Symbiont replacement and subsequent parallel genome erosion reshape a dual obligate symbiosis in the aphid Lachnus tropicalis

Symbiont replacement and subsequent parallel genome erosion reshape a dual obligate symbiosis in the aphid Lachnus tropicalis | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Symbiont replacement and subsequent parallel genome erosion reshape a dual obligate symbiosis in the aphid Lachnus tropicalis View ORCID Profile Tomonari Nozaki , View ORCID Profile Yuuki Kobayashi , Mika Ikeda , View ORCID Profile Shuji Shigenobu doi: https://doi.org/10.1101/2025.09.22.677894 Tomonari Nozaki 1 Laboratory of Evolutionary Genomics, National Institute for Basic Biology , Okazaki, Aichi 444-8585, Japan 2 Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies , SOKENDAI, Okazaki, Aichi 444-8585, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Tomonari Nozaki For correspondence: nozaki.t{at}nibb.ac.jp Yuuki Kobayashi 1 Laboratory of Evolutionary Genomics, National Institute for Basic Biology , Okazaki, Aichi 444-8585, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yuuki Kobayashi Mika Ikeda 1 Laboratory of Evolutionary Genomics, National Institute for Basic Biology , Okazaki, Aichi 444-8585, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Shuji Shigenobu 1 Laboratory of Evolutionary Genomics, National Institute for Basic Biology , Okazaki, Aichi 444-8585, Japan 2 Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies , SOKENDAI, Okazaki, Aichi 444-8585, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Shuji Shigenobu Abstract Full Text Info/History Metrics Supplementary material Preview PDF Abstract Many insects rely on obligate microbial symbioses, often involving multiple partners. Although symbiont replacement is well-documented, how newly acquired and resident obligate symbionts adapt after such events remains unclear. Here, we investigate the dual obligate symbiosis of the aphid Lachnus tropicalis , where an ancestral Serratia lineage was replaced by a newly acquired another Serratia lineage while the primary symbiont Buchnera remained. Our metagenomic sequencing yielded complete genomes of Buchnera (0.42 Mb) and Serratia (2.8 Mb), revealing developing metabolic complementarity. Although the Serratia genome retained abundant gene sets for amino acid synthesis, it also contained pseudogenes in leucine and methionine pathways, which would be compensated for by Buchnera or the host. Comparison with L. roboris , which harbors the ancestral Serratia lineage, showed that the newly acquired Serratia in L. tropicalis exhibits identical tissue localization and vertical transmission pattern, suggesting the smooth succession of the prior’s microniche. Notably, Buchnera in L. tropicalis exhibited a slightly more degenerated genome than its counterpart in L. roboris , indicating that symbiont replacement can accelerate gene loss even in ancient symbionts. Overall, our findings provide new insights into the dynamics of novel mutualism establishment and highlight symbiont replacement as a driver of host-symbiont co-evolution. 1. Introduction Many insects have established highly integrated symbiotic relationships with microorganisms such as bacteria and fungi ( 1 , 2 , 3 ). To date, a large number of highly integrated insect–microbe symbiotic systems have been discovered, highlighting microbial symbiosis as an evolutionary driver ( 4 , 5 ). Some mutualistic insect–bacterial relationships are ancient, implying enduring partnerships ( 6 , 7 , 8 ). However, “symbiont replacements,” in which older relationships are abandoned for newly acquired microbial partners, have been documented as evolutionary outcomes in many insect groups, including those harboring ancient symbionts ( 4 , 9 ). Whether this phenomenon results from selection and adaptive evolution, or simply an escape from the “symbiont rabbit hole” to compensate for overly degenerated genomes, remains unresolved ( 5 , 8 , 10 , 11 ). Comparative studies focusing on before and after replacement, including the states of the replaced and replacing symbionts, the host, any remaining co-symbionts, and the mechanisms by which new stable symbiotic systems are established and maintained, are crucial for advancing this debate. Before symbiont replacement, existing partners may show signs of instability, such as genomic fragmentation ( 12 ), which can precede replacement by new partners, as observed in cicadas ( 13 ). After replacement, newly integrated symbionts typically undergo rapid microniche adaptation, including genome degeneration and restricted localization owing to bottlenecks and isolation ( 8 , 11 , 14 , 15 , 16 ). This process is also hypothesized to accelerate genomic degeneration in ancient co-resident symbionts, particularly if the new partner has broader nutritional capacities, leading to microniche reallocation ( 16 , 17 ). Despite these emerging insights, the full extent of the genomic consequences and their validation across diverse systems remains unresolved. Moreover, it is unclear how host mechanisms for symbiosis (such as localization restriction, vertical transmission, and nutrient exchange across host–symbiont membranes) change post-replacement, or how new symbionts integrate into established systems. Indeed, newly acquired symbionts exhibit varied localization and transmission modes, suggesting flexibility in both host and symbiont ( 18 , 19 , 20 ). Answering these questions requires detailed comparative studies across recently replaced and closely related symbiotic systems. Aphid (Hemiptera: Aphididae) symbiotic systems and their functions have been well-studied ( 21 , 22 ), and growing research has detailed independently evolved, complex symbioses involving multiple obligate symbionts across subfamilies ( 23 , 24 , 25 , 26 , 27 ). Within the subfamily Lachninae, the widespread association with Serratia symbiotica and comprehensive symbiont diversity studies have led to specific symbiont replacement hypotheses ( 26 , 28 , 29 , 30 ). Detailed genome-based studies of Cinara spp. and related clades suggest a dynamic process: the common ancestor of Lachninae established a complex symbiosis with both Buchnera and Serratia ( 30 , 32 , 33 ). During subsequent diversification, Buchnera was maintained, but the ancestral Serratia was repeatedly replaced by diverse bacterial lineages, including Sodalis , Fukatsuia , Erwinia, and other Serratia strains ( 30 , 31 ). However, the precise events before and after these replacements remain unclear. For example, understanding host changes upon new symbiont entry, how new partners adapt to the insect body and novel bacteriome niches, and how resident Buchnera are impacted requires detailed comparative analyses of closely related species. Within the aphid subfamily Lachninae, the genus Lachnus represents a unique case of symbiont replacement. Previous studies have indicated a co-obligate symbiotic system in more basal Lachnus species, such as Lachnus roboris , comprising Buchnera alongside a Serratia symbiotica lineage known as “Clade B” ( Figure 1A , S1, S2, Supplementary Information Chapter 1; 26, 28, 29, 30). This Serratia lineage is characterized by coccoid morphology and reduced genomes, a pattern observed in strains from Cinara cedri and Tuberolachnus salignus ( 32 , 33 ). Conversely, Lachnus tropicalis ( Figure 1B ) and other East and Southeast Asian species harbor a different Serratia lineage, Clade A (rod-shaped and retaining relatively large genomes), as the partner symbiont alongside Buchnera ( Figure 1A , S1). Based on the symbiont replacement hypothesis in Lachnus ( Figure 1A , Supplementary Information Chapter 1; 30), these Clade A Serratia strains are considered relatively newly integrated partners. Therefore, the genus Lachnus is an ideal system for comprehensively describing and comparing pre- and post-replacement symbiotic systems, offering crucial insights into the factors driving symbiont replacement and its evolutionary consequences. Download figure Open in new tab Figure 1. (a) Simplified phylogenetic tree of Lachnus and related species, showing the associated Serratia clades (“A” or “B”) harbored by aphids in addition to Buchnera. This tree suggests a symbiont replacement event from Serratia Clade B to Clade A in the L. tropicalis group ( 29 , 30 ). (b) Colony of the black chestnut aphid, Lachnus tropicalis (Okazaki, Aichi). (c) Microbial diversity associated with L . tropicalis from different populations in Japan, based on amplicon sequencing of the hypervariable V3/V4 region of the 16S rRNA gene. In this study, we first comprehensively characterized the symbiotic system of L. tropicalis , the great chestnut aphid. We used amplicon and metagenomic sequencing to describe the microbiome and obtain the complete genomes of its bacterial symbionts, Buchnera aphidicola ( Buchnera Lt) and Serratia symbiotica ( Serratia Lt). As expected, our analysis revealed that Serratia Lt exhibited the characteristics of a recently acquired symbiont and was well-integrated into the pre-existing symbiosis with the aphid and Buchnera . We combined these genomic insights with detailed observations of symbiont localization and vertical transmission to elucidate how Serratia Lt took over the microniche of its ancestral counterpart. This description was then contextualized by comparison with the symbiotic system of L. roboris , which harbors ancestral Serratia , based on a thorough review of the existing literature ( 26 , 30 , 34 ). Furthermore, using the recently sequenced L. roboris Buchnera genome ( 35 ), we investigated the evolutionary consequences for Buchnera following symbiont replacement. 2. Materials and methods (a) Characterization of the symbiotic system in L. tropicalis (i) Sample collection Between 2021 and 2024, we collected L. tropicalis from three localities in Japan: Okazaki (Aichi Prefecture), Tsuruoka (Yamagata Prefecture), and Tsukuba (Ibaraki Prefecture). When aphid colonies were observed on twigs of Fagaceae trees, individuals were carefully collected using aspirators or forceps. Upon collection, they were morphologically identified as L. tropicalis based on the distinct forewing pattern of winged adults and further confirmed by sequencing the mitochondrial cytochrome c oxidase subunit I gene region, commonly used for aphid species identification. Aphid samples were preserved in 99.5% ethanol at 4 °C or at room temperature (approximately 20–28 °C) until DNA extraction for amplicon sequencing. For metagenomic sequencing and imaging analyses, fresh samples were collected from the National Institute for Basic Biology (NIBB) Campus (Okazaki, Aichi). (ii) 16S ribosomal DNA (rDNA) amplicon sequencing for L. tropicalis microbiome To clarify the bacterial diversity associated with L. tropicalis , we conducted amplicon sequencing of the hypervariable V3/V4 region of the bacterial 16S ribosomal RNA (rRNA) gene using 12 individuals from the three geographically distinct localities mentioned above. Libraries were constructed according to the 16S rRNA Metagenomic Sequencing Guide provided by Illumina (USA) and sequenced on the Illumina MiSeq platform. Detailed methods are provided in the Supplementary Information (Supplementary Information Chapter 2). Raw reads were deposited in the DDBJ database under accession numbers DRR709987-DRR709998 (PRJDB35790). Raw paired-end reads were analyzed using QIIME 2 (version 2020.8) ( 37 ) with the plugin “dada2” ( 37 ) for quality filtering, trimming of read length, merging paired reads, and removing chimeric sequences. We excluded dada2-derived amplicon sequence variants (ASVs) with 99% sequence identity. The four resulting ASVs were manually assigned to genus-level taxa using the BLAST function in the National Center for Biotechnology Information (NCBI) database. (iii) Metagenomic sequencing of the endosymbionts in L. tropicalis To characterize the genomic features of L. tropicalis endosymbionts ( Buchnera Lt and Serratia Lt), we performed metagenomic sequencing and subsequently assembled bacterial genomes using a hybrid assembly approach. Briefly, high-quality genomic DNA was extracted from fresh aphid samples; Nanopore and Illumina libraries were then prepared and sequenced using the R9.4.1 flow cell on the GridION system and the Illumina HiSeq X Ten platform, respectively. The total number of raw Nanopore reads was 2,038,881. The raw Nanopore reads were deposited in the DDBJ database under the accession number DRR718948 (PRJDB35790). The total number of raw Illumina paired-end reads obtained was 203,514,513. The raw Illumina reads were deposited in the DDBJ database under accession number DRR718949. To generate complete symbiont genomes from hologenomic samples, we carried out a hybrid assembly strategy involving long-read backbone assembly and short-read error correction. Detailed experimental procedures and assembly strategies are described in the Supplementary Information (Supplementary Information Chapter 3). The assembled genome and plasmid sequences were deposited in the DDBJ database under accession numbers: AP043953 and AP043954 for Buchnera Lt, and AP043955-AP043957 for Serratia Lt. Annotation of the corrected genomes was performed using DDBJ Fast Annotation and Submission Tool (DFAST) version 1.2.18 ( 38 ). We manually corrected the DFAST annotation for some genes, re-evaluating pseudogenes that appeared functional based on comparisons with related genomes. To characterize the gene repertoires of both symbionts in L. tropcialis , we examined the Cluster of Orthologous Genes (COG) category tags ( 39 ). This information was compared with that of related genomes (see Supplementary Information Chapter 3). The genome was visualized using Proksee ( 40 ), and the resulting images were processed with Inkscape version 1.4 (86a8ad7, 2024-10-11) ( 41 ). Metabolic pathways of the two symbiont genomes were reconstructed using the Kyoto Encyclopedia of Genes and Genomes Mapper tool ( 42 ), considering pseudogenization information obtained from the DFAST results (for details, see Supplementary Information Chapter 4). (iv) Phylogenomic analysis To infer the phylogeny of Buchnera and Serratia in L. tropicalis based on their genomic information, separate phylogenetic trees were constructed for each bacterial genus using GToTree v1.8.14 ( 43 ) and its prepackaged single-copy gene set for Gammaproteobacteria (172 targets). Briefly, protein-coding genes were predicted from input genome FASTA files (listed in Tables S7 and S8; details in Supplementary Information Chapter 3) using Prodigal v2.6.3 ( 44 ). Targeted single-copy genes were identified with HMMER3 v3.4 ( 45 ), individually aligned using MUSCLE v5.1 ( 46 ), and trimmed with TrimAl v1.5. rev0 ( 47 ), and concatenated. Phylogenetic trees were subsequently estimated using IQ-TREE v2.4.0 ( 48 ). The resulting tree files were visualized using Interactive Tree of Life (iTOL) v6 ( 49 ) and manually refined with Inkscape. (v) Histological observations of L. tropicalis bacteriome and symbiont localization To characterize the cellular features of the L. tropicalis bacteriome, we conducted morphological observations of the dissected bacteriomes with 4’,6-diamidino-2-phenylindole (DAPI) and Phalloidin staining for nuclei/DNA and F-actin, respectively. Furthermore, to visualize the tissue localization and vertical transmission of both symbionts in L. tropicalis , we conducted fluorescence in situ hybridization (FISH) on the bacteriome and viviparous embryos, using symbiont-specific probes targeting the 16S rRNA gene sequences ( 50 ). All stained or hybridized samples were observed under a confocal microscope FV1000 (Olympus, Japan). Detailed procedures and definitions of the embryonic developmental stages are described in the Supplementary Information (Supplementary Information Chapter 5). (b) Comparative analysis of L. roboris and L. tropicalis symbiotic systems To compare symbiotic systems before and after symbiont replacement, we surveyed existing information on L. roboris . This European and Middle Eastern species forms a clade distinct from its Asiatic counterparts, including L. tropicalis ( 51 , 52 ). We used the symbiotic system of L. roboris , which harbors both Buchnera and an ancestral lineage of Serratia symbiotica (Clade B), as a model for the pre-replacement state (Supplementary Information Chapter 6). This Serratia is closely related to symbionts found in Cinara cedri and Tuberolachnus salignus (Figure S2; 29, 30, 32) (see Supplementary Information Chapter 1). We reviewed bacteria taxa consistently detected in the microbiome ( 26 , 28 , 29 ) and re-analyzed the recently sequenced Buchnera draft genome ( 35 ). We downloaded the L. roboris Buchnera genome (Zenodo: https://zenodo.org/records/10513209 ) and re-annotated it using DFAST. To infer genomic differences between Buchnera from L. roboris and L. tropicalis , we used Proksee for visualization and sequence comparison, along with BLAST+ v2.16.0 ( 53 ) and FastANI v1.34 ( 54 ). To detect the presence or absence of genes in both Buchnera genomes, we performed an orthology analysis using OrthoFinder v3.1.0 (55, with Buchnera APS (GCF_000009605) as the outgroup. Notably, detailed histological observations exist for L. roboris (under its synonym Pterochlorus roboris ) concerning symbiont tissue localization and vertical transmission ( 34 ). We thoroughly reviewed this work and compared its features with those of the L. tropicalis symbiotic system (see Supplementary Information Chapter 5). As specific microbial species such as Buchnera and Serratia were not formally described in 1927, we first correlated Klevenhausen’s descriptions with our current understanding of symbiont identities (see Results). 3. Results (a) Description of the symbiotic system in L. tropicalis (i) Microbiome of L. tropicalis In our 16S rDNA amplicon sequencing analysis of L. tropicalis collected from three geographically distinct localities in Japan (Table S3), we consistently detected Buchnera and Serratia across all sampled localities and individuals ( Figure 1C ). Both symbionts were abundant within the L. tropicalis microbiome (mean ± standard deviation: Buchnera 25.5% ± 17.4%; Serratia 73.9% ± 17.3%). The Serratia partial sequence (427 bp) showed a 100% match with the deposited 16S rDNA sequences of Serratia symbionts from L. tropicalis , L. siniquercus, and L. yunlongensis (FJ655545, KP866556, KP866555, KP866552, and KF751207). Therefore, Serratia detected in the analysis belongs to Serratia symbiotica “Clade A,” which contains pathogenic, facultative, and obligate symbionts in aphids ( 56 , 57 ). This result was consistent with phylogenetic analysis using the nearly full-length 16S rDNA extracted from the Serratia genome assembled in this study (Figure S2). (ii) Genomic characterization of Buchnera and Serratia in L. tropicalis We performed shotgun hologenome sequencing of L. tropicalis , and our metagenomic assembly yielded complete genomes for two bacterial symbionts: Buchnera Lt and Serratia Lt ( Figures 2 and S3, Table 1 ; for more details, see Supplementary Information Chapter 3). Download figure Open in new tab Figure 2. (a) Circular maps of Lachnus tropicalis symbiont genomes. The chromosomes of the primary symbiont Buchnera aphidicola Lt and Serratia symbiotica Lt, as well as their plasmids: pLeu for Buchnera , and pSsLt-1 and pSsLt-2 for Serratia . The rings, from outermost to innermost, represent: (i) predicted protein-coding genes, tRNAs, tmRNAs, and rRNAs on the plus strand; (ii) genome backbone; (iii) predicted protein-coding genes, tRNAs, tmRNAs, and rRNAs on the minus strand; (iv) GC content (deviation from the average); and (v) genome coordinates in megabases. Both chromosomes are oriented with the reading frame of the dnaA gene as the first CDS on the forward strand. The Buchnera plasmid pLeu is oriented at repA , while the Serratia plasmids begin at arbitrary positions. (b) Metabolic complementation for the biosynthesis of 10 essential amino acids (EAAs) and B-vitamins (B2 and B7) in the L. tropicalis endosymbiotic system. The Serratia Lt genome shows a relatively broad capacity for EAA synthesis, but pseudogenization was detected in the methionine ( metC and metE ) and leucine ( leuA , leuC , and leuB ) pathways. These functions are presumably complemented by Buchnera (for metE ) or the aphid host (for metC ). All leucine genes are located on the Buchnera plasmid pLeu, underscoring the complementary nature of the two genomes. Conversely, the synthesis of histidine and tryptophan is entirely dependent on Serratia . View this table: View inline View popup Download powerpoint Table 1. Summary of assembled genomes of Buchnera and Serratia in Lachnus tropicalis . The Buchnera Lt genome comprised a 419,912 bp circular chromosome (21.3% GC content, 85.9% coding density) and a 6,487 bp pLeu plasmid encoding five leucine biosynthesis genes ( Figure 2A , Table 1 ). Although considerably smaller than the mono-symbiotic Buchnera genomes (approximately 600 kb) ( 58 ) found in many aphid species ( 6 , 22 , 59 ), this reduction is typical for Buchnera in Lachninae aphids ( 23 , 31 , 32 , 33 ), all of which co-exist with another obligate symbiont ( S. symbiotica or other bacteria; Table S4). DFAST annotation revealed that the Buchnera Lt chromosome encodes 380 protein-coding genes (CDSs), three rRNAs, 32 transfer RNAs (tRNAs), and 32 pseudogenes. Notably, the pTrp plasmid, common in most Buchnera lineages, was not detected. We confirmed this absence through three independent analyses: plasmid assembly using “plassembler” ( 60 ), long-read assembly (no reads exceeding 5kb), and short-read mapping on pTrp of Buchnera APS and Buchnera from Cinara cedri using “bbmap.” All analyses failed to detect pTrp, indicating that Buchnera Lt lacks the tryptophan plasmid. COG analysis showed Buchnera Lt had gene repertoires similar to Buchnera in Cinara cedri (Figure S4). However, Buchnera Lt exhibited more pseudogenes (9.07%) than Buchnera genomes from pea aphids (0% in APS) and Cinara cedri (0.82%) (Figure S4, Table S4), suggesting ongoing genomic degeneration. The Serratia Lt genome consisted of a 2,870,422 bp circular chromosome (52.3% GC content, 80.1% coding density) and two plasmids, pSsLt-1 and pSsLt-2 ( Figure 2A , Table 1 ). Its total genome size (2.97 Mb) is comparable to that of Serratia in Acyrthosiphon pisum (2.82 Mb), a facultative symbiont ( 61 ), and Serratia in Peryphyllus lyropictus (3.15 Mb), a recently acquired co-obligate partner ( 25 ). Overall, the Serratia Lt genome encoded 3,172 proteins, including 1,146 pseudogenes, 19 rRNAs, and 58 tRNAs. Its normal GC content, typical number of rRNA operons (five full sets and two partial sets of 16S and 23S rRNA), and high pseudogene count indicate a relatively recent establishment as an aphid endosymbiont (Table S5). Furthermore, COG analysis revealed that Serratia in L. tropicalis retained as many genes as Serratia strains IS and CWBI-2 and did not exhibit the functional degeneration observed in Serratia from C. cedri (Figure S4). Our phylogenomic analysis, utilizing the newly sequenced genomes together with deposited related species (Tables S6 and S7), confirmed the phylogenetic placement of L. tropicalis Buchnera and Serratia . Buchnera Lt clustered within Lachninae and was most closely related to Buchnera in L. roboris (Figure S5). Serratia Lt was placed in Clade A of S. symbiotica , with its closest relative being Serratia in Cinara tujaphilina (Figure S6). We then compared the gene repertoires of Buchnera Lt and Serratia Lt to determine their co-obligate associations with host aphids. This analysis revealed complementary metabolic pathways for essential amino acids (EAAs) and B vitamins, demonstrating a clear metabolic complementarity between the two symbionts ( Figures 2B , S7, S8; Tables S8, S9; Supplementary Information Chapter 4). Notably, the Buchnera Lt genome lacked histidine biosynthesis genes and the tryptophan plasmid, representing the most degraded EAA synthesis capacity observed in this bacterial clade. Although Serratia in L. tropicalis possessed abundant EAA gene sets, its genome contained pseudogenes for leucine biosynthesis (compensated by Buchnera ’s plasmid) and for later steps in methionine production (likely covered by Buchnera and the host aphid) ( Figure 2B , S7). For cofactor biosynthesis, including B vitamins, Serratia Lt retained nearly all genes required to complete these pathways ( Figures 2B , S8). To infer the evolutionary stage of the symbionts, we also examined genes related to cell wall synthesis, cell division, and cellular motility in Serratia Lt and Buchnera Lt. As expected, Buchnera Lt exhibited extensive genome degradation typical of Buchnera in Lachninae, Chaitophorinae, and Hormaphidinae ( 23 , 24 , 25 , 26 , 27 ). In contrast, Serratia Lt showed an ongoing process of functional degeneration in these pathways, suggesting that it is transitioning toward a more highly integrated symbiotic lifestyle (Tables S10, S11, S12; Supplementary Information Chapter 4). (iii) Symbiont localization, vertical transmission, and bacteriome formation in L. tropicalis Aphid symbiotic organ (bacteriome) generally consists of two types of cells: bacteriocytes, which house the obligate symbiont Buchnera , and sheath cells, which often harbor facultative symbionts ( 34 , 62 , 63 , 64 ). Bacteriocytes are large polyploid cells (approximately 256 ploidy in Acyrthosiphon pisum ) that serve as interfaces for nutritional interactions. Although some aphids with “multiple obligate symbionts,” such as Cinara cedri and Ceratovacuna japonica , harbor each symbiont in distinct bacteriocytes, sheath cells are typically either free of symbionts or house facultative ones ( 20 , 24 , 65 ) (Figure S9). Our morphological observations and FISH revealed that both Buchnera and Serratia were localized within the bacteriome of L. tropicalis ( Figure 3 ). Consistent with other aphids, the primary aphid symbiont, Buchnera , resided in large polyploid bacteriocytes. In contrast, Serratia was localized in smaller sheath cells. We also observed that both symbionts exhibited distinct modes of maternal vertical transmission ( Figures 4A–I , S10, and S11). Detailed observations of embryos from viviparous individuals showed that, following transmission, the two symbionts were distributed separately into embryonic bacteriome cells in a complex and integrated manner (Supplementary Information Chapter 5). Download figure Open in new tab Figure 3. Symbiont localization and bacteriome structure in Lachnus tropicalis and L. roboris . (a–d) Symbiont localization and bacteriome structure in Lachnus tropicalis . (a) Fluorescent in situ hybridization (FISH) visualization of Buchnera (green) and Serratia (red) in vivo . Buchnera is harbored in large, polyploid bacteriocytes, whereas Serratia occupies flattened sheath cells. (b) Differential interference contrast image of the same tissue shown in (A). Arrows indicate sheath cells, and arrowheads denote fat cells. (c, d) DAPI-Phalloidin staining of the bacteriome. DNA (magenta) and F-actin (green) highlight cellular structures. Buchnera (round-shaped) and Serratia (rod-shaped) cells were confirmed to be housed in the bacteriocytes and sheath cells (arrows), respectively. Fat cells (arrowheads) contain no symbionts. (e) Comparison of bacteriome structure and symbiont localization between L. tropicalis (this study) and L. roboris ( 34 ). In both species, Buchnera is localized within bacteriocytes, while Serratia symbionts are confined to sheath cells. Notably, these observations revealed no major differences between the two species, except for the distinct cellular morphology of Serratia symbionts. Download figure Open in new tab Figure 4. Vertical transmission, bacteriome formation, and symbiont distribution during viviparous embryogenesis in Lachnus tropicalis and L. roboris . (a–h) Schematic illustrations of L. tropicalis embryonic development, showing symbiont localization. Buchnera is indicated in green, and Serratia (Clade A, rod-shaped) in magenta. (a) Transmission stage. (b) Invagination (anatorepsis) stage. (c) Flip (katatrepsis) stage. (d–g) Final growth stage, during which Serratia cells sequentially infect sheath cells from a dorsally located infection mass. (h) Reconstruction of the bacteriome arrangement in adults (based on anatomical observations), reflecting the organization established during embryogenesis. (i) Schematic illustration of the Serratia infection mass and subsequent infection of sheath cells, showing the presence of several Buchnera cells within the infection mass. More detailed descriptions are provided in Supplementary Information Chapter 4, Figures S10 and S11. (a’,b’, d’, f’, g’, i’) Illustrations of the corresponding stages in L. roboris , based on 34. Each primed letter (such as a’) corresponds to the equivalent stage observed in L. tropicalis . Buchnera and bacteriocytes are shown in green, while Serratia (Clade B, round-shaped), its infection mass, and Serratia -containing sheath cells are depicted in cyan. Notably, no observable differences were found between L. roboris and L. tropicalis , except for the distinct cellular morphology of Serratia . (b) Comparison of symbiotic systems of L. tropicalis and L. roboris We re-examined the existing literature on the symbiotic system of L. roboris, the species with the most documented research within the genus (Supplementary Information Chapter 6). This included a review of early histological observations by Klevenhausen ( 34 ), who first described three morphologically distinct symbionts of the aphid: a common round-shaped symbiont, a small round-shaped symbiont, and a rod-shaped symbiont. Building on this histological groundwork, recent phylogenetic analyses and amplicon sequencing have definitively reinterpreted these findings. The symbionts have been identified as Buchnera and Serratia belonging to Clade B, along with guest symbionts such as Wolbachia (Figures S1, S2; 26, 28, 29, 30). Serratia is characterized by its round shape, unique tissue localization, vertical transmission mode, and sophisticated distribution in sheath cells during embryonic development ( Figure 4 ; 34). We first compared the anatomical features, including tissue localization, vertical transmission of symbionts, and bacteriome formation during embryogenesis, between the Buchnera/Serratia (Clade B) symbiosis in L. roboris and the Buchnera / Serratia (Clade A) symbiosis in L. tropicalis ( Table 2 ). We found no significant differences in symbiont localization ( Figure 3E ). In both aphid species, only Buchnera occupied the bacteriocytes, the main cell type comprising the symbiotic organs of aphids. In contrast, both Serratia lineages were localized in the sheath cells, which are flattened cells surrounding the bacteriocytes. Vertical transmission modes were nearly identical between the two Lachnus species ( Figure 4 ). Buchnera cells were first transferred to infect early-stage embryos. Subsequently, Serratia cell populations were transmitted, splitting the Buchnera mass in half. After transmission, the mass of Serratia cells formed a dome-like structure positioned over the Buchnera mass at the anterior pole of the embryo. View this table: View inline View popup Download powerpoint Table 2. Summary of comparison of symbiotic system in two Lachnus species Bacteriome formation and symbiont distribution were also strikingly similar across both species ( Figure 3 , Table 2 ). Buchnera populations proliferated and cellularized as bacteriocytes, consistent with observations in the pea aphid and cedar bark aphid, Cinara cedri ( 20 , 63 , 65 , 66 ). Serratia cells, conversely, proliferated but remained as a cohesive symbiont mass (“secondary infection mass” in Klevenhausen [34]) during the early stages of embryonic development ( Figure 4 ). As embryonic development progressed, the Serratia mass temporarily divided and elongated. The definitive symbiotic localization was then established as Serratia cells invaded the sheath cells. Initially, they invaded the sheath cells immediately adjacent to the Serratia mass. Subsequently, the entire Serratia infection mass ruptured, leading to the infection of all sheath cells. Notably, we observed the same phenomenon in L. tropicalis as previously reported in L. roboris , where a portion of the Buchnera population became engulfed within the Serratia mass, subsequently degenerated, and was expelled from the aphid ( Figure 4I , I’). Although the functional significance of this phenomenon remains unclear, these consistent findings underscore that both aphid species follow nearly identical mechanisms for symbiont distribution, proliferation within the host, and arrangement within the symbiotic organs. Furthermore, we compared the genomic features of Buchnera in L. roboris ( Buchnera Lr) and L. tropicalis ( Buchnera Lt) ( Figure 5 ). First, FastANI was performed to assess genomic relatedness; the average nucleotide identity (ANI) value was 83.0, indicating an intragenus-level relationship despite evolutionary divergence. Reciprocal mapping between them indicated that many regions and their orders were evolutionarily conserved, with 119 of 141 ontologically query fragments ontologically matched ( Figure 5A ). Gene content and number were largely conserved between the two Buchnera genomes, with Buchnera Lr and Lt containing 380 and 386 CDSs, respectively. Notably, the histidine synthesis pathway was also not detected in Buchnera Lr, suggesting that its loss is not exclusively tied to symbiont replacement events. Our orthological analysis of the genomes of Buchnera Lr, Lt, and an outgroup, Buchnera APS, identified 349 orthogroups shared among all three strains and 20 groups exclusive to Lr and Lt. When comparing only Buchnera Lr and Lt, the analysis revealed that each orthogroup generally corresponded to a single gene in both Lachnus Buchnera genomes. A single exception was the 16S rRNA methyltransferase gene in Buchnera Lt, which was pseudogenized into two separate CDSs but remained within one orthogroup. A large number of shared genes were detected, with 369 genes in Buchnera Lr and 370 genes in Buchnera Lt belonging to the common 369 orthogroups. The remaining genes consisted of four genes detected only in Buchnera Lr and nine in Buchnera Lt (all hypothetical genes), as well as seven orthogroups (containing seven genes) shared exclusively with APS in each strain. These numbers fully account for the total CDS counts predicted by DFAST for both Buchnera Lr (380 CDSs) and Lt (386 CDSs). A notable difference in gene content was that Buchnera Lr lacked genes encoding elongation factor P ( efp ), leucine synthesis ( leuA–lepD ), and repA , whereas Buchnera Lt retained them. Conversely, Buchnera Lt had lost the tryptophan synthesis pathway genes, along with the heat shock protein ibpB , phosphofructokinase pfkA , and ribose-phosphate pyrophosphokinase prs . The presence of chromosomal tryptophan synthesis genes ( trpA – trpD ) in Buchnera Lr highlights its capacity to synthesize this amino acid, a function lacking in Buchnera Lt ( Table 2 ). We assumed that both pLeu ( leuA – lepD ) and pTrp ( trpE and trpG ) plasmids are present in the Buchnera Lr genome but were not detected due to assembly limitations, which are common in short-read-only assemblies ( Figure 5B and Supplementary Information Chapter 6). These differences in gene content, particularly the loss of the tryptophan pathway in Buchnera Lt, highlight the distinct evolutionary trajectories of the two Lachnus lineages and raise intriguing questions regarding the factors that facilitated these changes. Download figure Open in new tab Figure 5. Genomic comparison of Buchnera from Lachnus roboris ( Buchnera Lr) and L. tropicalis ( Buchnera Lt). (a) FastANI analysis. Red bands represent reciprocal mapping between the Buchnera Lr (query) and Buchnera Lt (reference) genomes, indicating conserved regions. The average nucleotide identity (ANI) of 83.0% suggests intragenus-level similarity. (b) Orthologous gene analysis. Orthology was analyzed between Buchnera Lr and Lt, using Buchnera APS as the outgroup. The Venn diagram illustrates shared and unique gene sets. The large overlapping region contains 369 orthogroups, each corresponding to a single gene, accounting for the majority of genes common to both Buchnera in Lachnus . The only exception is the 16S rRNA methyltransferase gene in Buchnera Lt, which was pseudogenized into two CDSs but still grouped into one orthogroup. This results in 370 shared genes in Buchnera Lt and 369 in Buchnera Lr, out of total CDS counts of 386 and 380, respectively. The remaining genes are unique to each strain: 16 in Buchnera Lt and 11 in Buchnera Lr. Notably, Buchnera Lr retains chromosomal tryptophan synthesis genes ( trpA – trpD ), which are absent in Buchnera Lt. Genes on the pLeu plasmid ( leuA – leuD ) in Buchnera Lt are shown in gray. It is assumed that both pLeu and pTrp ( trpE and trpG ) plasmids are also present in the Buchnera Lr genome but were not detected presumably due to technical limitations (see Results and Supplementary Information Chapter 6). 4. Discussion In this study, we investigated the evolutionary consequences of symbiont replacement within the aphid genus Lachnus , comparing the ancestral symbiotic system of L. roboris with the derived system of L. tropicalis (Figures S1, S2). L. roboris , a European species, harbors both Buchnera and Serratia symbiotica belonging to a more symbiotically advanced lineage (Clade B, Figure S2). In contrast, L. tropicalis and its sister Asian species have acquired a distinct Serratia lineage (Clade A, see Supplementary Information Chapter 1 for more details), which we hypothesized would replace the ancestral Serratia ( 29 , 30 ). We characterized the symbiotic system of L. tropicalis , encompassing its ancient aphid symbiont Buchnera and the relatively recently acquired Serratia symbiotica . Microbiome and genomic analyses revealed that both symbionts were deeply metabolically integrated into the aphid host, indicating their obligate symbiotic nature. Genomic characterization suggests that Serratia symbiotica in L. tropicalis ( Serratia Lt) is a recently integrated symbiont, as evidenced by its large genome size (ca. 3.0 Mb), abundant pseudogenes, neutral GC content, and a high number of rRNA and tRNA genes (Figure S4, Table S6). In contrast, the genome of Buchnera in L. tropicalis ( Buchnera Lt) exhibited features similar to those of related Buchnera species (Table S5). We also performed histological observations to determine the tissue localization and vertical transmission modes of the symbionts in L. tropicalis ( Figures 3 and 4 ; for details, see Figures S10 and S11, Supplementary Information Chapter 5). Next, we compared the symbiotic systems of L. tropicalis and L. roboris by integrating existing knowledge of L. roboris , including microbiome analyses ( 26 , 28 , 29 , 30 ), the sequence of the Buchnera genome ( 35 ), and detailed historical histological descriptions of symbiont localization and vertical transmission during embryogenesis ( 34 ). We found that, consistent with almost all other aphid species, Buchnera was housed in bacteriocytes in both aphid species, and Serratia was localized to the sheath cells in both species ( Figure 3E , S9). Furthermore, no substantial differences were observed in the vertical transmission modes of Buchnera and Serratia , or in their allocation to the newly formed embryonic bacteriome between the two Lachnus species ( Figure 4 ). These histological findings suggest that despite the distinct clades of Serratia (Clade B vs. Clade A) and their differing bacterial morphologies (cocci vs. bacilli), there are remarkably few histological differences between the ancestral and newly acquired Serratia symbionts. This implies that the new Serratia has effectively utilized, or “taken over,” the microniche of the ancestral Serratia . Although further research is needed to understand the mechanisms underlying this successful niche succession, the consistent presence of Serratia Clade A across diverse phylogenetic backgrounds (Figures S2, S6B) strongly suggests that its inherent adaptability and flexibility likely play crucial roles in its ability to take over these established symbiotic niches. Future histological studies, such as those in Cinara (where ancestral Serratia was often replaced by a different genus; 31, 67) or Ceratovacuna (where ancestral Arsenophonus symbionts were replaced by other lineages; 22, 27), could further elucidate the mechanisms of this niche succession. Finally, to investigate the genomic consequences of symbiont replacement on primary and remaining symbionts, we compared the Buchnera genome sequences of L. roboris and L. tropicalis ( Figure 5 ). We observed no major differences in genome size, CDS numbers, or syntenic relationships. Indeed, their ANI values were relatively high (>80%, indicative of intragenus-level relationships). However, Buchnera Lt had lost the tryptophan synthesis pathway genes on both the plasmid and chromosome, a function now compensated for by Serratia in L. tropicalis . In contrast, the histidine synthesis pathway (also covered by Serratia in L. tropicalis ) was absent in L. roboris Buchnera . These results strongly suggest that, even for Buchnera , an ancient and deeply integrated symbiont, replacement events involving the acquisition of new symbionts with broader capacities can facilitate further genomic degeneration. Although the concept of symbiont replacement as a driver of symbiont genome degeneration has been proposed in previous studies ( 16 , 17 ), our case provides a particularly compelling and well-documented example that uniquely demonstrates genomic consequences for the ancient symbiont Buchnera . Our genomic analyses of L. tropicalis further elucidated the ongoing metabolic integration between its ancient ( Buchnera aphidicola ) and recently acquired ( Serratia symbiotica Clade A) symbionts ( Figures 2B , S7, S8, and Supplementary Information Chapter 4). Although Serratia broadly contributes to EAA and cofactor synthesis (such as histidine, phenylalanine, tryptophan, the initial steps of methionine, and nearly all B-vitamin pathways), a complementary, non-redundant relationship is clearly emerging. For instance, Serratia Lt abandoned parts of the methionine and leucine pathways, whereas the tryptophan pathway, originally maintained by Buchnera , was taken over by Serratia . This is noteworthy because other Clade A Serratia strains, such as CWBI-2.3 and 24.1, still possess the complete methionine and leucine pathways ( 57 ). This suggests that Serratia Lt lost these genes during its integration as a symbiont, likely because the Buchnera pathway, historically preserved in L. roboris and other Lachninae species ( Figure 5 , 32, 33), was a more efficient option. Similar dynamics were likely to develop for valine, leucine, and isoleucine. On the other hand, many redundant genes persisted in the arginine, threonine, lysine, and chorismate pathways. It is therefore reasonable to predict that, in future evolutionary processes, these overlapping pathways will be streamlined for efficiency. Further genomic analyses of Buchnera and Serratia in other Lachnus species, combined with gene expression studies of both symbionts and the aphid host, could reveal broader patterns of gene replacement by Serratia and retention by Buchnera . Such expression studies could also detect cases where redundant genes are retained but largely inactive, representing a pre-loss state and potentially indicative of genetic assimilation. Symbiont replacement is a pivotal evolutionary event; however, its genomic antecedents and immediate drivers remain challenging to decipher ( 8 ). Although our research provides a unique example within the aphid genus Lachnus , a key limitation is the absence of genomic data for Serratia Clade B in L. roboris , leaving the precise state of ancestral Serratia prior to replacement unknown. Drawing parallels with other Sternorrhynchans, in which ancient symbionts such as Hodgkinia in cicadas ( 68 ) and certain Sulcia lineages in planthoppers show highly fragmented subgenomes ( 17 , 69 ), it remains unclear whether Serratia Clade B in Lachnus exhibited similar genomic erosion before its replacement. Alternatively, factors such as host plant shifts or range expansion may have favored Serratia Clade A as relatively more efficient, leading to selective uptake ( 8 ). It is tempting to speculate that this successful replacement contributed to the adaptive radiation of Lachnus , particularly the rapid diversification of L. tropicalis and other Serratia Clade A-harboring species in East Asia ( 28 , 29 , 30 , 51 , 52 ). Further investigations of these ecological implications are crucial for a comprehensive understanding of the broader evolutionary impacts of replacement events. Future research should prioritize sequencing symbiont genomes from related Lachnus species and integrating life-history data to critically analyze the events surrounding this replacement. Author Contributions T.N. contributed to conceptualization, data curation, formal analysis, funding acquisition, investigation, methodology, project administration, resources, validation, visualization, writing the original draft, and writing—review and editing. Y.K. contributed to data curation, investigation, methodology, resources, writing the original draft, and writing—review and editing. M.I. contributed to methodology, resources, and writing—review and editing. S.S. contributed to conceptualization, funding acquisition, investigation, project administration, writing the original draft, and writing—review and editing. All authors approved the final version of the manuscript and agreed to be accountable for this work. Competing Interests The authors declare no conflicts of interest. Generative AI disclosure The authors verify and take full responsibility for the use of generative AI in the preparation of this manuscript. Generative AI (Google, 2025), specifically the Gemini model, was used as a writing assistant to improve grammar and sentence flow in parts of the manuscript. The scientific content, data analysis, and overall structure were developed solely by the authors. Funding This study was financially supported by KAKENHI from the Japan Society for the Promotion of Science to T. N. (grant numbers 19J01756, 22K14901, and 25K18554) and S. S. (grant numbers KAKENHI 17H03717, 17H06384, and 20H00478). Additional support was provided by a Grant-in-Aid for Scientific Research on Innovative Areas (Research in a Proposed Research Area No. 3902). Data Accessibility All datasets generated and analyzed in this study are publicly available. Raw sequencing reads, including 16S rRNA amplicon sequences (DRR709987–DRR709998), Nanopore long reads (DRR718948), and Illumina short reads (DRR718949), have been deposited in the DDBJ Sequence Read Archive (DRA) under BioProject ID PRJDB35790. The primary raw sequencing data are further associated with BioSample ID: SAMD01601843. The assembled genome sequences of Buchnera aphidicola isolate Lt-NIBB (BioSample ID: SAMD01609681, Accession numbers: AP043953 and AP043954 ) and Serratia symbiotica isolate Lt-NIBB (BioSample ID: SAMD01609682, Accession numbers: AP043955 - AP043957 ) from L. tropicalis are also available in the DDBJ/GenBank/ENA database under BioProject ID PRJDB35790. All other relevant data supporting these findings are provided in this article and supplementary material. Acknowledgements We thank Shunta Yorimoto for critical discussions and Wen Hsin-I and Katushi Yamaguchi for technical support with genomic library preparation and sequencing. We are also grateful to Jinyoung Choi, Filip Husnik, Ryuichi Koga, Takema Fukatsu, Akari, and Arisa Nozaki for sample collection and helpful advice. Finally, we thank Hiraku Yamada and the other members of the Laboratory of Evolutionary Genomics at the NIBB for their assistance with the experiments. Computational resources were provided by the Data Integration and Analysis Facility, NIBB. Funder Information Declared Japan Society for the Promotion of Science, https://ror.org/00hhkn466 , 19J01756 , 22K14901 , 25K18554 References 1. ↵ Klepzig KD , Adams AS , Handelsman J , Raffa KF . 2009 Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans . Environ. Entomol . 38 , 67 – 77 . 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Share Symbiont replacement and subsequent parallel genome erosion reshape a dual obligate symbiosis in the aphid Lachnus tropicalis Tomonari Nozaki , Yuuki Kobayashi , Mika Ikeda , Shuji Shigenobu bioRxiv 2025.09.22.677894; doi: https://doi.org/10.1101/2025.09.22.677894 Share This Article: Copy Citation Tools Symbiont replacement and subsequent parallel genome erosion reshape a dual obligate symbiosis in the aphid Lachnus tropicalis Tomonari Nozaki , Yuuki Kobayashi , Mika Ikeda , Shuji Shigenobu bioRxiv 2025.09.22.677894; doi: https://doi.org/10.1101/2025.09.22.677894 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Evolutionary Biology Subject Areas All Articles Animal Behavior and Cognition (7635) Biochemistry (17690) Bioengineering (13892) Bioinformatics (41935) Biophysics (21451) Cancer Biology (18587) Cell Biology (25499) Clinical Trials (138) Developmental Biology (13377) Ecology (19899) Epidemiology (2067) Evolutionary Biology (24318) Genetics (15609) Genomics (22506) Immunology (17736) Microbiology (40394) Molecular Biology (17181) Neuroscience (88601) Paleontology (666) Pathology (2832) Pharmacology and Toxicology (4824) Physiology (7641) Plant Biology (15152) Scientific Communication and Education (2045) Synthetic Biology (4294) Systems Biology (9825) Zoology (2271)