Contig.60858.P4.TypeA.Set1 Contig.67596.P4.TypeA.Set1 Contig.127642.P4.TypeA.Set1 ESCO001.0523.01502.001C.P4.TypeA.Set3Contig.34030.P4.TypeA.Set1 Contig.01591.P4.TypeA.Set1 Contig.91320.P4.TypeA.Set1 Contig.26631.P4.TypeA.Set1 ESCO001.0523.01212.001C.P4.TypeA.Set2Contig.164984.P4.TypeA.Set1 Contig.80728.P4.TypeB.variant000002.Set1 Contig.70823.P4.TypeB.variant000002.Set1 Contig.13046.P4.TypeB.variant000002.Set1Contig.163927.P4.TypeA.Set1 Contig.12031.P4.TypeA.Set1 Contig.39332.P4.TypeA.Set1 Contig.177240.P4.TypeA.Set1 Contig.33896.P4.TypeA.Set1 Contig.63871.P4.TypeA.Set1 Contig.110647.P4.TypeA.Set1 Contig.157087.P4.TypeA.Set1 Contig.84380.P4.TypeA.Set1 Contig.63547.P4.TypeA.Set1 Contig.117060.P4.TypeA.Set1 Contig.00774.P4.TypeA.Set1 Contig.190738.P4.TypeA.Set1 Contig.49820.P4.TypeA.Set1 Contig.150166.P4.TypeA.Set1 Contig.29758.P4.TypeA.Set1 Contig.166314.P4.TypeA.Set1 Contig.08363.P4.TypeA.Set1 Contig.08364.P4.TypeA.Set1 Contig.38729.P4.TypeA.Set1 Contig.101720.P4.TypeA.Set1 Contig.22894.P4.TypeA.Set1 Contig.120579.P4.TypeA.Set1 Contig.104395.P4.TypeA.Set1 Contig.119757.P4.TypeA.Set1 Contig.41881.P4.TypeA.Set1 Contig.61543.P4.TypeA.Set1 Contig.19056.P4.TypeA.Set1 Contig.102076.P4.TypeA.Set1 ESCO001.0523.01100.001C.P4.TypeB.variant0002.Set1 Contig.194125.P4.TypeA.Set1 Contig.27251.P4.TypeA.Set1 Contig.196427.P4.TypeA.Set1 Contig.135117.P4.TypeA.Set1 Contig.80731.P4.TypeA.Set1 Contig.06136.P4.TypeA.Set1 Contig.126687.P4.TypeB.variant000002.Set1 Contig.14419.P4.TypeB.variant000002.Set1 ESCO001.0523.02005.001C.P4.TypeA.Set1 ESCO001.0523.00279.001C.P4.TypeA.Set1Contig.139825.P4.TypeA.Set1 Contig.81038.P4.TypeA.Set1 Contig.07973.P4.TypeA.Set1 Contig.109170.P4.TypeA.Set1 Contig.120740.P4.TypeA.Set1 Contig.163945.P4.TypeB.variant000002.Set1Contig.199206.P4.TypeA.Set1 Contig.146348.P4.TypeA.Set1 Contig.70627.P4.TypeA.Set1 Contig.74020.P4.TypeA.Set1 Contig.157054.P4.TypeA.Set1 Contig.180963.P4.TypeA.Set1 Contig.63510.P4.TypeA.Set1 ESCO001.0523.01914.001C.P4.TypeA.Set1Contig.68862.P4.TypeA.Set1 Contig.145937.P4.TypeA.Set1 Contig.22365.P4.TypeA.Set1 Contig.38524.P4.TypeA.Set1 Contig.120838.P4.TypeA.Set1 Contig.139707.P4.TypeA.Set1 Contig.98715.P4.TypeA.Set1 Contig.205935.P4.TypeA.Set1 Contig.15214.P4.TypeA.Set1 Contig.40745.P4.TypeA.Set1 Contig.94082.P4.TypeA.Set1 Contig.75039.P4.TypeA.Set1 ESCO001.0523.00317.001C.P4.TypeA.Set1Contig.04244.P4.TypeA.Set1 Contig.41832.P4.TypeA.Set1 Contig.136503.P4.TypeA.Set1 Contig.43399.P4.TypeA.Set1 Contig.117075.P4.TypeA.Set1 Contig.92565.P4.TypeA.Set1 Contig.145978.P4.TypeA.Set1 Contig.21058.P4.TypeA.Set1 Contig.05164.P4.TypeA.Set1 ESCO001.0523.01259.001C.P4.TypeA.Set3Contig.179618.P4.TypeA.Set1 Contig.112830.P4.TypeA.Set1 Contig.110853.P4.TypeA.Set1 Contig.145813.P4.TypeA.Set1 Contig.141677.P4.TypeA.Set1 Contig.20649.P4.TypeA.Set1 Contig.91729.P4.TypeA.Set1 Contig.11568.P4.TypeA.Set1 Contig.35406.P4.TypeA.Set1 Contig.42414.P4.TypeA.Set1 Contig.37689.P4.TypeA.Set1 Contig.21900.P4.TypeA.Set1 Contig.25244.P4.TypeA.Set1 Contig.29734.P4.TypeB.variant000002.Set1 Contig.27270.P4.TypeB.variant000002.Set1Contig.179651.P4.TypeA.Set1 Contig.135137.P4.TypeA.Set1 Contig.93173.P4.TypeB.variant000002.Set1Contig.83513.P4.TypeA.Set1 Contig.131100.P4.TypeA.Set1 Contig.63888.P4.TypeB.variant000002.Set1Contig.14509.P4.TypeA.Set1 Contig.44122.P4.TypeA.Set1 Contig.161520.P4.TypeB.variant000002.Set1 Contig.139723.P4.TypeB.variant000002.Set1 ESCO001.0523.00528.001C.P4.TypeA.Set1Contig.104203.P4.TypeA.Set1 ESCO001.0523.02247.001C.P4.TypeA.Set2 Contig.140231.P4.TypeB.variant000002.Set1 Contig.08474.P4.TypeA.Set1 Contig.132556.P4.TypeA.Set1 Contig.53272.P4.TypeA.Set1 Contig.191844.P4.TypeA.Set1 Contig.11020.P4.TypeA.Set1 Contig.23559.P4.TypeA.Set1 Contig.28435.P4.TypeB.variant000002.Set1Contig.164980.P4.TypeA.Set1 Contig.92391.P4.TypeA.Set1 Contig.03234.P4.TypeA.Set1 Contig.00598.P4.TypeA.Set1 ESCO001.0523.01292.001C.P4.TypeB.variant0001.Set1 Contig.128818.P4.TypeA.Set1 Contig.63501.P4.TypeA.Set1 Contig.91340.P4.TypeA.Set1 Contig.99832.P4.TypeA.Set1 Contig.10432.P4.TypeA.Set1 Contig.70408.P4.TypeA.Set1 Contig.80364.P4.TypeA.Set1 Contig.163048.P4.TypeA.Set1 Contig.179601.P4.TypeB.variant000002.Set1 Contig.35395.P4.TypeA.Set1 Contig.14455.P4.TypeA.Set1 Contig.180080.P4.TypeB.variant000002.Set1 Contig.128354.P4.TypeA.Set1 ESCO001.0523.00970.001C.P4.TypeA.Set1 Contig.141086.P4.TypeA.Set1 Contig.140893.P4.TypeA.Set1 ESCO001.0523.00616.001C.P4.TypeA.Set2 ESCO001.0523.00616.001C.P4.TypeA.Set1 Contig.181272.P4.TypeA.Set1 Contig.57726.P4.TypeA.Set1 Contig.54438.P4.TypeA.Set1 Contig.04225.P4.TypeA.Set1 Contig.165087.P4.TypeA.Set1 Contig.85767.P4.TypeA.Set1 Contig.140837.P4.TypeA.Set1 Contig.17780.P4.TypeA.Set1 Contig.01450.P4.TypeA.Set1 Contig.38537.P4.TypeA.Set1 Contig.105047.P4.TypeA.Set1 ESCO001.0523.00556.001C.P4.TypeA.Set1 Contig.26073.P4.TypeA.Set1 Contig.31665.P4.TypeB.variant000002.Set1 Contig.01892.P4.TypeB.variant000002.Set1 Contig.153082.P4.TypeB.variant000002.Set1 Contig.82336.P4.TypeB.variant000002.Set1 Contig.41510.P4.TypeA.Set1 Contig.125897.P4.TypeB.variant000002.Set1 Contig.71844.P4.TypeB.variant000002.Set1 Contig.38891.P4.TypeA.Set1 Contig.64686.P4.TypeB.variant000002.Set1 Contig.20723.P4.TypeA.Set1 Contig.59377.P4.TypeA.Set1 Contig.16039.P4.TypeB.variant000002.Set1 Contig.77014.P4.TypeB.variant000002.Set1 Contig.79358.P4.TypeB.variant000002.Set1 Contig.22919.P4.TypeB.variant000002.Set1 Contig.154194.P4.TypeA.Set1 Contig.01778.P4.TypeA.Set1 ESCO001.0523.00717.001C.P4.TypeA.Set1 ESCO001.0523.00717.001C.P4.TypeA.Set2 Contig.11634.P4.TypeA.Set1 Contig.14295.P4.TypeA.Set1 Contig.202123.P4.TypeA.Set1 Contig.107551.P4.TypeA.Set1 Contig.179634.P4.TypeA.Set1 Contig.179633.P4.TypeA.Set1 Contig.41370.P4.TypeB.variant000002.Set1 Contig.03526.P4.TypeB.variant000002.Set1 Contig.129009.P4.TypeA.Set1 Contig.11755.P4.TypeA.Set1 Contig.181807.P4.TypeA.Set1 Contig.08131.P4.TypeB.variant000002.Set1 ESCO001.0523.01259.001C.P4.TypeA.Set1 Contig.60473.P4.TypeA.Set1 Contig.204639.P4.TypeA.Set1 Contig.146664.P4.TypeA.Set1 Contig.133945.P4.TypeA.Set1 Contig.205936.P4.TypeA.Set1 Contig.52751.P4.TypeA.Set1 Contig.161486.P4.TypeA.Set1 ESCO001.0523.00008.001C.P4.TypeA.Set1 Contig.162877.P4.TypeA.Set1 Contig.157444.P4.TypeA.Set1 ESCO001.0523.00283.001C.P4.TypeA.Set1 Contig.41803.P4.TypeA.Set1 Contig.110288.P4.TypeA.Set1 ESCO001.0523.01502.001C.P4.TypeA.Set2 Contig.41821.P4.TypeA.Set1 Contig.125462.P4.TypeA.Set1 ESCO001.0523.01972.001C.P4.TypeA.Set1 Contig.83366.P4.TypeA.Set1 Contig.167064.P4.TypeA.Set1 Contig.106620.P4.TypeA.Set1 Contig.99364.P4.TypeA.Set1 Contig.116279.P4.TypeA.Set1 Contig.28551.P4.TypeA.Set1 Contig.19311.P4.TypeA.Set1 Contig.85299.P4.TypeA.Set1 Contig.199197.P4.TypeB.variant000002.Set1 ESCO001.0523.00695.001C.P4.TypeA.Set1 Contig.89548.P4.TypeA.Set1 Contig.07934.P4.TypeB.variant000002.Set1 Contig.19295.P4.TypeB.variant000002.Set1 Contig.184718.P4.TypeB.variant000002.Set1 Contig.132644.P4.TypeB.variant000002.Set1 ESCO001.0523.00731.001C.P4.TypeA.Set1 Contig.32434.P4.TypeA.Set1 Contig.44314.P4.TypeA.Set1 Contig.44315.P4.TypeA.Set1 Contig.62866.P4.TypeA.Set1 Contig.01525.P4.TypeA.Set1 Contig.72923.P4.TypeA.Set1 Contig.44692.P4.TypeA.Set1 ESCO001.0523.02389.001C.P4.TypeA.Set1 Contig.38877.P4.TypeA.Set1 Contig.38587.P4.TypeA.Set1 Contig.38838.P4.TypeA.Set1 Contig.42836.P4.TypeA.Set1 Contig.38450.P4.TypeA.Set1 Contig.14344.P4.TypeA.Set1 Contig.48614.P4.TypeA.Set1 Contig.38880.P4.TypeA.Set1 Contig.39041.P4.TypeA.Set1 Contig.45223.P4.TypeA.Set1 Contig.206093.P4.TypeA.Set1 Contig.116035.P4.TypeA.Set1 Contig.03192.P4.TypeA.Set1 Contig.150137.P4.TypeA.Set1 Contig.179571.P4.TypeB.variant000002.Set1 Contig.01419.P4.TypeB.variant000002.Set1 Contig.179586.P4.TypeB.variant000002.Set1 Contig.37621.P4.TypeB.variant000002.Set1 ESCO001.0523.02444.001C.P4.TypeA.Set1 Contig.181642.P4.TypeA.Set1 Contig.106958.P4.TypeA.Set1 Contig.03067.P4.TypeA.Set1 Contig.08669.P4.TypeA.Set1 Contig.203898.P4.TypeA.Set1 Contig.58431.P4.TypeA.Set1 Contig.88520.P4.TypeA.Set1 Contig.42978.P4.TypeA.Set1 Contig.39105.P4.TypeA.Set1 Contig.89578.P4.TypeA.Set1 Contig.34553.P4.TypeA.Set1 Contig.110472.P4.TypeA.Set1 Contig.148886.P4.TypeA.Set1 ESCO001.0523.01039.001C.P4.TypeA.Set2 Contig.191587.P4.TypeA.Set1 Contig.04212.P4.TypeA.Set1 Contig.59297.P4.TypeA.Set1 ESCO001.0523.01301.001C.P4.TypeA.Set1 ESCO001.0523.00820.001C.P4.TypeA.Set1 Contig.31800.P4.TypeA.Set1 Contig.41523.P4.TypeA.Set1 ESCO001.0523.01381.001C.P4.TypeA.Set1 Contig.158507.P4.TypeA.Set1 Contig.12076.P4.TypeB.variant000002.Set1 Contig.104646.P4.TypeB.variant000002.Set1 Contig.07951.P4.TypeB.variant000002.Set1 Contig.110213.P4.TypeB.variant000002.Set1 Contig.87918.P4.TypeB.variant000002.Set1 Contig.12005.P4.TypeA.Set1 Contig.209836.P4.TypeA.Set1 Contig.91723.P4.TypeA.Set1 ESCO001.0523.02130.001C.P4.TypeA.Set1 Contig.01780.P4.TypeA.Set1 Contig.27240.P4.TypeA.Set1 Contig.18966.P4.TypeA.Set1 Contig.77080.P4.TypeA.Set1 Contig.62830.P4.TypeA.Set1 Contig.32958.P4.TypeA.Set1 Contig.56859.P4.TypeA.Set1 Contig.126648.P4.TypeB.variant000002.Set1 Contig.105188.P4.TypeA.Set1 Contig.98986.P4.TypeA.Set1 Contig.01392.P4.TypeA.Set1 Contig.109871.P4.TypeA.Set1 Contig.156171.P4.TypeA.Set1 Contig.191498.P4.TypeA.Set1 Contig.180767.P4.TypeA.Set1 Contig.86177.P4.TypeA.Set1 Contig.68843.P4.TypeA.Set1 Contig.118542.P4.TypeA.Set1 Contig.146895.P4.TypeA.Set1 Contig.199481.P4.TypeA.Set1 Contig.80879.P4.TypeA.Set1 Contig.41887.P4.TypeA.Set1 Contig.181534.P4.TypeA.Set1 Contig.68153.P4.TypeA.Set1 ESCO001.0523.01448.001C.P4.TypeA.Set2 Contig.09116.P4.TypeA.Set1 Contig.120396.P4.TypeA.Set1 Contig.03481.P4.TypeA.Set1 Contig.174567.P4.TypeA.Set1 Contig.70379.P4.TypeA.Set1 Contig.14284.P4.TypeA.Set1 Contig.69553.P4.TypeB.variant000002.Set1 Contig.107029.P4.TypeA.Set1 Contig.92957.P4.TypeB.variant000002.Set1 Contig.153211.P4.TypeB.variant000002.Set1 Contig.107584.P4.TypeB.variant000002.Set1 Contig.145056.P4.TypeB.variant000002.Set1 Contig.07845.P4.TypeB.variant000002.Set1 Contig.09904.P4.TypeA.Set1 Contig.30974.P4.TypeB.variant000002.Set1 Contig.135148.P4.TypeB.variant000002.Set1 Contig.43877.P4.TypeB.variant000002.Set1 Contig.164015.P4.TypeB.variant000002.Set1 Contig.56322.P4.TypeB.variant000002.Set1 Contig.107734.P4.TypeA.Set1 Contig.112052.P4.TypeB.variant000002.Set1 Contig.176230.P4.TypeA.Set1 Contig.58118.P4.TypeA.Set1 Contig.164557.P4.TypeA.Set1 Contig.92063.P4.TypeA.Set1 Contig.162593.P4.TypeB.variant000002.Set1 Contig.100815.P4.TypeB.variant000002.Set1 Contig.04247.P4.TypeA.Set1 Contig.141665.P4.TypeB.variant000002.Set1 Contig.06583.P4.TypeA.Set1 Contig.62160.P4.TypeB.variant000002.Set1 Contig.204537.P4.TypeB.variant000002.Set1 Contig.29287.P4.TypeA.Set1 Contig.100029.P4.TypeA.Set1 Contig.146185.P4.TypeA.Set1 Contig.21306.P4.TypeA.Set1 ESCO001.0523.00660.001C.P4.TypeB.variant0002.Set1 Contig.105118.P4.TypeA.Set1 Contig.79337.P4.TypeA.Set1 Contig.179932.P4.TypeA.Set1 ESCO001.0523.01815.001C.P4.TypeA.Set1 ESCO001.0523.01034.001C.P4.TypeB.variant0004.Set1 Contig.120773.P4.TypeA.Set1 Contig.199523.P4.TypeA.Set1 Contig.20971.P4.TypeA.Set1 Contig.44960.P4.TypeA.Set1 Contig.65385.P4.TypeA.Set1 Contig.176127.P4.TypeA.Set1 Contig.201503.P4.TypeA.Set1 Contig.60706.P4.TypeA.Set1 Contig.176605.P4.TypeA.Set1 Contig.159601.P4.TypeA.Set1 Contig.65545.P4.TypeA.Set1 Contig.137362.P4.TypeA.Set1 Contig.106781.P4.TypeA.Set1 Contig.54824.P4.TypeA.Set1 Contig.17649.P4.TypeA.Set1 Contig.140234.P4.TypeA.Set1 Contig.167122.P4.TypeA.Set1 Contig.167085.P4.TypeB.variant000002.Set1Contig.11851.P4.TypeB.variant000002.Set1 Contig.05280.P4.TypeB.variant000002.Set1 Contig.206311.P4.TypeB.variant000002.Set1 Contig.193489.P4.TypeA.Set1 Contig.197128.P4.TypeB.variant000002.Set1 Contig.145512.P4.TypeA.Set1 Contig.178725.P4.TypeA.Set1 Contig.102479.P4.TypeA.Set1 Contig.106386.P4.TypeA.Set1 Contig.101718.P4.TypeA.Set1 Contig.140098.P4.TypeA.Set1Contig.27134.P4.TypeA.Set1 Contig.107384.P4.TypeA.Set1Contig.11912.P4.TypeA.Set1 Contig.200383.P4.TypeA.Set1Contig.68318.P4.TypeA.Set1 Contig.176555.P4.TypeA.Set1 Contig.109897.P4.TypeA.Set1Contig.41536.P4.TypeA.Set1 Contig.94060.P4.TypeA.Set1 Contig.95274.P4.TypeA.Set1 Contig.111063.P4.TypeA.Set1 Contig.10296.P4.TypeA.Set1 SAEN001.0523.00325.001C.P4.TypeA.Set1 Contig.61830.P4.TypeA.Set1 Contig.28388.P4.TypeA.Set1 Contig.22427.P4.TypeA.Set1 Contig.143540.P4.TypeA.Set1 ESCO001.0523.01413.001C.P4.TypeA.Set1 Contig.18038.P4.TypeA.Set1 Contig.44031.P4.TypeA.Set1 Contig.109240.P4.TypeA.Set1Contig.41634.P4.TypeA.Set1 Contig.70420.P4.TypeA.Set1 ESCO001.0523.01593.001C.P4.TypeA.Set1 Contig.109769.P4.TypeA.Set1 Contig.162060.P4.TypeA.Set1Contig.23525.P4.TypeA.Set1 Contig.93811.P4.TypeA.Set1 Contig.142515.P4.TypeA.Set1Contig.42826.P4.TypeA.Set1 Contig.01232.P4.TypeA.Set1 Contig.93819.P4.TypeA.Set1 Contig.35255.P4.TypeA.Set1 Contig.28762.P4.TypeA.Set1 Contig.19706.P4.TypeA.Set1 Contig.114468.P4.TypeA.Set1 Contig.105472.P4.TypeA.Set1Contig.23409.P4.TypeA.Set1 Contig.176227.P4.TypeA.Set1Contig.87921.P4.TypeA.Set1 Contig.118543.P4.TypeA.Set1 Contig.164031.P4.TypeA.Set1 Contig.162328.P4.TypeA.Set1 ESCO001.0523.00350.001C.P4.TypeB.variant0001.Set2 ESCO001.0523.01394.001C.P4.TypeB.variant0002.Set1 Contig.128215.P4.TypeB.variant000002.Set1 Contig.101813.P4.TypeB.variant000002.Set1 ESCO001.0523.00133.001C.P4.TypeB.variant0002.Set1 Contig.30132.P4.TypeA.Set1 Contig.33909.P4.TypeA.Set1 ESCO001.0523.02093.001C.P4.TypeA.Set1 Contig.107255.P4.TypeA.Set1 Contig.196089.P4.TypeA.Set1Contig.37590.P4.TypeA.Set1 Contig.52405.P4.TypeA.Set1 Contig.61853.P4.TypeA.Set1 Contig.02667.P4.TypeA.Set1 Contig.181596.P4.TypeA.Set1 ESCO001.0523.02079.001C.P4.TypeA.Set1 ESCO001.0523.01321.001C.P4.TypeA.Set2 Contig.41860.P4.TypeA.Set1 Contig.139930.P4.TypeA.Set1 Contig.186949.P4.TypeA.Set1 Contig.153434.P4.TypeA.Set1 Contig.111884.P4.TypeA.Set1Contig.74033.P4.TypeA.Set1 ESCO001.0523.00639.001C.P4.TypeA.Set1 Contig.104952.P4.TypeB.variant000002.Set1Contig.64654.P4.TypeB.variant000002.Set1 Contig.135114.P4.TypeA.Set1Contig.74044.P4.TypeA.Set1 Contig.107637.P4.TypeA.Set1Contig.29757.P4.TypeA.Set1 Contig.13075.P4.TypeB.variant000002.Set1 Contig.40660.P4.TypeA.Set1 Contig.44245.P4.TypeA.Set1 Contig.11317.P4.TypeB.variant000002.Set1 Contig.136682.P4.TypeA.Set1 Contig.14525.P4.TypeB.variant000002.Set1 ESCO001.0523.01754.001C.P4.TypeA.Set1 Contig.175052.P4.TypeA.Set1 Contig.129946.P4.TypeA.Set1Contig.20770.P4.TypeA.Set1 Contig.83869.P4.TypeA.Set1 Contig.11899.P4.TypeA.Set1 Contig.13511.P4.TypeA.Set1 Contig.145841.P4.TypeA.Set1Contig.74630.P4.TypeA.Set1 Contig.77682.P4.TypeA.Set1 Contig.137039.P4.TypeA.Set1Contig.12114.P4.TypeA.Set1 Contig.29583.P4.TypeA.Set1 Contig.04623.P4.TypeA.Set1 Contig.210412.P4.TypeA.Set1 SAEN001.0523.01235.001C.P4.TypeA.Set2 Contig.133100.P4.TypeA.Set1Contig.26927.P4.TypeA.Set1 Contig.206317.P4.TypeA.Set1 Contig.201913.P4.TypeA.Set1 Contig.151834.P4.TypeA.Set1Contig.11905.P4.TypeA.Set1 Contig.21105.P4.TypeA.Set1 Contig.30562.P4.TypeA.Set1 Contig.183065.P4.TypeA.Set1 Contig.119670.P4.TypeA.Set1Contig.08299.P4.TypeA.Set1 Contig.124075.P4.TypeA.Set1Contig.59646.P4.TypeA.Set1 Contig.58291.P4.TypeA.Set1 Contig.13459.P4.TypeA.Set1 ESCO001.0523.01381.001C.P4.TypeA.Set2 Contig.20700.P4.TypeA.Set1 Contig.20588.P4.TypeA.Set1 Contig.13083.P4.TypeB.variant000002.Set1 Contig.159437.P4.TypeA.Set1Contig.55639.P4.TypeA.Set1 Contig.00013.P4.TypeA.Set1 Contig.180430.P4.TypeA.Set1Contig.58436.P4.TypeA.Set1 ESCO001.0523.01713.001C.P4.TypeA.Set1 Contig.13107.P4.TypeA.Set1 Contig.94108.P4.TypeA.Set1 Contig.128304.P4.TypeA.Set1Contig.29692.P4.TypeA.Set1 ESCO001.0523.01157.001C.P4.TypeA.Set1 Contig.209893.P4.TypeA.Set1Contig.93138.P4.TypeA.Set1 Contig.34506.P4.TypeA.Set1 Contig.89545.P4.TypeA.Set1 Contig.121198.P4.TypeA.Set1 Contig.44457.P4.TypeB.variant000002.Set1 Contig.145150.P4.TypeA.Set1 Contig.105847.P4.TypeA.Set1Contig.26874.P4.TypeA.Set1 Contig.83904.P4.TypeA.Set1 Contig.09895.P4.TypeA.Set1 Contig.45102.P4.TypeB.variant000002.Set1 Contig.110289.P4.TypeA.Set1 Contig.200847.P4.TypeA.Set1Contig.08426.P4.TypeA.Set1Contig.03024.P4.TypeA.Set1Contig.05405.P4.TypeA.Set1 Contig.163460.P4.TypeA.Set1 ESCO001.0523.00462.001C.P4.TypeB.variant0004.Set1 Contig.35388.P4.TypeA.Set1Contig.06038.P4.TypeA.Set1Contig.15158.P4.TypeA.Set1 Contig.59710.P4.TypeB.variant000002.Set1 Contig.93799.P4.TypeA.Set1 ESCO001.0523.02303.001C.P4.TypeA.Set1 Contig.108489.P4.TypeA.Set1 ESCO001.0523.02526.001C.P4.TypeA.Set1ESCO001.0523.01914.001C.P4.TypeA.Set2ESCO001.0523.01505.001C.P4.TypeA.Set1 Contig.176684.P4.TypeA.Set1Contig.02997.P4.TypeA.Set1 Contig.121961.P4.TypeA.Set1Contig.116378.P4.TypeA.Set1Contig.203212.P4.TypeA.Set1 ESCO001.0523.00567.001C.P4.TypeB.variant0006.Set1 ESCO001.0523.01267.001C.P4.TypeA.Set1 Contig.154156.P4.TypeA.Set1Contig.80763.P4.TypeA.Set1Contig.06146.P4.TypeA.Set1Contig.30175.P4.TypeA.Set1Contig.49409.P4.TypeA.Set1Contig.74049.P4.TypeA.Set1Contig.49659.P4.TypeA.Set1Contig.06260.P4.TypeA.Set1 Contig.105897.P4.TypeA.Set1Contig.13098.P4.TypeA.Set1 SAEN001.0523.00224.001C.P4.TypeA.Set1Contig.18016.P4.TypeB.variant000002.Set1Contig.42524.P4.TypeB.variant000002.Set1Contig.18714.P4.TypeB.variant000002.Set1 Contig.206308.P4.TypeB.variant000002.Set1 Contig.33025.P4.TypeA.Set1Contig.20644.P4.TypeA.Set1Contig.40732.P4.TypeA.Set1 Contig.148561.P4.TypeA.Set1Contig.01230.P4.TypeA.Set1Contig.18981.P4.TypeA.Set1Contig.34582.P4.TypeA.Set1 Contig.133954.P4.TypeA.Set1 ESCO001.0523.01646.001C.P4.TypeA.Set1ESCO001.0523.02549.001C.P4.TypeA.Set1ESCO001.0523.01247.001C.P4.TypeA.Set1 ESCO001.0523.01257.001C.P4.TypeB.variant0006.Set2 Contig.196896.P4.TypeA.Set1Contig.71409.P4.TypeA.Set1Contig.05359.P4.TypeA.Set1Contig.00779.P4.TypeA.Set1 Contig.170264.P4.TypeA.Set1 ESCO001.0523.02063.001C.P4.TypeA.Set2 Contig.44302.P4.TypeA.Set1Contig.62869.P4.TypeA.Set1Contig.02613.P4.TypeA.Set1Contig.99800.P4.TypeA.Set1 ESCO001.0523.00643.001C.P4.TypeA.Set1 Contig.61215.P4.TypeA.Set1 Contig.191996.P4.TypeB.variant000002.Set1 Contig.69807.P4.TypeA.Set1 Contig.112118.P4.TypeA.Set1Contig.06145.P4.TypeA.Set1 ESCO001.0523.01409.001C.P4.TypeA.Set1 Contig.131098.P4.TypeA.Set1Contig.61786.P4.TypeA.Set1 ESCO001.0523.01486.001C.P4.TypeA.Set3 Contig.63449.P4.TypeA.Set1 ESCO001.0523.02411.001C.P4.TypeA.Set1 Contig.23745.P4.TypeA.Set1Contig.05647.P4.TypeA.Set1 Contig.117077.P4.TypeA.Set1Contig.181552.P4.TypeA.Set1Contig.187200.P4.TypeA.Set1 ESCO001.0523.00663.001C.P4.TypeA.Set1ESCO001.0523.00381.001C.P4.TypeA.Set1ESCO001.0523.02504.001C.P4.TypeA.Set1 Contig.164012.P4.TypeA.Set1Contig.21299.P4.TypeA.Set1 Contig.195775.P4.TypeA.Set1Contig.41560.P4.TypeA.Set1 ESCO001.0523.00194.001C.P4.TypeA.Set1 Contig.189472.P4.TypeA.Set1Contig.91282.P4.TypeA.Set1 Contig.108375.P4.TypeA.Set1Contig.135284.P4.TypeA.Set1Contig.10287.P4.TypeA.Set1Contig.20817.P4.TypeA.Set1 Contig.190712.P4.TypeA.Set1Contig.168815.P4.TypeA.Set1Contig.111067.P4.TypeA.Set1Contig.53864.P4.TypeA.Set1 ESCO001.0523.02102.001C.P4.TypeA.Set2 ESCO001.0523.02024.001C.P4.TypeB.variant0006.Set1 ESCO001.0523.01259.001C.P4.TypeA.Set4ESCO001.0523.01668.001C.P4.TypeA.Set1ESCO001.0523.00568.001C.P4.TypeA.Set1Contig.85534.P4.TypeB.variant000002.Set1Contig.04159.P4.TypeB.variant000002.Set1Contig.40888.P4.TypeC.variant000008.Set1SAEN001.0523.00004.001C.P4.TypeA.Set1SAEN001.0523.00595.001C.P4.TypeA.Set2 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Contig.126114.P4.TypeA.Set1Contig.121978.P4.TypeA.Set1Contig.80359.P4.TypeA.Set1 Contig.113512.P4.TypeA.Set1Contig.203165.P4.TypeA.Set1Contig.188784.P4.TypeA.Set1Contig.81875.P4.TypeA.Set1 Contig.103754.P4.TypeB.variant000005.Set1 Contig.02948.P4.TypeA.Set1 Contig.180847.P4.TypeA.Set1Contig.60162.P4.TypeA.Set1 Contig.130671.P4.TypeA.Set1 Contig.206649.P4.TypeB.variant000002.Set1Contig.59167.P4.TypeB.variant000002.Set1Contig.40578.P4.TypeB.variant000005.Set1 Contig.133403.P4.TypeB.variant000002.Set1 Contig.64707.P4.TypeA.Set1 Contig.105703.P4.TypeC.variant000003.Set1Contig.111973.P4.TypeB.variant000002.Set1Contig.13133.P4.TypeB.variant000002.Set1 ESCO001.0523.00194.001C.P4.TypeB.variant0001.Set2ESCO001.0523.02506.001C.P4.TypeB.variant0001.Set1 Contig.05042.P4.TypeA.Set1 Contig.26086.P4.TypeC.variant000008.Set1Contig.185308.P4.TypeB.variant000005.Set1Contig.153107.P4.TypeB.variant000005.Set1 KLPN001.0523.00479.001C.P4.TypeB.variant0002.Set1 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Contig.29289.P4.TypeA.Set1Contig.136458.P4.TypeB.variant000002.Set1 Contig.22441.P4.TypeA.Set1 Contig.35358.P4.TypeA.Set1 Contig.100800.P4.TypeB.variant000002.Set1 Contig.31646.P4.TypeB.variant000002.Set1 Contig.32358.P4.TypeB.variant000002.Set1 Contig.22281.P4.TypeB.variant000002.Set1 Contig.57712.P4.TypeA.Set1 Contig.10242.P4.TypeA.Set1 Contig.39471.P4.TypeB.variant000002.Set1 Contig.84813.P4.TypeA.Set1 Contig.10229.P4.TypeA.Set1 Contig.04109.P4.TypeB.variant000002.Set1 Contig.39505.P4.TypeB.variant000002.Set1 Contig.71036.P4.TypeA.Set1 KLPN001.0523.01324.001C.P4.TypeB.variant0002.Set1 Contig.133149.P4.TypeB.variant000002.Set1 Contig.42484.P4.TypeA.Set1 Contig.08350.P4.TypeA.Set1 Contig.94988.P4.TypeA.Set1 KLPN001.0523.00788.001C.P4.TypeB.variant0002.Set1 Contig.01537.P4.TypeA.Set1 Contig.40074.P4.TypeB.variant000002.Set1 Contig.37726.P4.TypeB.variant000002.Set1 KLPN001.0523.00578.001C.P4.TypeB.variant0002.Set2 Contig.63811.P4.TypeB.variant000002.Set1 Contig.43317.P4.TypeB.variant000002.Set1 Contig.156948.P4.TypeB.variant000002.Set1 Contig.58139.P4.TypeB.variant000002.Set1 Contig.34771.P4.TypeB.variant000002.Set1 Contig.44443.P4.TypeA.Set1 KLPN001.0523.00941.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01182.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00677.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00338.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01014.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00681.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00568.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00494.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00334.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00253.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00270.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00531.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01191.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01171.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00402.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00177.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01380.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00818.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00100.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00148.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01506.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00837.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01420.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00844.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00009.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01406.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01052.001C.P4.TypeB.variant0002.Set1 Contig.34764.P4.TypeB.variant000002.Set1 Contig.43766.P4.TypeB.variant000002.Set1 Contig.68778.P4.TypeB.variant000002.Set1 KLPN001.0523.00433.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00766.001C.P4.TypeB.variant0002.Set1 Contig.140959.P4.TypeB.variant000002.Set1 Contig.129167.P4.TypeB.variant000002.Set1 Contig.143999.P4.TypeB.variant000002.Set1 KLPN001.0523.00934.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00768.001C.P4.TypeB.variant0002.Set1 Contig.37763.P4.TypeB.variant000002.Set1 KLPN001.0523.00432.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00442.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01266.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01358.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01261.001C.P4.TypeB.variant0002.Set1 Contig.22467.P4.TypeB.variant000002.Set1 KLPN001.0523.01146.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01113.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01004.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00669.001C.P4.TypeB.variant0002.Set1 Contig.02241.P4.TypeB.variant000002.Set1 Contig.69982.P4.TypeB.variant000002.Set1 Contig.17860.P4.TypeB.variant000002.Set1 Contig.45871.P4.TypeB.variant000002.Set1 KLPN001.0523.00594.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00153.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00728.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01331.001C.P4.TypeB.variant0002.Set1 Contig.41696.P4.TypeB.variant000002.Set1 Contig.39502.P4.TypeB.variant000002.Set1 Contig.27074.P4.TypeB.variant000002.Set1 KLPN001.0523.00243.001C.P4.TypeB.variant0002.Set1 Contig.143804.P4.TypeB.variant000002.Set1 Contig.22401.P4.TypeB.variant000002.Set1 Contig.54012.P4.TypeB.variant000002.Set1 KLPN001.0523.01339.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00285.001C.P4.TypeB.variant0002.Set1 Contig.15883.P4.TypeB.variant000002.Set1 Contig.43717.P4.TypeB.variant000002.Set1 Contig.37602.P4.TypeB.variant000002.Set1 Contig.158793.P4.TypeB.variant000002.Set1 Contig.141363.P4.TypeB.variant000002.Set1 Contig.35360.P4.TypeB.variant000002.Set1 Contig.24314.P4.TypeB.variant000002.Set1 Contig.42451.P4.TypeB.variant000002.Set1 Contig.142059.P4.TypeB.variant000002.Set1 Contig.38243.P4.TypeB.variant000002.Set1 Contig.08566.P4.TypeB.variant000002.Set1 Contig.26847.P4.TypeB.variant000002.Set1 Contig.02213.P4.TypeA.Set1 Contig.02215.P4.TypeA.Set1 Contig.27555.P4.TypeA.Set1 Contig.02015.P4.TypeB.variant000002.Set1 KLPN001.0523.00886.001C.P4.TypeB.variant0002.Set1 Contig.141324.P4.TypeA.Set1 Contig.13777.P4.TypeA.Set1 Contig.107201.P4.TypeA.Set1 Contig.22391.P4.TypeB.variant000002.Set1 Contig.43477.P4.TypeA.Set1 KLPN001.0523.00314.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00014.001C.P4.TypeB.variant0002.Set2 Contig.07954.P4.TypeA.Set1 Contig.41675.P4.TypeA.Set1 KLPN001.0523.00757.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00714.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00354.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00333.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01179.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00545.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00338.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00950.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00140.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00943.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00345.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01156.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01405.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01171.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00997.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00686.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00420.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00951.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00806.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00494.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00402.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00112.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00650.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00177.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01219.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00147.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01479.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00531.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01028.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01378.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00920.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01472.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01167.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00562.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01223.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01181.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01185.001C.P4.TypeB.variant0002.Set1 Contig.116341.P4.TypeA.Set1 KLPN001.0523.01407.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01506.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00118.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00424.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00980.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.00974.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00837.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01014.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00530.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.01015.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01474.001C.P4.TypeB.variant0002.Set1 Contig.107075.P4.TypeB.variant000002.Set1 Contig.34929.P4.TypeB.variant000002.Set1 KLPN001.0523.00578.001C.P4.TypeB.variant0002.Set1 Contig.110275.P4.TypeB.variant000002.Set1 Contig.88428.P4.TypeB.variant000002.Set1 Contig.174612.P4.TypeB.variant000002.Set1 Contig.22289.P4.TypeA.Set1 Contig.43409.P4.TypeB.variant000002.Set1 Contig.172071.P4.TypeB.variant000002.Set1 Contig.156418.P4.TypeB.variant000002.Set1 Contig.38758.P4.TypeB.variant000002.Set1 Contig.208876.P4.TypeB.variant000002.Set1 Contig.18701.P4.TypeB.variant000002.Set1 Contig.34937.P4.TypeB.variant000002.Set1 KLPN001.0523.00983.001C.P4.TypeB.variant0002.Set1 Contig.02262.P4.TypeB.variant000002.Set1 Contig.22891.P4.TypeB.variant000002.Set1 KLPN001.0523.00856.001C.P4.TypeB.variant0002.Set1 Contig.124199.P4.TypeB.variant000002.Set1 Contig.08548.P4.TypeA.Set1 KLPN001.0523.01459.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00578.001C.P4.TypeB.variant0002.Set3 KLPN001.0523.00516.001C.P4.TypeB.variant0002.Set2 KLPN001.0523.01140.001C.P4.TypeB.variant0002.Set1 Contig.55031.P4.TypeB.variant000002.Set1 KLPN001.0523.00499.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00255.001C.P4.TypeB.variant0002.Set1 Contig.40567.P4.TypeB.variant000002.Set1 Contig.35407.P4.TypeB.variant000002.Set1 Contig.139429.P4.TypeB.variant000002.Set1 Contig.26977.P4.TypeB.variant000002.Set1 Contig.01641.P4.TypeB.variant000002.Set1 Contig.00192.P4.TypeB.variant000002.Set1 Contig.127986.P4.TypeB.variant000002.Set1 Contig.31629.P4.TypeB.variant000002.Set1 Contig.26585.P4.TypeB.variant000002.Set1 Contig.37736.P4.TypeA.Set1 Contig.08433.P4.TypeB.variant000002.Set1 Contig.02714.P4.TypeB.variant000002.Set1 Contig.25958.P4.TypeA.Set1 Contig.110559.P4.TypeA.Set1 Contig.21646.P4.TypeB.variant000002.Set1 Contig.34166.P4.TypeB.variant000002.Set1 Contig.27553.P4.TypeB.variant000002.Set1 Contig.104236.P4.TypeB.variant000002.Set1 Contig.112490.P4.TypeB.variant000002.Set1 Contig.05696.P4.TypeB.variant000002.Set1 KLPN001.0523.01323.001C.P4.TypeB.variant0002.Set1 Contig.107221.P4.TypeB.variant000002.Set1 Contig.04951.P4.TypeB.variant000002.Set1 Contig.170928.P4.TypeA.Set1 Contig.84833.P4.TypeB.variant000002.Set1 KLPN001.0523.00748.001C.P4.TypeB.variant0002.Set2 Contig.22271.P4.TypeB.variant000002.Set1 Contig.36748.P4.TypeB.variant000002.Set1 Contig.19722.P4.TypeB.variant000002.Set1 Contig.150677.P4.TypeB.variant000002.Set1 KLPN001.0523.00768.001C.P4.TypeB.variant0002.Set2 Contig.41710.P4.TypeB.variant000002.Set1 KLPN001.0523.01303.001C.P4.TypeB.variant0002.Set1 Contig.104225.P4.TypeB.variant000002.Set1 Contig.107064.P4.TypeB.variant000002.Set1 Contig.104100.P4.TypeB.variant000002.Set1 Contig.21637.P4.TypeB.variant000002.Set1 Contig.02264.P4.TypeB.variant000002.Set1 Contig.27540.P4.TypeB.variant000002.Set1 Contig.36739.P4.TypeB.variant000002.Set1 Contig.31624.P4.TypeB.variant000002.Set1 Contig.35325.P4.TypeB.variant000002.Set1 KLPN001.0523.00014.001C.P4.TypeB.variant0002.Set1 KLPN001.0523.00014.001C.P4.TypeB.variant0002.Set3 KLPN001.0523.00448.001C.P4.TypeB.variant0002.Set1 Contig.27639.P4.TypeB.variant000002.Set1 Contig.147714.P4.TypeA.Set1 Contig.29655.P4.TypeB.variant000002.Set1 KLPN001.0523.00553.001C.P4.TypeB.variant0002.Set3 Contig.05332.P4.TypeB.variant000002.Set1 Contig.11399.P4.TypeB.variant000002.Set1 Contig.65217.P4.TypeB.variant000002.Set1 Contig.56939.P4.TypeB.variant000002.Set1 Contig.05732.P4.TypeB.variant000002.Set1 KLPN001.0523.00371.001C.P4.TypeB.variant0002.Set1 Contig.15966.P4.TypeB.variant000002.Set1 Contig.08556.P4.TypeB.variant000002.Set1 Contig.33436.P4.TypeB.variant000002.Set1 KLPN001.0523.01410.001C.P4.TypeB.variant0002.Set1 Contig.146662.P4.TypeB.variant000002.Set1 Contig.169927.P4.TypeB.variant000002.Set1 Contig.57699.P4.TypeB.variant000002.Set1 Contig.01966.P4.TypeB.variant000002.Set1 Contig.01815.P4.TypeB.variant000002.Set1 Contig.123732.P4.TypeB.variant000002.Set1 Contig.22469.P4.TypeB.variant000002.Set1 Contig.22286.P4.TypeB.variant000002.Set1 Contig.107203.P4.TypeB.variant000002.Set1 KLPN001.0523.00044.001C.P4.TypeB.variant0002.Set1 Contig.136480.P4.TypeA.Set1 Contig.79431.P4.TypeA.Set1 Contig.44427.P4.TypeA.Set1 Contig.109278.P4.TypeA.Set1 Contig.141327.P4.TypeA.Set1 Contig.142987.P4.TypeB.variant000002.Set1 Contig.80017.P4.TypeB.variant000002.Set1 Contig.80925.P4.TypeB.variant000002.Set1 Contig.26082.P4.TypeB.variant000002.Set1 KLPN001.0523.00479.001C.P4.TypeB.variant0002.Set2 Contig.157193.P4.TypeB.variant000002.Set1 Contig.159739.P4.TypeB.variant000002.Set1 Contig.31622.P4.TypeA.Set1 Contig.84494.P4.TypeA.Set1 KLPN001.0523.00150.001C.P4.TypeB.variant0002.Set1 Contig.70464.P4.TypeB.variant000002.Set1 Contig.08584.P4.TypeB.variant000002.Set1 Contig.11002.P4.TypeA.Set1 Contig.162852.P4.TypeA.Set1 Contig.08518.P4.TypeA.Set1 Contig.22272.P4.TypeA.Set1 Contig.43393.P4.TypeA.Set1 KLPN001.0523.00015.001C.P4.TypeB.variant0002.Set2 Contig.35361.P4.TypeA.Set1 KLPN001.0523.00797.001C.P4.TypeB.variant0002.Set1 Contig.37725.P4.TypeB.variant000002.Set1 Contig.143803.P4.TypeB.variant000002.Set1 Contig.33438.P4.TypeA.Set1 Contig.182330.P4.TypeA.Set1 Contig.32352.P4.TypeA.Set1 Contig.43977.P4.TypeB.variant000002.Set1 Contig.22327.P4.TypeB.variant000002.Set1 Contig.02263.P4.TypeA.Set1 Contig.41976.P4.TypeA.Set1 Contig.185226.P4.TypeA.Set1 Contig.44913.P4.TypeA.Set1 Contig.01534.P4.TypeA.Set1 Contig.28772.P4.TypeA.Set1 Contig.11670.P4.TypeA.Set1 Contig.203374.P4.TypeA.Set1 Contig.37772.P4.TypeA.Set1 Contig.08513.P4.TypeB.variant000002.Set1 Contig.26994.P4.TypeA.Set1 Contig.36798.P4.TypeA.Set1 Contig.11997.P4.TypeB.variant000002.Set1 Contig.45134.P4.TypeB.variant000002.Set1 Contig.22879.P4.TypeB.variant000002.Set1 Contig.40562.P4.TypeB.variant000002.Set1 KLPN001.0523.00630.001C.P4.TypeB.variant0002.Set1 Contig.43371.P4.TypeB.variant000002.Set1 Contig.32373.P4.TypeA.Set1 Contig.85629.P4.TypeA.Set1 Contig.63507.P4.TypeA.Set1 Contig.41712.P4.TypeB.variant000002.Set1 Contig.15878.P4.TypeA.Set1 KLPN001.0523.01220.001C.P4.TypeB.variant0002.Set1 Contig.26844.P4.TypeA.Set1 Contig.03601.P4.TypeA.Set1 Contig.08284.P4.TypeB.variant000002.Set1 Contig.153578.P4.TypeB.variant000002.Set1 Contig.146953.P4.TypeB.variant000002.Set1 Contig.102911.P4.TypeB.variant000002.Set1 KLPN001.0523.00285.001C.P4.TypeB.variant0002.Set2 Contig.11118.P4.TypeC.variant000008.Set1 Contig.56137.P4.TypeB.variant000002.Set1 Contig.114669.P4.TypeB.variant000002.Set1 Contig.23678.P4.TypeA.Set1 Contig.39503.P4.TypeA.Set1 Contig.185392.P4.TypeA.Set1 Contig.41699.P4.TypeB.variant000002.Set1 Contig.03598.P4.TypeB.variant000002.Set1 Contig.45866.P4.TypeB.variant000002.Set1 Contig.05305.P4.TypeB.variant000002.Set1 Contig.160951.P4.TypeB.variant000002.Set1 Contig.37742.P4.TypeB.variant000002.Set1 Contig.21363.P4.TypeA.Set1 Contig.31650.P4.TypeB.variant000002.Set1 Contig.95273.P4.TypeB.variant000002.Set1 Contig.40576.P4.TypeB.variant000002.Set1 Contig.10259.P4.TypeB.variant000002.Set1 Contig.26974.P4.TypeB.variant000002.Set1 Contig.79040.P4.TypeB.variant000002.Set1 Contig.103071.P4.TypeB.variant000002.Set1 Contig.07918.P4.TypeB.variant000002.Set1 Contig.43384.P4.TypeB.variant000002.Set1 Contig.174614.P4.TypeB.variant000002.Set1 Contig.148648.P4.TypeB.variant000002.Set1 Contig.01662.P4.TypeB.variant000002.Set1 Contig.16165.P4.TypeA.Set1 Contig.41753.P4.TypeA.Set1 Contig.102957.P4.TypeA.Set1 Contig.43111.P4.TypeA.Set1 Contig.84808.P4.TypeA.Set1 Contig.22285.P4.TypeA.Set1 Contig.112496.P4.TypeA.Set1 Contig.134790.P4.TypeB.variant000002.Set1 KLPN001.0523.00808.001C.P4.TypeB.variant0002.Set1 Contig.155449.P4.TypeB.variant000002.Set1 Contig.132726.P4.TypeB.variant000002.Set1 Contig.194875.P4.TypeB.variant000002.Set1 Contig.23760.P4.TypeB.variant000002.Set1 KLPN001.0523.00281.001C.P4.TypeB.variant0002.Set1 Contig.45863.P4.TypeA.Set1 Contig.27556.P4.TypeB.variant000005.Set1 Contig.167671.P4.TypeB.variant000005.Set1 Contig.42335.P4.TypeB.variant000005.Set1 Contig.41926.P4.TypeB.variant000005.Set1 Contig.32827.P4.TypeB.variant000005.Set1 Contig.07361.P4.TypeB.variant000005.Set1 Contig.21504.P4.TypeB.variant000005.Set1 Contig.37781.P4.TypeA.Set1 KLPN001.0523.01330.001C.P4.TypeB.variant0002.Set1 Contig.201446.P4.TypeB.variant000002.Set1 KLPN001.0523.01305.001C.P4.TypeB.variant0002.Set1 Contig.05825.P4.TypeB.variant000002.Set1 Contig.103080.P4.TypeA.Set1 Contig.104247.P4.TypeA.Set1 Contig.39475.P4.TypeA.Set1 Contig.02813.P4.TypeA.Set1 Contig.189679.P4.TypeA.Set1 Contig.103757.P4.TypeA.Set1 Contig.122925.P4.TypeA.Set1 Contig.103791.P4.TypeA.Set1 Contig.142021.P4.TypeA.Set1 Contig.43124.P4.TypeA.Set1 Contig.121885.P4.TypeA.Set1 Contig.103817.P4.TypeA.Set1 Contig.116259.P4.TypeA.Set1 Contig.103816.P4.TypeA.Set1 Contig.104901.P4.TypeA.Set1 Contig.57681.P4.TypeB.variant000005.Set1 Contig.21520.P4.TypeA.Set1 Contig.143154.P4.TypeA.Set1 Contig.146696.P4.TypeA.Set1 Contig.05753.P4.TypeA.Set1 Contig.09119.P4.TypeA.Set1 Contig.09958.P4.TypeB.variant000002.Set1 Contig.65391.P4.TypeA.Set1 Contig.180546.P4.TypeA.Set1 Contig.92005.P4.TypeC.variant000008.Set1 Contig.63629.P4.TypeA.Set1 Contig.62768.P4.TypeA.Set1 Contig.76240.P4.TypeA.Set1 Contig.183957.P4.TypeA.Set1 Contig.07890.P4.TypeA.Set1 Contig.103077.P4.TypeA.Set1 Contig.04072.P4.TypeA.Set1 Contig.33644.P4.TypeA.Set1 Contig.181405.P4.TypeA.Set1 Contig.119063.P4.TypeA.Set1 Contig.119059.P4.TypeA.Set1 Contig.11649.P4.TypeA.Set1 Contig.12056.P4.TypeA.Set1 Contig.65927.P4.TypeB.variant000005.Set1 Contig.143962.P4.TypeA.Set1 Contig.29987.P4.TypeB.variant000005.Set1 Contig.26866.P4.TypeB.variant000002.Set1 Contig.120985.P4.TypeA.Set1 Contig.72838.P4.TypeA.Set1 Contig.01840.P4.TypeB.variant000002.Set1 Contig.106020.P4.TypeA.Set1 Contig.78883.P4.TypeB.variant000002.Set1 Contig.05268.P4.TypeC.variant000008.Set1 Contig.124883.P4.TypeA.Set1 Contig.35263.P4.TypeA.Set1 Contig.36749.P4.TypeA.Set1 Contig.142815.P4.TypeA.Set1 Contig.152144.P4.TypeA.Set1 Contig.103280.P4.TypeA.Set1 Contig.103766.P4.TypeA.Set1 Contig.08360.P4.TypeA.Set1 Contig.124701.P4.TypeA.Set1 Contig.126877.P4.TypeA.Set1 Contig.103815.P4.TypeA.Set1 Contig.43322.P4.TypeA.Set1 Contig.25088.P4.TypeA.Set1 Contig.94170.P4.TypeA.Set1 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Tree scale: 1 Tree scale: 1 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint indicate P4 from metagenomes, without an assigned host). Note that since these are dereplicated P4 220 genomes, some P4 might be representative of a group of elements with multiple bacterial hosts (we 221 consider only the host of the representative genome). The ten outward circles represent the presence 222 (orange) or absence (white) of the ten most frequent defence systems in P4 (complete defence systems, 223 from DefenseFinder). The outermost circle indicates whether each P4 element has any other complete 224 defence system, apart from the ten most frequent in the family of elements (black shows cases where 225 another defence system is present). B. Left, number of pairs of P4 genomes with similar defence genes 226 (wGRR≥0.95) in function of the similarity between core genes (x-axis). Right, number of pairs of P4 genomes 227 with distinct defence genes (wGRR ≤0.05) in function of the similarity between core gene s (x-axis). C. 228 Spearman correlation values between the wGRR of defence genes and the bitscore values from BlastP of 229 individual core genes of P4-like satellites, for the set of all pairs of P4s. Colours of a stronger shade indicate 230 higher Spearman correlation values. E. Same as in A, but for P2 genomes and their defence systems. F. 231 Same as in B, but for P2 genomes. G. Same as in C, but for the defence and core genes of P2-like phages. 232 233 Pseudogenes of defence systems are rare in P4 and P2 234 235 Turnover of defence systems could occur in two ways. They could be first inactivated by 236 mutations or indels and subsequently replaced (Deletion -reacquisition model). 237 Alternatively, functional systems could be swapped by others before becoming defective 238 (Swap model). The first scenario suggests that systems are lost because they are not 239 selected for anymore, i.e., they are nearly neutral or even deleterious (costs outweigh 240 gains). The second scenario only requires that the new defence system is at least as 241 adaptive as the old one in the current population context . These models have diYerent 242 testable predictions. The deletion-reacquisition model predicts the frequent presence of 243 pseudogenes of defence systems whereas the swap model predicts the opposite. We 244 assessed the fraction, type, and past function of pseudogenes in P4 and P2 using 245 PseudoFinder25 (see Methods). The vast majority of P4 and P2 have at least one 246 pseudogene (94% and 98%, respectively, Fig 3), showing that defective genes remain long 247 enough to be identifiable in large numbers in these genomes. We note that, in some 248 cases, several identified pseudogenes can originate from a single gene. Although 249 pseudogenes are frequently found in defence -associated loci (Fig S8), only a very small 250 percentage of them had sequence similarity with defence-associated genes ( less than 251 1% in P4 and c.a. 2% in P2). Many more had sequence similarity to core genes (24% in P4, 252 typically Ash pseudogenes) and especially to unknown function genes (Fig 3 insets, see 253 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint File S1 for PFAM annotations). These results suggest that defence systems are frequently 254 swapped before being inactivated. Moreover, m ost pseudogenes in P4 and P2 are 255 detected as very small intergenic sequences (c.a. 90% in either P4 or P2, Fig S9), which 256 confirms that the putative defence systems detected in these elements are intact, likely 257 functional genes. 258 259 260 261 262 Figure 3. Quantification and characterization of pseudogenes in P4 -like satellites and P2 -like 263 prophages. Histograms show the distribution of pseudogenes detected by PseudoFinder per P4 -like 264 satellite (left) and P2-like prophage (right). The charts as insets show the proportion of the pseudogenes 265 annotated as defence (orange), core of each element (blue and red for P4 and P2, respectively), or with 266 other (or no) annotations (grey). 267 268 269 P4 hotspots contain numerous novel or chimeric defence systems 270 271 We found many genes of defen ce systems that lacked the typical cognate components 272 in the defen ce hotspots ( Fig S5B). These could be inactivated systems, but our 273 observation that pseudogenes of defence systems are rare make this hypothesis unlikely. 274 Instead, they might be functional novel systems resulting from re-assembly of others26,27. 275 To test this hypothesis, we selected 11 candidate systems based on their diYerent 276 characteristics (Fig 4, see File S2 for a description of the putative systems ): s ome are 277 potential variants of known systems (e.g., a Lamassu system missing a known eYector); 278 02004006008001000 # of P4 elements # of P2 elements # of pseudogenes 0 2 4 6 8 10 12 14 0 100 200 300 400 Other (74.7%) Core (24.5%) Core (7.5%) Other (90.1%) Defense (0.7%) Defense (2.4%) .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint others are mixtures of genes from diYerent systems (e.g., two genes from the PD Lambda 279 2 system, and another from the Rst_gop_cll system) ; and others are potential 280 minimizations of known systems (e.g., a Thoeris system with a single ThsA gene ). We 281 synthesized and cloned each putative system in a low copy plasmid under the control of 282 a pTet promoter, which were introduced into E. coli MG1655. A n empty plasmid was 283 transformed to the same background as a control. We then challenged these strains with 284 a collection of 28 virulent phages to test the antiviral protection of each putative defence 285 system (see Methods, Fig S10, File S2 ). 8 out of 1 1 provided protection against several 286 virulent phages (Fig 4, top 11 rows). Failure to observe protection can arise from multiple 287 causes. The most likely explanations are: (i) the defence system is functional but does 288 not target any of the 28 phages included in the present panel; or (ii) the system is 289 functional in its native host but is not properly expressed, assembled, or active in the 290 heterologous E. coli host used here. Interestingly, a system similar to the Lamassu 291 variant, which did not provide protection against the phages tested here, was recently 292 shown to be provide an anti -phage function 28. The high success rate we obtained in 293 detecting resistance against this limited phage panel strongly suggests that most of the 294 putative systems not recognized as complete by either DefenseFinder or PADLOC are 295 functional. 296 297 Some P4 (27%) and P2 (19%) lack identifiable defence genes (Fig 1B) but have genes of 298 unknown function at their main defence loci. We hypothesised that some of these could 299 be novel antiviral systems. We selected at random 8 P4 satellites with genes of unknown 300 function to test their anti-phage phenotypes, as above (Fig 4, bottom 8 rows, Fig S10). 6 301 out the 8 conferred protection against multiple virulent phages. phages. As previously, 302 this high success rate indicates that most of these unannotated loci are likely bona fide, 303 functional defence systems. We named the novel functional systems according to deities 304 from Lusitanian mythology, while waiting for a uniform standardised system of 305 nomenclature, and they are described in detail in File S3. 306 307 When possible, we characterized the novel systems using available data, sensitive 308 sequence similarity detection programs ( wjth HHPred), and structural similarity (with 309 ESMFold and FoldSeek, File S3). The Crouga system has some evidence of being an RM-310 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint like system, with one of its proteins containing PFAM domains (ResIII, DEAD and Helicase 311 C) associated with other RM systems 29. The Bandua system has two proteins with 312 domains typically associated with immune functions (a nuclease and a kinase, 313 respectively). Neither protein is recognized by current antiviral annotation pipelines. The 314 Aernus system has one protein annotated with kinase and nuclease domains, and a 315 second one annotated as a mannitol repressor. It is unknown at this point if the latter has 316 any impact in antiviral capabilities. The single protein in the Toga system has several hits 317 with protein domains associated (through FoldSeek) with the Gao_Ppl 30 and the SMC 318 defence systems31, albeit not being recognized by any of the current models for either 319 system. The Reve system is another single gene system, with ATPase and KAP family P -320 loop domains 32. Finally, the last system we tested has two proteins , one with 321 pentapeptide repeats and an IRK potassium channel domain, which could be involved in 322 membrane depolarization, while the other protein contains a Nucleotidyltransferase like 323 domain and a HEPN-like domain, suggesting it acts on host or phage RNA. A system with 324 similar components was described by others during the course of this study as Hailong33, 325 which is currently not detected by DefenseFinder or PADLOC. Hence, and despite being 326 part of the non -defence annotated genes in P4, we refer to it as Hailong to avoid 327 introducing redundant nomenclature. 328 329 The novel systems described above, together with the unannotated Hailong system, are 330 clear evidence that at least some genes of unknown function in P4 have antiviral 331 phenotypes, with most (e.g., Bandua, Aernus, Toga and Reve) providing strong protection 332 against Drexlerviridae and/or Siphoviridae phages). W e thus wondered whether other 333 genes in the defence-less elements could have similar properties. For this, we collected 334 all the genes of unknown function from P2 and P4 detected only in complete genomes, 335 to use the information on their larger chromosomal context, and analysed them using a 336 recent machine learning approach to detect antiviral domains (see Methods). We 337 observed a significant signal for the association of antiviral defences in 30% of the 338 proteins of unknown function in P4 (62%, with the method that considers the genomic 339 context), and in 15% of the unknown proteins in P2 (32%, with the method that considers 340 the genomic context) (Fig S11). We note that all the confirmed novel systems are part of 341 those predicted to have an antiviral function, due to their genetic context. The 342 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint computational predictions, together with experimental validations, demonstrate that 343 P4-like satellites constitute major loci for both established and yet -to-be-discovered 344 functional defence systems. Moreover, many of the proteins of unknown function that 345 cluster in P4 - and P2 -associated defence hotspots are predicted to encode antiviral 346 activities. 347 348 349 350 351 Figure 4. Putative and unknown defence systems in P4 provide protection against phage infection. On 352 the left are the g enomes of P4 with putative defence systems (light orange genes , top 11 rows) and the 353 genomes of P4 with genes of unknown function in their defence loci (grey genes, bottom 8 rows) . For the 354 former, the names of the genes, as well as the complete systems with which they are associated, are shown 355 in front of each genome. The regions synthetized in plasmids are boxed (exact sequences in Datasets E1 356 and E2). Heatmap of the phage resistance phenotype shows the mean fold resistance of two independent 357 replicates of each putative and unknown system against a panel of 28 E. coli phages. The degree of 358 protection is indicated by the colour (log) scale, with darker red colours indicating higher levels of 359 protection, relative to the same bacterial background with an empty plasmid. Only the infections w here 360 both replicates show increased protection, and the mean of the two replicates is ≥ 10-fold di_erence, are 361 shown as coloured squares. Asterisks indicate smaller plaque morphologies, relative to the infection of the 362 strain with the empty plasmid. Plaque-forming units were measured for each phage on cells harbouring 363 either a control plasmid or a defence system (Fig S10). Fold-resistance was calculated as the ratio between 364 these two values. All systems were expressed from pTet promoter in the presence of anhydrotetracycline 365 (aTc, 0.5 µg/ml) and measured at 37°C, except for T7 -like phages, which were measured at room 366 temperature. The raw data for the ratios system/control are shown in File S4. 367 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 368 P4 and P2 exchange defences with other MGEs but not with each other 369 370 If defence systems are constantly swapped in both P4 and P2, where do these genes 371 come from? To address this question, we searched for closely related homologs (>85% 372 identity, see Methods) of defence genes from either P4 or P2 in 32798 bacterial and in 373 27022 phage genomes. For 6% of defence genes in P4, and for 2% of the defence genes 374 in P2, we found at most one homolog , indicating that some of the se defence genes are 375 likely variants specific to the P4 and P2 in our dataset (Fig S12). Many of the remaining P4 376 and P2 defence genes have homologs in multiple genomic contexts ( Fig 5A ). Similar 377

were found when including the putative novel defence systems from the first 378 section (File S5, Fig S13). To avoid comparing elements that might have similar systems 379 because of recent common ancestry, we excluded the pairs of very similar (wGRR>=0.95) 380 P4 or P2 elements. Nevertheless, the analysis reveals that most homologs of defence 381 genes of P4 (76%) and P2 (47%) are in bacterial regions predicted to be respectively P4-382 like satellites and P2 phages. These include P4 and P2 in bacterial hosts (e.g., 383 Citrobacter, Enterobacter or Pectobacterium, Fig S1 4) where these elements’ 384 delimitation in bacterial chromosomes was not possible for lack of information on their 385 att sites (called P2* and P4* , see Methods). These elements had hence not been included 386 in our focal dataset of phages and satellites. P2 and P4 often co -occur in genomes and 387 are induced and replicated at the same time . One could thus expect that they would 388 exchange defen ce systems. Surprisingly, we found only one case of closely related 389 defence genes between P4 and P2, even when including all putative defence systems (Fig 390 S15). Hence, hitchers and helpers have not recently exchanged defence systems. 391 392 The highly similar homologs of P4 and P2 defence genes found in bacterial regions that 393 are not identified as P4 or P2 -like could be the result of recent genetic exchanges with 394 other MGEs . We found no homologs in the other families of satellites known in 395 Enterobacteria (PICI and cfPICI9,17,File S5). Both P4 and P2 defence homologs were found 396 in (non-P2 like) pro phages, albeit this was much more frequent for P2, which also has 397 defence homologs in 31 temperate and 11 virulent phage genomes (all P2-like). 398 Chromosomal regions with integrative conjugative elements 34, which are known to 399 encode antiviral systems 35, account for very few of the homologs of P4 or P2 defence 400 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint genes. P4 and especially P2 defence systems have relatively more homologs in plasmids. 401 Some of the latter could correspond to phage-plasmids (P-Ps), since they are plasmid 402 replicons identified as phages by geNomad36, although they are not part of the current 403 dataset of known P-Ps37. The MGEs and bacterial regions with homologs of defence genes 404 of P4 and P2 are sometimes within bacteria that are phylogenetically distant from the 405 hosts of P4 and P2, such as Pseudomonas or Vibrio (Fig S14). These results suggest that 406 exchange of defence systems tends to occur between similar types of elements, but can 407 also involve distinct MGEs. 408 409 Genetic exchanges with other MGEs may allow to introduce novel types of defences in P2 410 or P4, which can then be exchanged within each group of elements . For instance, the 411 phylogeny of a variant of the AVS_V system, detected in P2 from K. pneumoniae, includes 412 homologs in non-P2 prophages and uncharacteristic genomic regions from diYerent 413 bacterial hosts, that form a separate clade (Fig 5 B). Intermingled with the two main 414 clades are two terminal branches, corresponding to an uncharacteristic genomic region 415 in Proteus and a single plasmid in Du<yella. The phylogeny suggests the acquisition of 416 the system by P2 was recent. It was then followed by the dissemination of this variant of 417 AVS_V within K. pneumoniae in P2 phages. Another defence system detected in P2, Lit, 418 is mostly found in plasmids and uncharacteristic genomic regions. While being rare in 419 prophages, a homolog is found in a single P2 -like prophage (Fig S1 6A). Given its 420 singularity, and the scarcity of this type of systems in P2 (Fig 1A), this likely illustrates a 421 recent acquisition of the Lit system by this P2. 422 423 Exchange of defence system s between diYerent types of MGEs also broadens the 424 mechanisms of dissemination of the former within bacterial species. For instance, the 425 phylogeny of a variant of the PD -T7-2 A is consistent with a unique, recent exchange of 426 this system between P4 and plasmids (whose direction cannot be ascertained from this 427 data alone). The system in the plasmids has diversified in two separate genetic variants 428 that disseminated in K. pneumoniae (Fig 5C). The phylogeny of the other gene of the 429 system (PD-T7-2 B ) shows yet another variant in P4 that is disseminating the defence 430 system in Escherichia and Klebsiella hosts, with a transfer to plasmids in the latter (Fig 431 S16B). Hence, events of exchange between MGEs show the establishment and further 432 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint diversification of defence homologs in diYerent MGEs, allowing the spread of defence 433 systems within and across species through diYerent mechanisms of horizontal gene 434 transfer. 435 436 Tree scale: 1bootstrap44587286100 Proteus Enterobacter KlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiella EnterobacterCitrobacterCitrobacterDuffyelaEscherichiaEscherichiaKasokonia KlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiellaKlebsiella Tree scale: 1bootstrap6166717681 2.5kb 2.5kb Identity (%) 0 100 A B C AVS_V PD-T7-2-A .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 437 Figure 5. Highly similar h omologs of defence genes of P4 and P2 are found in completely diMerent 438 genomic contexts. A. Graph based representation of the number of instances where homologs of defence 439 genes (from complete defence systems) in P4 and P2 are found in di_erent genomic contexts . These 440 include other MGEs (plasmids, phage-plasmids, conjugative integrated elements, prophages and virulent 441 phages) or regions of the bacterial genomes that are uncharacteristic. Thickness of the arrows represents 442 the proportion of homologous matches detected between defence genes from P4 or P2 and the other 443 di_erent genomic contexts (thicker arrows correspond to a higher proportion of matches). The exact values 444 for each combination are shown in File S5. B. Phylogeny of the AVS_V gene, comprised of the gene found 445 as a defence system in a focal P2 in Klebsiella, and its homologs detected in either other P2s (red circles at 446 the tree leaves), plasmids (green circles), prophages (violet circles) or uncharacteristic genomic regions 447 (grey circles). The genes corresponding to each of the elements (or to the segments that include the 448 uncharacteristic genomic regions as grey circles ) are shown in front of the tree, with larger plasmids 449 truncated for visibility. C. Phylogeny of the PD -T7-2-A gene, comprised of the gene found in a PD -T7-2 450 defence system in a focal P4 in Klebsiella, and its homologs detected in either other P4s (blue circles at the 451 tree leaves), plasmids or uncharacteristic genomic regions. The genes corresponding to each of the 452 elements (or to the segments that include the uncharacteristic genomic regions) are shown in front of the 453 tree, with larger plasmids truncated for visibility. 454 455 Cryptic genomic islands have homologs of defence genes from P4 and P2 456 457 A large fraction of homologs of P4s or P2s identifiable defence systems are found in 458 bacterial uncharacteristic genomic regions (UGRs) that do not correspond to known 459 MGEs. Their genomic context (20 genes each side) often contained tRNAs genes, which 460 are well-known points of integration of MGEs38 (Fig S17A). Functional annotation with 461 EggNOG Mapper and PFAM revealed that some of these genes are typical from P4 or 462 prophages (Fig S17C and D, see blue and red dots). These regions also contained many 463 pseudogenes of proteins typical of MGEs (Fig S17A and B). Since these results suggested 464 that some UGRs could be defective satellites or phages , we systematically annotated 465 them using the core markers of P4 and P2 (see Methods) and PseudoFinder. In total, 745 466 URGs encode highly similar homologs of bacterial antiviral genes detected in P4s (Fig 6A, 467 File S5) and many of them ( 27%) have at least one P4 -specific marker(s). All 745 UGRs 468 have at least one pseudogene, and about half have pseudogenes (typically intergenic) 469 homologous to a P4 core gene. Conversely, in the 775 UGRs that encode highly similar 470 homologs of bacterial defence genes detected in P2s, P2 -like markers are found in ca. 471 20% of them. Although almost all (>98%) of these UGRs have at least one pseudogene, 472 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint only 5% of them correspond to a P2 -like core gene. The above observations remain 473 qualitatively similar when including the putative defence systems (Fig S18). UGRs with P4 474 or P2 core markers are thus very likely defective versions of these elements. Within them, 475 we found numerous pseudogenes of mobility functions, but the neighbouring defence 476 genes remain ed almost identical to those of intact elements, and are thus likely 477 functional (Fig 6B -C). These results mean that defective P4 and P2 either engaged in 478 genetic exchanges of defence systems with their functional counterparts, or are non-479 mobile satellites and prophages with stabilized (and conserved) defence genes . 480 Moreover, and consistent with the absence of genetic exchanges between hitcher and 481 helper (Fig 5), homologs of defence genes in P4 and P2 are also not found in defective 482 elements of the opposite type. 483 484 Almost 50% of UGRs with homologs to P4 defences and 80% of the UGRs with homologs 485 to P2 defences lack any P4- and P2-specific markers, considering both the genes and 486 pseudogenes within these regions. They are thus cryptic genomic islands, completely 487 distinct from P4/P2, and of unknown mobility. The detection of defence homologs in such 488 dissimilar islands is consistent with the observed putative exchanges of P4 and P2 489 defences with MGEs of diYerent types, where we do not expect to find large regions of 490 homology (Fig 5). 491 492 493 494 Figure 6. Quantification of pseudogenes and P4 -like/P2-like markers in uncharacteristic genomic 495 regions with homologs to defence genes encoded by P4 and P2. A. Characterization of uncharacteristic 496 genomic regions (URGs) that encode homologs to defence genes found in P4 (left bars, blue) and URGs 497 that encode homologs to defence genes found in P2 (right bars, red). We quantified the proportion of these 498 URGs that encode P4/P2 markers predicted as pseudogenes by PseudoFinder (last two bars). B. Examples 499 of P4-like satellites, and the homology of their defence systems with URGs that contain incomplete (likely 500 A B C With at least one P4 marker 745 uncharacteristic genomic regions with homologs to defence genes in P4 775 uncharacteristic genomic regions with homologs to defence genes in P2 With at least one P2 marker With at least one pseudogene With at least one pseudogene P4 marker With at least one pseudogene P2 marker Septu PD-T7-2 Hachiman 2.5Kb 2.5Kb ThsB (Thoeris) PD-Lambda-5 PDC-S06 PDC-S49 MTase (RM Type II) Identity (%) 0 100 050100 Percentage 0 50 100 Percentage .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint defective) P4-like satellites. In each genomic comparison, the coloured arrows indicate P4-like core genes 501 that were detected as intergenic pseudogenes in the URGs. C. Examples of P2 -like prophages, and the 502 homology of their defence systems with URGs that contain incomplete (likely defective) P2-like prophages. 503 In each genomic comparison, the coloured arrows indicate P2 -like core genes that were detected as 504 intergenic pseudogenes in the genomic regions. 505 506 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint

507 508 The systematic detection of defence genes in prophages and satellites is a strong 509 statement on the selective importance of antiviral functions for the ecology and evolution 510 of these MGEs . Given the prevalence of P4 and P2 in Enterobacteria17, and the large 511 proportion of their accessory genes that we show here to be dedicated to defence, these 512 MGEs constitute a significant fraction the bacterial repertoire of defences. Yet, the 513 elements’ pangenome dynamics show that the sampling of their natural diversity is not 514 yet exhausted, even when considering, for the first time, the vast diversity of P4 elements 515 in metagenomes using Logan18. Our experimental validation of anti-phage activity for 13 516 novel systems encoded by P4 confirms that the contribution of defence functions to the 517 pangenomes of P4 and P2, as well as to the antiviral repertoire of their bacterial hosts, 518 will keep surprising us. 519 520 The diversity of antiviral functions in P4 and P2 is driven by events of genetic swaps at 521 defence-specific hotspots, enlightening the underlying processes of natural selection in 522 MGE-defence associations . A novel system will fix in a population of MGEs if it has 523 adaptive value . Targeted phages may, over time, adapt to resist this novel system , 524 reducing the selective advantage of retaining it in the MGE genome . It has remained 525 unclear if this process typically runs until the defen ce systems become neutral (or even 526 deleterious, e.g., due to autoimmunity 39) or if defen ces are replaced before hand. Our 527 observation of rapid replacement of the systems and the lack of defen ce-associated 528 pseudogenes at these loci suggest that recombination quickly swaps functional systems 529 without the latter passing by a period of inactivation. Although many small intergenic 530 regions predicted as pseudogenes are in defence loci, they are likely remnants of an 531 intense process of recombination. What little may remain of antiviral genes in these 532 regions lost any recognisable homology with known defences , even if they could 533 potentially give rise to novel defence genes40. These findings have two implications. First, 534 defence systems may be lost when they are still adaptive: it suYices that the novel system 535 is more adaptive for the swap to be fixed in the population by natural selection. Second, 536 it suggests that systems spend little time, if any, as neutral components of the MGE 537 genome. 538 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 539 P4 and P2 exchange their defen ce systems with elements of the same type and , less 540 frequently, with other MGEs. Yet, they do not exchange with each other. This is puzzling 541 because P4 and P2 frequently co -occur within bacterial hosts , and are co -induced, 542 replicate and package their DNA simultaneously41. This should provide plenty of 543 opportunities for genetic exchanges 9,42, particularly since phage induction, replication 544 and recombination are mechanistically concomitant43,44. Three factors may explain this 545 result. First, exchanges by homologous recombination require high sequence identity 546 that is lacking between P2 and P4 45. Yet, we do observe exchanges between these 547 elements and other unrelated MGEs, like plasmids. Second, because P4 and P2 often co-548 occur in genomes, there might be selection against the presence of redundant defences 549 in the two elements. DiYerent types of defences in P2 and P4 would maximize the range 550 of anti-phage defence of the consortium . Identical defences would be redundant , and 551 one set could be easily lost by genetic drift. Third, if P2 have defence systems to prevent 552 P4 infection , or to avoid the hijacking of P2 particles by P4 , these systems might be 553 counter-selected in P4 . Conversely, P4 might carry defence systems that increase the 554 fitness of P4 by decreasing the ability of P2 to use its own capsids. If they exist, such 555 genes are not expected to be acquired by P2 phages. 556 557 Despite the lack of exchanges between P2 and P4, we found very similar defence systems 558 in distinct MGEs or genomic islands , suggesting that genetic exchanges between very 559 diYerent elements is possible. It is diYicult to estimate the direction of these exchanges, 560 although in some cases the defence was very likely acquired by P4 or P2 from other 561 MGEs. When a phage or a satellite acquires a defence gene from a plasmid, the system 562 can now be exchanged more easily with other satellites or phages46. These exchanges 563 can also contribute to the flow of antiviral genes between phylogenetically distant 564 bacteria, if the MGEs involved in these exchanges have diYerent host range s. We also 565 found defence homologs in defective MGEs. It will be interesting to investigate if this 566 corresponds to their domestication, resulting in the stabilization of the defence genes in 567 bacterial genomes, or if defective elements still actively swap their defences with other 568 MGEs. 569 570 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint Defence genes in P4 and P2 have evolutionary histories that are strikingly diYerent from 571 the rest of the elements’ genomes. Antiviral defences, in accordance with the idea that 572 they are “guns for hire”, change genomic contexts of MGEs as quasi-independent 573 entities47. Yet, they do so in ways that resemble the change of bacterial chromosome 574 contexts by MGEs : frequent recombination breaks genetic linkage between defence 575 genes and the core genes of the elements , like MGEs are unlinked from the bacterial 576 chromosome lineage48; defence genes integrate predictable (hotspot) locations, like 577 MGEs in bacterial chromosomes 49 (through a presumably diYerent mechanism) ; the 578 modularity of defence systems can promote the emergence of hybrids through 579 recombination, resembling the modularity of the evolution of prophages50,51; defence 580 genes are a large fraction of the satellite and the phage’s pangenomes , similar to the 581 contribution of MGEs to bacterial pangenomes 52; and defence genes provide accessory 582 functions to both phages and satellites, which in turn do the same to their bacterial 583 hosts2. The key diYerence is that defence systems are not known to encode mobilization 584 functions. Instead, our results suggest that P2 and P4 hotspots function as factories of 585 novel systems by recombination processes that still need to be elucidated. It also 586 remains to clarify how mutations and natural selection act on these chimeras to 587 eventually lead to their fixation as functional hybrid systems. In summary, our work 588 shows that P2 and P4 can be seen as genetic platforms that accumulate, diversify, and 589 then disseminate bacterial defence systems across microbial populations. 590 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint

591 592 Genomic and metagenomic datasets 593 594 We retrieved all the complete genomes of the NCBI non -redundant RefSeq database 595 (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/, last accessed in May 2023), which consists 596 of 32799 complete bacterial genomes. The metagenomes used for the detection of P4 -597 elements were retrieved by aligning a query set of 538 clustered P4 protein sequences to 598 Logan v1.1 contigs using DIAMOND253, as described in the Logan manuscript18. We also 599 retrieved from GenBank a dataset with 27022 complete bacteriophage genomes 600 (retrieved March 2024). The lifestyle of each of these bacteriophages was inferred using 601 Bacphlip54. 602 603 Identification and delimitation of genomic regions of P4-like satellites or P2-like 604 prophages in complete bacterial genomes 605 606 P4-like satellites were initially detected from the RefSeq bacterial genomes as described 607 previously17. This resulted in 3437 P4-like genomes of Type A or B. All prophages encoded 608 by bacterial genomes were detected using geNomad (version 1.5.2, default 609 parameters)36. In total, we detected 88288 prophages in the RefSeq bacterial genomes. 610 We then designed a MacSyFinder 55 model corresponding to a prototypical P2 -like 611 prophage. The components of the model include the GpQ-L operon, which is conserved 612 in P2 -like prophages56, as well as an integrase and a primase (GpA). This model was 613 directly applied to the prophages detected by geNomad, resulting in 8165 P2-like 614 prophages of Type A, B or C. The latter two types of P2 -like prophages are often missing 615 either the integrase, or the primase. We speculate that these two components are either 616 less conserved than the profiles used for the GpQ-L operon, or excluded by geNomad 617 during the predicted prophage region. The proteomes of these elements were retrieved 618 by extracting all the genes within the farthest core components. This general set of non-619 att delim ited 3437 P4-like satellites and 8165 P2-like prophages constitutes what we 620 name, respectively, the broad P4* and P2* categories. 621 622 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint A stricter definition of the genomic regions corresponding to P4 and P2 was achieved by 623 identifying att sites (attL and attR) at the borders of the se elements in three bacterial 624 species, Escherichia coli (Ec), Klebsiella pneumoniae (Kp), and Salmonella enterica (Se), 625 which constitute the most abundant hosts of P4 and P2 elements17. To do so, we started 626 by identifying genomic spots containing P2 or P4 core genes across bacterial 627 chromosomes. The genomic positions of P4 and P2 elements described above were 628 mapped relative to persistent genes in the three host species (Ec: 2527 genomes, Kp: 629 1510 genomes, and Se:1256 genomes) to facilitate MGE delimitation and comparison 630 across genomes. The pangenome of each species (i.e., the full bacterial species gene 631 repertoire, not to be confused with the P2/P4 pangenome) was computed using the 632 pangenome module of PanACoTA v1.4.1 -dev57, applying a minimum sequence identity 633 and coverage threshold of 80%. Persistent gene families—those present in a single copy 634 in at least 90% of genomes —were extracted using the corepers module of PanACoTA. 635 Intervals were defined as the regions between two consecutive persistent genes within 636 genomes. P2 and P4 core genes are not persistent across species and are confined to 637 these intervals, providing an upper bound for their genomic positions. In total, 6,008 638 intervals containing P2 or P4 core genes (excluding integrases) were identified across the 639 three species (2258 in Ec, 2,66 in Kp, and 1384 in Se). Intervals from genomes of the same 640 species were grouped into genomic spots if flanked by the same pair of persistent gene 641 families, allowing comparison of equivalent regions across genomes. The number of 642 genomic spots occupied by P2 and P4 was generally low in each species (30 in Ec, 16 in 643 Kp, and 21 in Se). 644 645 P2 and P4 integrate the bacterial chromosome using a Tyrosine recombinase (integrase), 646 which mediates site-specific recombination between the host attB site and the MGE attP 647 site. Integration duplicates part of attB at the element edges, generating attL and attR58, 648 which can be identified by sequence similarity within genomic spots. For each spot 649 described above, the shortest interval observed in the species was extracted as the 650 ancestral MGE-free state containing attB; when this assumption does not hold, att sites 651 cannot be reliably identified. Each such interval was then compared using sequence 652 alignments with longer intervals containing P2 or P4 elements, expected to harbour short 653 repeats of attB at their edges. To ensure at least two significant sequence alignments per 654 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint comparison and to account for possible integrations within persistent genes, intervals 655 were extracted including the flanking persistent genes and oriented so that these genes 656 point in the same direction, restricting the search to the positive strand for computational 657 eYiciency. Sequence similarity between the shortest interval (query, attB) and each 658 longer interval (subject, candidate attL/attR) within the same spot was screened using 659 BLASTn of BLAST 2.9.0+ 59 (-evalue 0.001 -strand plus). Alignments with ≥80% identity 660 were retained, and redundant hits fully contained within longer alignments were 661 discarded. Pairs of hits on the subject aligning to overlapping regions of the query were 662 interpreted as duplications associated with integration. The overlapping region on the 663 query defines the putative attB site, and the corresponding regions on the subject define 664 attL and attR. Pairs of att sites flanking all P4/P2 core genes were then selected to 665 precisely predict element boundaries, resulting in the delimitation of 2175 elements in 666 Ec, 2230 in Kp, and 1357 in Se, corresponding to 96 % of intervals containing P2/P4 core 667 genes. This approach does not rely on genomic context, such as the presence or position 668 of tyrosine recombinase genes (unlike methods such as TIGER 60). Although integrases 669 were not considered while detecting P4 and P2 spots , they are present in nearly all 670 delimited elements – with only 76 exceptions - and in most cases (5638), the integrase is 671 located within 2kb of an element boundary, demonstrating the robustness of our method. 672 Att site pairs (sequences), element size, and integrase presence are provided in File S6. 673 674 From the P4/P2 intervals with an att identification, we further filtered the elements 675 according to their size (<20kb for P4 and <50kb for P2) and discarded P4 that were lacking 676 more than two core genes (i.e, only considered P4 of Type A or B, according to 677 SatelliteFinder). Delimiting and filtering the elements in the 3 main bacterial species, 678 resulted in a total of 2168 P4-like satellites and 3574 P2-like prophages originating from 679 complete bacterial genomes. 680 681 Identification and delimitation of genomic regions of metagenomes that correspond to 682 P4-like satellites 683 684 To detect P4-like satellites in the metagenomic contigs, the latter were initially processed 685 as described previously in18. The 7 P4 core genes were detected in a set of 210895 “P4-686 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint like contigs” . An initial step of dereplication of data was performed in these full contigs, 687 using MMSeqs2 61 with an identity cutoY of 0.999 and a (default) minimum of 80% 688 coverage. This resulted in 16205 unique “P4-like contigs” . The collection of att sites 689 detected for the P4-like satellites in the 3 main bacterial species (described above) were 690 then used to subsequently delimit the regions in each contig that correspond to a P4-like 691 satellite. Briefly, we used blastn with the blastn-short option to detect the att sites in each 692 contig, retaining matches with ≥ 70% identity. To consider possible variation in att sites, 693 we did not enforce the match with both a specific attL and attR sequence, but instead 694 searched for either one of these sequences (i.e., two attL or two attR sequences would 695 suYice). We then extracted the shortest regions that correspond to nucleic sequences 696 that are surrounded by two of these att sequences, requesting a minimum of 5kb and a 697 maximum of 20kb in length for the whole att-defined region, according to the expected 698 distribution of sizes of P4 -like elements. This resulted in 6039 unique P4-like replicons. 699 To confirm that these regions correspond to the expected P4 -like satellites with enough 700 components, we first used Prodigal to extract the proteins, and then used SatelliteFinder 701 to characterize the putative P4s. This resulted in a total of 6026 P4-like satellites, where 702 most sequences ( 6001) correspond to P4 -like satellites of Type A or B ( Fig S 1). This 703 suggests that our delimitation of P4 -like regions using the known att-sites, whilst likely 704 conservative and resulting in the discarding of some valid elements, is appropriate to 705 properly define the regions of P4-like satellites. 706 707 Dereplication of P4 and P2 genomes 708 709 To dereplicate the final dataset used for the analyses, we merged the nucleotide 710 sequences from the att-defined P4-like satellites in E. coli, K. pneumoniae and S. enterica 711 with all the att-defined P4-like contigs from the metagenomes. We then clustered these 712 replicons using MMSeqs2 with the same identity cutoY as before ( 0.999) but with a 713 stricter 99% coverage threshold, to avoid the merging of elements that have only one 714 gene that is distinct. A similar approach was done for the att-defined P2-like prophages 715 in the 3 main bacterial species. This resulted in a final dataset of 3085 dereplicated P4-716 like satellites and 1511 dereplicated P2-like prophages, which we use for all the analysis 717 described in the manuscript. 718 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 719 Identification of defence genes and systems 720 721 The detection of defence genes and systems were done with DefenseFinder version 2.0.0 722 (defense-finder-models database v2.02) 19, using the default options. We included the 723 flag -a to detect the anti -defence systems as well , albeit none were detected in P4 -like 724 satellites, and very few in P2-like prophage (see main text for details). We used PADLOC 725 version 2.0.0 20 to complement the detection of complete defence systems by 726 DefenseFinder. To retrieve genes associated with putative defence systems, we extracted 727 the best hit for each gene from the * .hmmer.tsv output file of DefenseFinder. 728 729 To identify the gene repertoire of defence systems in the bacterial hosts of P4 (restricted 730 to P4 detected in complete bacterial genomes) and P2 elements, we identified the 731 defence systems in the bacterial genomes of the three main species ( E. coli, K. 732 pneumoniae and S. enterica) that encoded at least one P4 and/or one P2, using the same 733 approaches as above. The defence gene families in bacterial hosts were computed by 734 collecting, for each species, the genes of the defence systems (either in DefenseFinder 735 or PADLOC) and clustering all the corresponding protein sequences using MMSeqs2 736 (again, the clustering was performed per each of the three species, and for each dataset, 737 DefenseFinder or PADLOC individually). A defence gene family was considered to be 738 associated with P4 or with P2 if at least one of the genes of the family is within an att-739 defined P4 or P2 genome of the three main species. 740 741 Calculation of P4 and P2 pangenome accumulation curves 742 743 We first clustered at 40% identity all proteins of the dereplicated P4 satellites, and all 744 proteins of the dereplicated P2 prophages, using the MMSeq2 cluster function, with the 745 parameters cluster_mode 1 and the default coverage. Then, for each category of 746 elements (P4 or P2), we randomized the order of the elements and calculated the number 747 of new gene families added by each consecutive element, annotating whether their 748 representative sequences correspond to a defence-associated gene or a core gene of the 749 respective element. 750 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 751 Calculation of genomic similarity between P4-like satellites and between P2-like 752 prophages 753 754 We searched for sequence similarity between all proteins of satellites using MMseqs2 755 with the sensitivity parameter set at 7.5 to align all versus all proteins. For specific 756 datasets (core or defen ce genes), the datasets were limited to the genes that were 757 annotated with the specific core markers or identified as defence -associated. We then 758 performed the combinations between diYerent datasets as well (e.g., defence vs core or 759 defence vs whole proteome). The outputs of MMSeqs2 were converted to the blast format 760 and we kept for analysis the hits respecting the following thresholds: e-value lower than 761 0.0001, at least 35% identity, and a coverage of at least 50% of the proteins (since 762 MMSeqs2 searches for local similarity). The hits were used to retrieve the bi -directional 763 best hits between pair of genomes, which were in turn used to compute a score of gene 764 repertoire relatedness weighted by sequence identity: 765 𝑤𝐺𝑅𝑅 = ∑ 𝑖𝑑(𝐴!, 𝐵!)" ! min (𝐴, 𝐵) 766 767 where A i and B i is the pair I of homologous proteins present in A and B, id( Ai,Bi) is their 768 sequence identity in the local alignment, and min( A,B) is the number of proteins of the 769 genome encoding the fewest proteins (A or B). wGRR is the fraction of bi-directional best 770 hits between two genomes weighted by the sequence identity of the homologs. It varies 771 between zero (no bi-directional best hits) and one (all genes of the smallest genome have 772 an identical homolog in the largest genome). Hence, a wGRR=1 means that the two 773 elements are identical (or one is entirely contained within the other), whereas wGRR=0 774 means the elements have no homologous protein -coding genes. wGRR integrates 775 information on the frequency of homologs and sequence identity. For example, when the 776 smallest genome has 10 proteins, a wGRR of 0.2 can result from two identical homologs 777 or five homologs each with a lower sequence similarity (40%). All wGRR calculations in 778 the manuscript were obtained through GRIS version 2 779 (https://gitlab.pasteur.fr/jgugliel/gris). 780 781 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint Calculation of the pairwise similarity of core genes of P4 or P2 782 783 To calculate the pairwise similarity between each core gene, we first collected and 784 concatenated in a fasta file all the individual core genes of P4-like satellites (7 core genes) 785 and P2-like prophages (7 core genes). Each of these files with concatenated proteins was 786 simultaneously used as both query and target database in Diamond BlastP , in order to 787 retrieve the best pairwise matches. The parameters used were the following: --query-788 cover 50, --ultra-sensitive and --max-target-seqs 0. We then retrieved the best matches 789 for each core gene between each pair of elements. 790 791 Identification of pseudogenes 792 793 Pseudogenes were detected using PseudoFinder version 1.1.0 25, using the default 794 parameters. We first generated the GenBank files from the sequences to be analysed (P4-795 like satellites, P2 -like prophages, or uncharacteristic genomic regions of bacterial 796 genomes). We used as a reference database the complete set of bacterial proteins from 797 the RefSeq bacterial collection used in this study (see Bacterial genomic and 798 metagenomic datasets ). We then analysed the p utative pseudogenes reported by 799 PseudoFinder either as an existing ORFs or as an intergenic region predicted to be a 800 pseudogene. To functionally annotate the latter, we used the ORF from the RefSeq 801 bacterial dataset that better matches each intergenic sequenced (as reported by 802 PseudoFinder, using BlastX). The putative pseudogenes (ORFs and intergenic) were then 803 functionally annotated with the HMM profiles corresponding to the P4 and P2 core genes 804 and analysed with DefenseFinder and PADLOC to detect defen ce-associated genes. 805 Additionally, we annotated the pseudogenes using EggNoggMapper version 2.1.1262, with 806 the -m diamond parameter and with all the other parameters left as default. 807 808 Cloning of candidate defence systems 809 810 Putative defence systems, as well as unknown P4 genes, were synthesized with their 811 native promoter and cloned into the low -copy plasmid pFR66, which carries a pSC101 812 origin of replication, a kanamycin resistance cassette, and a superfolder GFP gene under 813 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint the control of a pTet promoter10. Thus, the GFP was replaced by the candidate defence 814 systems, placing them under the control of the anhydrotetracycline (aTc) inducible pTet 815 promoter. Fifty µl of E. coli K-12 MG1655 chemically competent cells prepared by 816 rubidium chloride method were transformed by heat shock at 42°C with one µl of plasmid 817 carrying the candidate defence system. After 1 h of recovery at 37°C in LB (Lysogeny 818 broth) medium, transformants were selected on LB plates supplemented with 819 kananamycin (Kan) at 50 µg/ml. All constructions were verified by Nanopore sequencing. 820 The fragments of candidate defence genes are shown in Dataset E1, whilst the complete 821 plasmid sequences are shown in Dataset E2. 822 823 Phage amplification 824 825 The panel of 28 phages tested, including both classical model phages and a 826 representative selection of phages from the BASEL collection63, as well as the T5 Mos 827 phage64, was amplified on E. coli K-12 MG1655. For amplification of phage stocks from -828 80°C, a frozen piece of phage stock mixed with 200 µl of an overnight culture of E. coli and 829 20 mL of warm (56°C) LB + CaCl2 5 mM + 0.5% agar was poured onto square plates (12 x 830 12 cm) containing LB + CaCl2 5 mM + 1% agar and incubated overnight at 37°C except for 831 the T7 -like phages that were incubated at room temperature. The top -agar layer was 832 recovered with 1 mL of PBS 1X from plates on which confluent lysis was observed and 833 transferred into a 50 mL conical tube. The top agar was then disrupted by vortexing until 834 broken into small pieces. Tubes were then left to incubate 10 min at room temperature 835 before centrifugation at 4,000 g for 5 min. Finally, the supernatant was recovered and 836 filtered with a 0.45 µM filter. The phage lysates were stored at 4°C. To determine the titer 837 of the phage lysates, the lysates were serially diluted and spotted onto lawns of E. coli 838 MG1655. 839 840 Phage plaque assays 841 842 E. coli K-12 MG1655 strains carrying each putative defence system or the control plasmid 843 pFR66 were grown overnight in LB supplemented with Kan 50 µg/ml. Bacterial lawns were 844 prepared by mixing 200 µL of a stationary culture with 100 µl of 1 mM CaCl2 and 20 mL of 845 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint LB containing 0.5% agar, and the mixture was poured onto square plates (12 x 12 cm) of 846 LB supplemented with Kan 50 µg/ml with or without 0.5 µg/ml aTc. Serial dilutions of high-847 titre (>108 pfu/mL) phage stocks were spotted onto each plate and incubated overnight 848 at 37°C or at room temperature for T7 -like phages. The next day, plaques were counted, 849 and fold resistance was calculated as the number of plaques in the presence of each 850 system divided by the number of plaques on the control plate. When plaques were too 851 small to be counted individually, the highest -concentration dilution showing no visible 852 plaques was conservatively scored as containing a single plaque. 853 854 Machine learning detection of antiviral domains in P4-like satellites and annotation of 855 novel defence systems 856 857 To annotate the candidate defence systems and characterize potential antiviral domains, 858 sequence and structural homology analyses were performed. Sequence homology was 859 first assessed using Pfam -A annotation using PyHMMER 65 (v0.11), a Pyhton library 860 binding to HMMER 66 (v3.4). To annotate protein regions without Pfam annotations, 861 HHpred67 was used with 3 iterations on Pfam -A (online version) to identify conserved 862 domains via profile -to-profile Hidden Markov Model (HMM) comparisons. Structural 863 predictions were used for both homology detection and representation. For homology 864 detection, 3D protein models were generated using ESM-Fold, and the resulting PDB files 865 were processed through the Foldseek web server68 to identify structural homologs within 866 the PDB and AlphaFold databases. In the second approach, AlphaFold 3.0.1 was 867 employed to generate structural predictions, evaluating monomeric or dimeric 868 configurations (when the system has 2 genes). When possible, we annotated whether the 869 novel systems were predicted as potentially defensive 69 (GeneCLR hit in File S3). These 870 integrated structural data were used to infer the presence of specialized antiviral eYector 871 or sensor domains by comparing the predicted folds to known defence -related protein 872 architectures. 873 874 Genes of unknown functions were scored by both the ESM -650MDF and the 875 geneCLRDF scores as defined in 69. The methods were run on representative sequences 876 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint when clustering the database at 95% of identity. Thus, we mapped the genes of unknown 877 function to their representative 95 and retrieved the corresponding scores. 878 879 Detection of homologs of P4/P2 defence genes in bacterial and bacteriophage genomes 880 881 We collected all defence-associated proteins in P4-like satellites and P2-like genomes, 882 and then used this set with Diamond BlastP to search for homologs in the complete 883 RefSeq bacterial genomes, including their plasmids. We used Diamond BlastP with the 884 parameters --query-cover 50, --ultra-sensitive and --max-target-seqs 0 . We then 885 retrieved all matches with at least 85% identity with the query sequence and consider 886 these as homologs of the matched defence genes. We did a similar analysis to search for 887 homologs of P4 or P2 defence-associated proteins in the dataset of 27022 bacteriophage 888 genomes described above. 889 890 The genomic context of the homologs detected in bacterial genomes is assigned as a 891 plasmid (if in a secondary replicon of the bacterial genome), a prophage (if in a region 892 detected as such by geNomad), a satellite (if in a region detected as such by 893 SatelliteFinder), a phage -plasmid (if the plasmid replicon correspond to known phage -894 plasmids37 or if geNomad detects a secondary replicon as a prophage) or an integrative 895 mobile element (i.e., Integrative Conjugative Elements – ICEs –, Integrative Mobilizable 896 Elements – IMEs – or iOriTs, if in a region detected as described in 34). If the defence 897 homolog was detected in a bacterial genomic region that does not correspond to any of 898 the categories above, we assigned it as an “uncharacteristic genomic region” . 899 900 To account for the possibility that homology of defen ce systems is caused by vertical 901 descent within the element, i.e., cases where an homolog of a P4/P2 defence gene was 902 found in a bacterial region that corresponds to that same P4/P2, we calculated the core 903 (minus the integrase) wGRR (see section above) between all P4 and P4* , and all P2 and 904 P2* , and discarded homologous matches with elements that had a wGRR of at least 0.95. 905 906 Phylogenetic analyses 907 908 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint To compute the phylogenies of P4 and P2 elements, we extracted all their respective core 909 proteins (except for the integrase), and aligned each set of proteins individually, using 910 using maYt -linsi70 (v. 7.490, default parameters). The individual alignments of core 911 proteins were then concatenated in two alignments (one with the P4 core proteins, 912 another with the P2 core proteins). For elements where some core genes were missing, a 913 sequence of gaps (“-“) was added. The resulting alignment was trimmed with clipkit71 (v. 914 1.3.0, default parameters). We then used IQ -Tree72 (v. 1.6.12) to build the phylogenetic 915 trees, with the options –bb 1000 to run the ultrafast bootstrap option with 1000 replicates 916 and -m TEST option for automatic model choice . The resulting tree files were visualized 917 and edited using the v5 webserver of iTOL73 918 919 The phylogenies of individual defence genes were inferred by aggregating in single fasta 920 files all the protein sequences corresponding to homologous matches of specific 921 defence genes (PD-T7-2, Lit and Avs_V). Systems with more than one gene (i.e., PD-T7-2) 922 were aggregated in separate files, and each gene was processed separately . The 923 alignments and phylogenies were assembled and visualized as described above. 924 925 Functional annotation of uncharacteristic genomic regions 926 927 Homologous matches of defence genes of P4/P2 in bacterial chromosomic regions that 928 do not correspond to known MGEs were defined as “uncharacteristic genomic regions” . 929 To analyse the genomic context of these homolog genes, we extracted 20 genes upstream 930 and 20 genes downstream. These regions were then further annotated with 931 DefenseFinder19 and PADLOC20, P4 and P2-specific HMM markers, and EggNogMapper62, 932 all with the same parameters described above in each section. We also used 933 PseudoFinder25, as described above, to detect pseudogenes in these uncharacteristic 934 genomic regions, and the intergenic pseudogenes detected were further classified with 935 P4 and P2 specific HMM profiles. To maintain specificity, we excluded from the search for 936 core markers the integrase of P4/P2, as well as Delta and AlpA of P4 , since homologs to 937 these components can be found in other MGEs. 938 939 Visualization of genomic regions 940 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 941 Genome visualization across the manuscript uses Clinker version 0.0.3 74 with the -i 942 parameter set at 0.3 at the other parameters were left as default. The JSON output files 943 were edited to better represent the colors of the gene clusters. 944 945

946 947 We thank all the Microbial Evolutionary Genomics Unit members for the regular 948 discussions throughout the project. The authors also wish to acknowledge the students 949 of the 2025 M2 Microbiology course at Institut Pasteur (Pierric Chup pa, Hugo Cibla, Léa 950 Dunand-Sauthier, Esteban Francois, Thibault Frisch, Theana Gardais, Chiara Gouviaux -951 Deletraz, Dorian JoYres, Ekaterina Korotaeva, Kevin Koule, Jeane Le Floch, Nicolas Le 952 Jalle, Laly Meyer, Laura Ochsenbein, Orane Pion, Maël Rochefort, Corentin Rohel, 953 Alexandre Roubaud, Inès Santos and Sofia Tagkalidou) , who collaborated in the 954 preliminary assays of infection the candidate defence systems. This work used the 955 computational and storage services (MAESTRO cluster) provided by the IT department at 956 Institut Pasteur, Paris. We acknowledge support from the Laboratoire d’Excellence IBEID 957 Integrative Biology of Emerging Infectious Diseases [ANR-10-LABX-62-IBEID], the Agence 958 Nationale de Recherc he [ANR 23 CE20 0046 01 TRIADE] and [ANR-20-CE12-0004 959 TransfoConflict] and the HORIZON programme [ HORIZON-MSCA-2024-PF-01 TriSH] . 960 This work used the computational and storage services (MAESTRO cluster) provided by 961 the IT department at Institut Pasteur, Paris. 962 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint

963 964 1. Clokie, M. R. J., Millard, A. D., Letarov, A. V . & Heaphy, S. Phages in nature. 965 Bacteriophage 1, 31–45 (2011). 966 2. Touchon, M., Moura de Sousa, J. A. & Rocha, E. P . Embracing the enemy: the 967 diversification of microbial gene repertoires by phage-mediated horizontal gene 968 transfer. Curr. Opin. Microbiol. 38, 66–73 (2017). 969 3. Shkoporov, A. N., Turkington, C. J. & Hill, C. Mutualistic interplay between 970 bacteriophages and bacteria in the human gut. Nat. Rev. Microbiol. 971 https://doi.org/10.1038/s41579-022-00755-4 (2022) doi:10.1038/s41579-022-00755-972 4. 973 4. Dedrick, R. M. et al. Prophage-mediated defence against viral attack and viral 974 counter-defence. Nat. Microbiol. 2, 16251 (2017). 975 5. Brenes, L. R. & Laub, M. T. E. coli prophages encode an arsenal of defense systems to 976 protect against temperate phages. Cell Host Microbe 33, 1004-1018.e5 (2025). 977 6. Beamud, B., Benz, F . & Bikard, D. Going viral: The role of mobile genetic elements in 978 bacterial immunity. Cell Host Microbe 32, 804–819 (2024). 979 7. Clabby, T., Tesson, F ., Gaborieau, B. & Bernheim, A. Why do bacteria accumulate 980 antiphage defence systems? Philos. Trans. R. Soc. B Biol. Sci. 380, 20240082 (2025). 981 8. Ares-Arroyo, M., Coluzzi, C., Moura De Sousa, J. A. & Rocha, E. P . C. Hijackers, 982 hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements. PLOS Biol. 983 22, e3002796 (2024). 984 9. Penadés, J. R., Seed, K. D., Chen, J., Bikard, D. & Rocha, E. P . C. Genetics, ecology 985 and evolution of phage satellites. Nat. Rev. Microbiol. 23, 410–422 (2025). 986 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 10. Rousset, F . et al. Phages and their satellites encode hotspots of antiviral 987 systems. Cell Host Microbe 30, 740-753.e5 (2022). 988 11. Puigbò, P ., Makarova, K. S., Kristensen, D. M., Wolf, Y . I. & Koonin, E. V . 989 Reconstruction of the evolution of microbial defense systems. BMC Evol. Biol. 17, 94 990 (2017). 991 12. Hussain, F . A. et al. Rapid evolutionary turnover of mobile genetic elements 992 drives bacterial resistance to phages. Science 374, 488–492 (2021). 993 13. Hatfull, G. F . Bacteriophage genomics. Curr. Opin. Microbiol. 11, 447–453 (2008). 994 14. Dion, M. B., Oechslin, F . & Moineau, S. Phage diversity, genomics and phylogeny. 995 Nat. Rev. Microbiol. 18, 125–138 (2020). 996 15. Kindt, J., Tzlil, S., Ben-Shaul, A. & Gelbart, W. M. DNA packaging and ejection 997 forces in bacteriophage. Proc. Natl. Acad. Sci. 98, 13671–13674 (2001). 998 16. Leclercq, S. & Cordaux, R. Do phages eYiciently shuttle transposable elements 999 among prokaryotes? Evolution 65, 3327–3331 (2011). 1000 17. de Sousa, J. A. M., Fillol-Salom, A., Penadés, J. R. & Rocha, E. P . C. Identification 1001 and characterization of thousands of bacteriophage satellites across bacteria. 1002 Nucleic Acids Res. gkad123 (2023) doi:10.1093/nar/gkad123. 1003 18. Chikhi, R. et al. Logan: Planetary-Scale Genome Assembly Surveys Life’s 1004 Diversity. Preprint at https://doi.org/10.1101/2024.07.30.605881 (2024). 1005 19. Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of 1006 prokaryotes. Nat. Commun. 13, 2561 (2022). 1007 20. Payne, L. J. et al. PADLOC: a web server for the identification of antiviral defence 1008 systems in microbial genomes. Nucleic Acids Res. 50, W541–W550 (2022). 1009 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 21. Fillol-Salom, A. et al. Bacteriophages benefit from mobilizing pathogenicity 1010 islands encoding immune systems against competitors. Cell 185, 3248-3262.e20 1011 (2022). 1012 22. Christie, G. E. & Calendar, R. Bacteriophage P2. Bacteriophage 6, e1145782 1013 (2016). 1014 23. Nilsson, A. S. & Haggård-Ljungquist, E. Evolution of P2-like phages and their 1015 impact on bacterial evolution. Res. Microbiol. 158, 311–317 (2007). 1016 24. Egorov, A. A., Hauryliuk, V . & Atkinson, G. C. Systematic annotation of hyper-1017 variability hotspots in phage genomes and plasmids. Preprint at 1018 https://doi.org/10.1101/2024.10.15.618418 (2024). 1019 25. Syberg-Olsen, M. J., Garber, A. I., Keeling, P . J., McCutcheon, J. P . & Husnik, F . 1020 Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes. Mol. Biol. Evol. 39, 1021 msac153 (2022). 1022 26. Mariano, G. & Blower, T. R. Conserved domains can be found across distinct 1023 phage defence systems. Mol. Microbiol. 120, 45–53 (2023). 1024 27. Georjon, H. & Bernheim, A. The highly diverse antiphage defence systems of 1025 bacteria. Nat. Rev. Microbiol. 21, 686–700 (2023). 1026 28. Haudiquet, M. et al. Structural basis for Lamassu-based antiviral immunity and 1027 its evolution from DNA repair machinery. Proc. Natl. Acad. Sci. 122, e2519643122 1028 (2025). 1029 29. Gorbalenya, A. E. & Koonin, E. V . Endonuclease (R) subunits of type-I and type-III 1030 restriction-modification enzymes contain a helicase-like domain. FEBS Lett. 291, 1031 277–281 (1991). 1032 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 30. Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in 1033 prokaryotes. Science 369, 1077–1084 (2020). 1034 31. Liu, H. W., Roisné-Hamelin, F . & Gruber, S. SMC-based immunity against 1035 extrachromosomal DNA elements. Biochem. Soc. Trans. 51, 1571–1583 (2023). 1036 32. Andersen, S. E. et al. Serine recombinases are conserved genetic markers of 1037 antiphage defense systems. Preprint at https://doi.org/10.1101/2025.10.07.681051 1038 (2025). 1039 33. Tan, J. M. J. et al. A DNA-gated molecular guard controls bacterial Hailong anti-1040 phage defence. Nature 643, 794–800 (2025). 1041 34. Ares-Arroyo, M., Junker, R., Nucci, A., Touchon, M. & Rocha, E. P . C. Genomic 1042 Islands as minimal hitchers of conjugative elements. Preprint at 1043 https://doi.org/10.64898/2026.01.13.699239 (2026). 1044 35. Johnson, C. M., Harden, M. M. & Grossman, A. D. Interactions between mobile 1045 genetic elements: An anti-phage gene in an integrative and conjugative element 1046 protects host cells from predation by a temperate bacteriophage. PLOS Genet. 18, 1047 e1010065 (2022). 1048 36. Camargo, A. P . et al. Identification of mobile genetic elements with geNomad. 1049 Nat. Biotechnol. 42, 1303–1312 (2024). 1050 37. Pfeifer, E., Moura de Sousa, J. A., Touchon, M. & Rocha, E. P . C. Bacteria have 1051 numerous distinctive groups of phage–plasmids with conserved phage and variable 1052 plasmid gene repertoires. Nucleic Acids Res. 49, 2655–2673 (2021). 1053 38. Reiter, W.-D., Palm, P . & Yeats, S. Transfer RNA genes frequently serve as 1054 integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17, 1907–1914 1055 (1989). 1056 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 39. Aframian, N., Omer Bendori, S., Hen, T., Guler, P . & Eldar, A. Expression level of 1057 anti-phage defence systems controls a trade-oY between protection range and 1058 autoimmunity. Nat. Microbiol. 10, 1954–1962 (2025). 1059 40. Frumkin, I., Vassallo, C. N., Chen, Y . H. & Laub, M. T. Emergence of antiphage 1060 functions from random sequence libraries reveals mechanisms of gene birth. Proc. 1061 Natl. Acad. Sci. 122, e2513255122 (2025). 1062 41. Christie, G. E. & Calendar, R. INTERACTIONS BETWEEN SATELLITE 1063 BACTERIOPHAGE P4 AND ITS HELPERS. Annu. Rev. Genet. 24, 465–490 (1990). 1064 42. Lindqvist, B. H., Dehò, G. & Calendar, R. Mechanisms of genome propagation 1065 and helper exploitation by satellite phage P4. Microbiol. Rev. 57, 683–702 (1993). 1066 43. Smith, G. R. Chi hotspots of generalized recombination. Cell 34, 709–710 (1983). 1067 44. Mosig, G. Recombination and recombination-dependent DNA replication in 1068 bacteriophage T4. Annu. Rev. Genet. 32, 379–413 (1998). 1069 45. Vulić, M., Dionisio, F ., Taddei, F . & Radman, M. Molecular keys to speciation: DNA 1070 polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. 1071 Acad. Sci. 94, 9763–9767 (1997). 1072 46. Moura de Sousa, J. A., Pfeifer, E., Touchon, M. & Rocha, E. P . C. Causes and 1073 Consequences of Bacteriophage Diversification via Genetic Exchanges across 1074 Lifestyles and Bacterial Taxa. Mol. Biol. Evol. 38, 2497–2512 (2021). 1075 47. Koonin, E. V ., Makarova, K. S., Wolf, Y . I. & Krupovic, M. Evolutionary 1076 entanglement of mobile genetic elements and host defence systems: guns for hire. 1077 Nat. Rev. Genet. 21, 119–131 (2020). 1078 48. Sheinman, M. et al. Identical sequences found in distant genomes reveal 1079 frequent horizontal transfer across the bacterial domain. eLife 10, e62719 (2021). 1080 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 49. Oliveira, P . H., Touchon, M., Cury, J. & Rocha, E. P . C. The chromosomal 1081 organization of horizontal gene transfer in bacteria. Nat. Commun. 8, 841 (2017). 1082 50. Baker, J., Limberger, R., Schneider, S. J. & Campbell, A. Recombination and 1083 modular exchange in the genesis of new lambdoid phages. New Biol. 3, 297–308 1084 (1991). 1085 51. Dragoš, A. et al. Pervasive prophage recombination occurs during evolution of 1086 spore-forming Bacilli. ISME J. 15, 1344–1358 (2021). 1087 52. Touchon, M. et al. Phylogenetic background and habitat drive the genetic 1088 diversification of Escherichia coli. PLOS Genet. 16, e1008866 (2020). 1089 53. Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life 1090 scale using DIAMOND. Nat. Methods 18, 366–368 (2021). 1091 54. Hockenberry, A. J. & Wilke, C. O. BACPHLIP: predicting bacteriophage lifestyle 1092 from conserved protein domains. PeerJ 9, e11396 (2021). 1093 55. Néron, B. et al. MacSyFinder v2: Improved modelling and search engine to 1094 identify molecular systems in genomes. Peer Community J. 3, e28 (2023). 1095 56. Casjens, S. R. & Grose, J. H. Contributions of P2- and P22-like prophages to 1096 understanding the enormous diversity and abundance of tailed bacteriophages. 1097 Virology 496, 255–276 (2016). 1098 57. Perrin, A. & Rocha, E. P . C. PanACoTA: a modular tool for massive microbial 1099 comparative genomics. NAR Genomics Bioinforma. 3, lqaa106 (2021). 1100 58. Rajeev, L., Malanowska, K. & Gardner, J. F . Challenging a paradigm: the role of 1101 DNA homology in tyrosine recombinase reactions. Microbiol. Mol. Biol. Rev. MMBR 1102 73, 300–309 (2009). 1103 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 59. Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 1104 10, 421 (2009). 1105 60. Mageeney, C. M. et al. New candidates for regulated gene integrity revealed 1106 through precise mapping of integrative genetic elements. Nucleic Acids Res. 48, 1107 4052–4065 (2020). 1108 61. Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence 1109 searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 1110 (2017). 1111 62. Cantalapiedra, C. P ., Hernández-Plaza, A., Letunic, I., Bork, P . & Huerta-Cepas, J. 1112 eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain 1113 Prediction at the Metagenomic Scale. Mol. Biol. Evol. 38, 5825–5829 (2021). 1114 63. MaYei, E. et al. Systematic exploration of Escherichia coli phage–host 1115 interactions with the BASEL phage collection. PLOS Biol. 19, e3001424 (2021). 1116 64. Burman, N. et al. A virally encoded tRNA neutralizes the PARIS antiviral defence 1117 system. Nature 634, 424–431 (2024). 1118 65. Larralde, M. & Zeller, G. PyHMMER: a Python library binding to HMMER for 1119 eYicient sequence analysis. Bioinformatics 39, btad214 (2023). 1120 66. Eddy, S. R. Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 1121 (2011). 1122 67. Gabler, F . et al. Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. 1123 Curr. Protoc. Bioinforma. 72, e108 (2020). 1124 68. Van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. 1125 Nat. Biotechnol. 42, 243–246 (2024). 1126 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint 69. Mordret, E. et al. Protein and genomic language models chart a vast landscape 1127 of antiphage defenses. Preprint at https://doi.org/10.1101/2025.01.08.631966 (2025). 1128 70. Katoh, K. & Standley, D. M. MAFFT Multiple Sequence Alignment Software 1129 Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. 30, 772–780 1130 (2013). 1131 71. Steenwyk, J. L., Buida, T. J., Li, Y ., Shen, X.-X. & Rokas, A. ClipKIT: A multiple 1132 sequence alignment trimming software for accurate phylogenomic inference. PLOS 1133 Biol. 18, e3001007 (2020). 1134 72. Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A Fast and 1135 EYective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol. 1136 Biol. Evol. 32, 268–274 (2015). 1137 73. Letunic, I. & Bork, P . Interactive Tree Of Life (iTOL) v5: an online tool for 1138 phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021). 1139 74. Gilchrist, C. L. M. & Chooi, Y .-H. clinker & clustermap.js: automatic generation of 1140 gene cluster comparison figures. Bioinformatics 37, 2473–2475 (2021). 1141 1142 .CC-BY-NC-ND 4.0 International licensemade available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprintthis version posted March 4, 2026. ; https://doi.org/10.64898/2026.02.27.708500doi: bioRxiv preprint