Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes

Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes | 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 Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes View ORCID Profile Masa-aki Yoshida , View ORCID Profile Emese Tóth , View ORCID Profile Koto Kon-Nanjo , View ORCID Profile Tetsuo Kon , View ORCID Profile Kazuki Hirota , View ORCID Profile Atsushi Toyoda , View ORCID Profile Hidehiro Toh , View ORCID Profile Hideyuki Miyazawa , View ORCID Profile Makoto Terauchi , Hideki Noguchi , View ORCID Profile Davin H. E. Setiamarga , View ORCID Profile Oleg Simakov doi: https://doi.org/10.1101/2025.05.16.652989 Masa-aki Yoshida a Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University , Oki, Shimane 685-0024, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Masa-aki Yoshida For correspondence: mayoshida{at}life.shimane-u.ac.jp davin{at}wakayama-nct.ac.jp oleg.simakov{at}univie.ac.at Emese Tóth b Department for Neuroscience and Developmental Biology, University of Vienna , Vienna 1030, Austria Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Emese Tóth Koto Kon-Nanjo b Department for Neuroscience and Developmental Biology, University of Vienna , Vienna 1030, Austria Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Koto Kon-Nanjo Tetsuo Kon b Department for Neuroscience and Developmental Biology, University of Vienna , Vienna 1030, Austria Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Tetsuo Kon Kazuki Hirota c Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN) , Gobo, Wakayama 644-0023, Japan d Graduate School of Science, The University of Tokyo, Bunkyo-ku , Tokyo 113-0033, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Kazuki Hirota Atsushi Toyoda e Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Atsushi Toyoda Hidehiro Toh e Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Hidehiro Toh Hideyuki Miyazawa f Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems , 1111 Yata, Mishima, Shizuoka 411-8540, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Hideyuki Miyazawa Makoto Terauchi f Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems , 1111 Yata, Mishima, Shizuoka 411-8540, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Makoto Terauchi Hideki Noguchi f Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems , 1111 Yata, Mishima, Shizuoka 411-8540, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Davin H. E. Setiamarga c Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN) , Gobo, Wakayama 644-0023, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Davin H. E. Setiamarga For correspondence: mayoshida{at}life.shimane-u.ac.jp davin{at}wakayama-nct.ac.jp oleg.simakov{at}univie.ac.at Oleg Simakov b Department for Neuroscience and Developmental Biology, University of Vienna , Vienna 1030, Austria Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Oleg Simakov For correspondence: mayoshida{at}life.shimane-u.ac.jp davin{at}wakayama-nct.ac.jp oleg.simakov{at}univie.ac.at Abstract Full Text Info/History Metrics Supplementary material Preview PDF Abstract Why some animal groups retain ancestral chromosomal complements while others change significantly is a fundamental question in evolutionary genomics. Few systems exist where accumulations of chromosomal changes can be studied in the context of morphological innovation. In coleoid cephalopods (octopus, squid, cuttlefish), an ancient coleoid chromosomal rearrangement event (ACCRE) has led to a substantial increase in the chromosome number and a new set of chromosomal homologies. Compared to typical molluscan or bilaterian genomes, ACCRE has enabled the origin of many novel regulatory regions in coleoid cephalopods. However, the discrepancies between extant octopodiform (octopus, ∼30 chromosomes) and decapodiform (squid and cuttlefish, ∼46 chromosomes) karyotypes and the direction of these evolutionary changes remain unexplained. Here we provide a draft genome assembly of the vampire squid Vampyroteuthis sp., the largest cephalopod genome sequenced to-date (over 10 gigabasepairs). Through syntenic comparisons, we infer that this basally branching octopodiform species shows partial retention of the chromosomal complement of Decapodiformes, indicating its more ancestral state and the derived nature of the octopod karyotype. Together with the analysis of a new chromosome-level assembly of the pelagic octopod Argonauta hians , we identified irreversible chromosomal fusion-with-mixing events followed by inter-chromosomal translocations in octopods. We show that this secondary reduction and mixing within octopod chromosomes has enabled the origin of a more entangled genomic configuration, shedding light onto the early evolutionary transitions within the clade. Our results offer broader insights into general patterns of chromosomal evolution following large-scale rearrangement events in animal genomes. Significance statement How changes to the ancient animal synteny result in novel chromosomal homologies is difficult to dissect due to the lack of intermediate states. Here we report that the genome of Vampyroteuthis , one of the largest animal genomes sequenced to-date (over 11 gigabasepairs), despite its phylogenetic position within the octopodiform cephalopods, partially retains squid and cuttlefish chromosomal complement, reflecting an ancestral karyotypic state that existed at the time of divergence between these cephalopod lineages. Our findings reveal karyotype reductions through chromosomal fusions were followed by inter-chromosomal translocations in octopods, leading to a more specialized genomic and gene regulatory architecture. These data show how chromosomal fusions can act as drivers of further inter-chromosomal rearrangements in animal genomes. Introduction Cephalopods (octopuses and squids) are known for their complex behaviors 1 , including problem solving, learning by observation, executing different tasks, and exceptional camouflaging ability 1 . Although similar in size to those of mammals, coleoid nervous systems are structurally distinct and have a long evolutionary history associated with advanced cognition and neural complexity. Coleoids diverged from nautiloids in the Late Ordovician (ca. 450 Ma) 2 ( Figure 1a ). While extant nautiloids retained their external shells, coleoids internalized or lost theirs, enabling greater maneuverability and adaptation to diverse marine environments 3 , 4 . Shell loss may also have driven the evolution of sophisticated neural processing leading to adaptive and complex behaviors such as rapid decision-making and camouflaging 5 . By the Late Permian to the Middle Triassic (∼260–235 Ma), coleoids had further diversified into Octopodiformes (vampire squids and octopuses) and Decapodiformes (squids and cuttlefishes) 2 , 6 – 8 ( Figure 1a ). Download figure Open in new tab Figure 1. Early origins of coleoid cephalopods and conflicting chromosome evolution scenarios. (a) Phylogenetic time tree of mitochondrial genomes with the major coleoid cephalopod clades and their closest outgroups. Node branches are labelled according to the major cephalopod evolutionary transitions. (b) Two conflicting scenarios how coleoid karyotypes evolved, reduction and expansion (via fission) scenarios. Fusion-with-mixing (FWM) provides a powerful synapomorphic character to profile irreversible changes. (c) Vampyroteuthis specimen used for sequencing. ACCRE: ancient coleoid chromosomal rearrangement event. The evolution of behavioral and neural complexities in coleoids, which was probably driven by clade-specific predation pressures and ecological adaptations 9 – 12 , likely required major genetic innovations. Recent studies have begun to uncover how large-scale changes in genome structure contributed to the evolution of their neural, cognitive, and other traits unique to coleoids. Comparative analyses show coleoids differ substantially in genome organization from both their primitive relatives and other mollusks 13 , 14 . While extant nautiluses retain the typical molluscan genomic structure 15 – 17 , coleoids underwent “ancient coleoid chromosomal rearrangement events 15 (ACCREs)”, causing topological reorganizations that restructured gene linkages and formed novel regulatory landscapes 18 . While ACCRE marked a key genomic transition in early coleoids, substantial lineage-specific changes between major coleoid lineages likely happened post-ACCRE. Octopuses and squids differ in chromosome numbers 15 , repeat content 19 , and expansions of gene families such as Protocadherins 20 and GPCRs 21 . Interestingly, while coleoid chromosomes have remained largely intact within both decapodiform and octopodiform lineages, their homologies are not strictly one-to-one, with some chromosomes showing many-to-many correspondences 15 . The discrepancy between predicted typical chromosome numbers (∼30 in Octopodiformes vs. ∼46 in Decapodiformes) also raises questions about whether chromosome numbers contracted or expanded during early coleoid evolution ( Figure 1b ). However, the lack of genomic data from early branching Octopodiformes or Decapodiformes has obscured the directionality of these transitions. The vampire squid ( Vampyroteuthis cf. infernalis ), a basal Octopodiformes, provides critical insight into the deep evolutionary history of coleoids 23 . This species is a globally distributed deep-sea pelagic cephalopod with an opportunistic detritivorous and zooplanktivorous feeding strategy 24 , 25 . This “living fossil” is the only extant representative of the vampyropods, an ancient clade within Octopodiformes ( Figure 1 ) that has existed since the Mesozoic Era, from at least the Middle Jurassic (e.g., Vampyronassa ; ca. 165 Ma) 23 , 24 with some evidence suggesting its origins in the Early Jurassic (e.g., Teudopsis and Simoniteuthis ; ca.183 Ma) 26 – 28 . Ancient vampyropods coexisted with the ammonites and the belemnites throughout the Jurassic (∼201–145 Ma) and Cretaceous (∼145–66 Ma), occupying various ecological niches across global marine environments 27 , 29 , 30 . However, most vampyropod lineages went extinct at the end of the Cretaceous (∼66 Ma), eventually leaving extant Vampyroteuthis as the sole surviving species 31 . Vampyroteuthis ’ unique phylogenetic position makes it a valuable model for resolving early genomic transition events and subsequent evolutionary trajectories in Octopodiformes and coleoids. To enhance resolution within Octopodiformes, we also present the chromosome-level genome assembly of the muddy argonaut Argonauta hians , a member of Argonautoidea, an octopodiform clade composed mainly of pelagic octopods characterized by the presence of the secondarily acquired shell-like calcified eggcases 32 , 33 . The inclusion of these two new genomes in our analyses enables us to reveal the directionality and trajectory of chromosomal rearrangements, genomic reorganizations, and size variation across early and modern cephalopods. Results We sequenced the draft genome of Vampyroteuthis sp. from an individual collected in the West Pacific Ocean. Genome sequencing was performed using the PacBio HiFi platform at approximately 40X coverage and assembled with hifiasm, resulting in a 14 Gb assembly. Different assembly settings were tested, yielding similar assembly sizes ( Supplementary Note ). A more stringent setting to both haplotype overestimation and to remove duplicates still resulted in similar completeness (BUSCO score of 95%) and an assembly size of over 11 Gb. Therefore, regardless of the assembly settings, the total length estimates confirm that the Vampyroteuthis genome constitutes the largest cephalopod genome sequenced to date ( Supplementary Figure 1) . Since we could not currently obtain additional samples for this rare deep-sea species, chromosomal conformational data is not yet attainable. However, while our Vampyroteuthis draft genome assembly consists of numerous sub-chromosomal level contigs (about 5,600 contigs, N50 of 9.96 Mb, and the longest contig of 51.7 Mb), it still contains sufficient syntenic information 22 , with 162 contigs containing 15 or more orthologous genes and the largest contig containing 130 orthologous genes. Meanwhile, the size of the genome of Argonauta hians was ∼1.57 Gb, similar to that of its congener A. argo 33 , but only half of that of Octopus (∼3 Gb) 14 . The draft genome of A. hians was assembled into putative 28 chromosomes, comparable in contiguity and resolution to other octopod genomes, which typically have 30 chromosomes ( Supplementary Figure 2 ). Gene mixing on fused chromosomes is irreversible, and thus any ancestral or fusion-with-mixing (FWM) would serve as a strong synapomorphy for the clade in question 33 , 35 , 36 . To investigate how genome architectures relate to chromosomal evolution, we conducted comparative analyses across multiple cephalopod lineages using a modified synteny approach (see Methods). This approach enabled us to profile the presence of chromosomal irreversible FWM ( Figure 2 ) and to confirm the highly rearranged nature of coleoid chromosomes relative to the nautilus ( Supplementary Figure 3 ) 15 . Despite its gigantic size due to massive expansion of repetitive elements, we also found that the Vampyroteuthis genome structure predominantly adheres to basic coleoid karyotype rather than the more ancestral nautilus or the general molluscan chromosomal complements ( Supplementary Figure 3 ) 22 . This pattern remained consistent even when alternative mapping and orthology search strategies were applied ( Supplementary Figure 4 ), confirming the robustness of this result. Download figure Open in new tab Figure 2 . Vampyroteuthis genome suggests ancestral coleoid karyotype was decapodiform-like, followed by karyotype reduction in Octopodiformes. Synteny dotplots showing Octopodiformes and Argonauta-Octopus shared FWM characters, relative to the Doryteuthis pealeii chromosomes. Doryteuthis chromosomes are ordered in the same way across the three species comparisons. The color codings indicate representative examples of the ancestral coleoid chromosome (green), ancestral Octopodiformes mixed chromosome (pink), and fused-and-mixed chromosomes in octopods (blue), respectively (corresponding to the phylogenetic nodes highlighted in Figure 1). Surprisingly, we found that the Vampyroteuthis chromosomal structure is more closely aligned with that of Decapodiformes, including those of the longfin squid Doryteuthis pealeii , the bobtail squid Euprymna scolopes , the diamond squid Thysanoteuthis rhombus , and the cuttlefish Sepia lycidas ( Figure 2 , Supplementary Figure 5 ), despite its well-supported phylogenetic placement in Octopodiformes and thus its affinities with the octopods. Although our Vampyroteuthis draft genome assembly is not at the chromosomal level, its contigs often correspond to single Doryteuthis chromosomes, reflecting a high degree of chromosomal retention. Conversely, Vampyroteuthis contigs exhibited complex relationships with the chromosomes of the other octopodiform species ( A. hians , the curled octopus Eledone cirrhosa , and the common octopus Octopus vulgaris ), indicating synapomorphic fusions and rearrangements shared across octopods ( Figure 2 , Supplementary Figure 5 ). Multiple Doryteuthis chromosomes and their one-to-one homologous Vampyroteuthis sets of contigs correspond to single octopod chromosomes and show highly entropic mixing. For example, O. vulgaris chromosome 22 corresponds to Doryteuthis chromosomes 8 and 9, each with its own non-overlapping set of Vampyroteuthis contigs, with the degree of entropic mixing of these two states along the Octopus chromosome of 0.193, as measured by the normalized turbulence 37 . This implies that FWM of two ancestral decapodiform-like chromosomes ( Doryteuthis chromosomes 8 and 9) occurred at the base of the octopod ( Eledone , Argonauta , Octopus ) lineage after its separation from Vampyroteuthis . For comparison, O. vulgaris chromosome 2 shows inter-chromosomal translocations with sharp syntenic boundaries and little mixing (<0.1 normalized turbulence for Doryteuthis chromosomes 9 and 29), suggesting a more recent origin of this translocation event. These chromosomal changes most likely accumulated gradually in the lineage leading to the octopods after their divergence from the Vampyroteuthis lineage ( Figure 2 , Supplementary Figure 5 ). Given the basal position of Vampyroteuthis among the Octopodiformes, the conservation of chromosomal structure across decapodiform lineages and Vampyroteuthis , along with the drastic chromosomal rearrangements shared by all octopods suggest the ancestral nature of the decapodiform karyotype. To further explore the extent of chromosomal fusion and mixing in the lineage leading to octopods, we examined how Doryteuthis chromosomes were mapped onto the Vampyroteuthis genome. The results revealed chromosomal rearrangements with a high degree of mixing within the Vampyroteuthis contigs. For example, contig ptg000753l is mapped to Doryteuthis chromosomes 7, 37, and 35 with normalized turbulence measure of 0.285 for Dpe35 and Dpe37, 0.290 for Dpe07 and Dpe37, and 0.193 for Dpe07 and Dpe35 37 . The pattern is observed for 33 out of the 46 Doryteuthis chromosomes, where parts of the chromosomes were mapped onto the same set of Vampyroteuthis contigs (Fisher’s exact test p-value <0.05), suggesting irreversible fusion-with-mixing. As the same chromosomes were found to be fused and mixed in all other octopodiform species, this suggests an ancient synapomorphy supporting the affinity of Vampyroteuthis with octopods. On top of this synapomorphic signature, further substantial chromosomal fusion-with-mixing occurred in the lineage leading to octopods ( Eledone , Argonauta , and Octopus ) ( Figure 2 ). Octopod homologs of only 3 Doryteuthis chromosomes (including the proposed sex chromosome 38 ) remain unfused, suggesting that 43 out of 46 cases where chromosomes underwent fusions on the branch leading to octopods. Of these, at least 10 chromosomes were previously unfused in Vampyroteuthis , indicating additional fusions after the divergence of octopods from the vampyropod lineage. Comparison with O. vulgaris karyotype showed that the argonaut underwent further fusions between chromosomes 3 and 8, as well as 6 and 7, reducing the chromosome number from 30 to 28, suggesting a general trend of chromosomal number reduction in octopuses. Our observations strongly suggest that the ancestral coleoid had a decapodiform-like karyotype, which later underwent additional fusions and karyotype reduction, first at the base of Octopodiformes, and then later in the octopods ( Figure 2 ). The alternative scenario of chromosomal fissions is highly unlikely, as it would require independent, convergent fissions of hundreds of genes to produce identical chromosomal splits observed in all Decapodiformes and Vampyroteuthis 35 . We could also confirm this pattern by partitioning the O. vulgaris genome into fragments containing the same gene content as those contained in our Vampyroteuthis assembly. Using the same syntenic analysis approach, this artificially “rearranged and fragmented” Octopus genome was still recapitulating octopod fusions ( Supplementary Figure 6 ), besides also showing a signal for the fusion of 42 out of 46 Doryteuthis chromosome homologs, compared to the 43 fused Doryteuthis chromosome homologs found in the complete O. vulgaris genome (Fisher’s exact test p-value <0.05). This suggests that the contiguity of the Vampyroteuthis assembly is unlikely to impact the inference of chromosomal fusions. These results suggest that Vampyroteuthis has a chromosomal structure partially shared with extant Decapodiformes, supporting the interpretation that it retains the more ancestral coleoid configuration, while octopods underwent additional FWMs. We also observed a complex syntenic pattern in octopod chromosomes that cannot be explained by simple FWMs ( Figure 3 ). Two possible scenarios might explain this complex syntenic pattern ( Figure 3b ). First, it may suggest that major inter-chromosomal translocations have occurred in the lineage leading to octopods ( Eledone , Argonauta , and Octopus ; Figure 2b ). The second possibility is that a large post-ACCRE ancestral coleoid karyotype independently fused into different configurations in Decapodiformes and Octopodiformes ( Figure 3b ). If the second scenario was the case, we would expect to find a decapodiform species with an unfused chromosomal pair that corresponds to separate chromosomes in Vampyroteuthis or octopods yet fused in other Decapodiformes. However, since we have yet to find such decapodiform species, our data most strongly support the first scenario ( Supplementary Figure 7 ). Although similar syntenic patterns can also arise after whole genome duplication 35 , we found no evidence of paralogous enrichment on any of the octopodiform chromosomes. Besides that, the observed chromosomal correspondence pattern does not indicate the presence of a consistent genome-wide doubling of ancestral chromosomes. Therefore, we believe it is unlikely for any whole-genome duplication event to have happened and be the cause of the syntenic patterns we observed. Additionally, comparisons within the octopods ( Supplementary Figure 8 ) show that Eledone , despite its basal position on the tree, showed additional modifications to its karyotype, including translocations to the otherwise highly conserved ancestral coleoid chromosomes Dpe03-Ovu12. On the other hand, genomes of A. hians and O. vulgaris were strikingly similar and shared more chromosomal characteristics with Vampyroteuthis , suggesting a more ancestral octopod karyotype ( Supplementary Figure 8 ). Download figure Open in new tab Figure 3. Chromosomal evolutionary pattern suggests additional ancestral translocations in octopods. (a) Dotplot representation for the three cases highlighted in Figure 1 , with the Y axis indicating the chromosomes of Doryteuthis . Green indicates conserved coleoid chromosomes, as suggested by the conservation of genes in the chromosomes of all compared coleoids, despite translocation of the genes’ location within the chromosomes (intrachromosomal rearrangements; “mixing in a chromosome”). Meanwhile, ancestral Octopodiformes (pink) indicate fusions of different Doryteuthis chromosomes, which happened in ancestral Octopodiformes. The third example (blue) shows the formation of complex patterns of fusion-with-mixing, where orthologous genes undergoing intrachromosomal translocations in specific regions of the chromosomes of Doryteuthis are present in multiple chromosomes in compared species. (b) Two main scenarios for the observed complex chromosomal evolutionary patterns. The first one involves a fusion-with-mixing of intact (in red) and partial (in blue) chromosomes following inter-chromosomal translocations (blue) that occurred in Octopodiformes after divergence from the decapodiform karyotypes. A second possible scenario suggests that following the split of Octopodiformes and Decapodiformes, each lineage experienced distinct fusion-with-mixing events involving multiple ancestral chromosomes. In Octopodiformes, two specific chromosomes fused and mixed (red and blue), while in Decapodiformes, a different pair of chromosomes (blue and yellow) underwent a similar fusion-with-mixing process. Why has the vampire squid maintained its more ancestral chromosomal state despite a dramatic increase in genome size? While several studies have implied the effects of transposable elements (TEs) accumulation on enhancing genome rearrangement rate, some of the largest genomes sequenced to date (e.g., lungfish 39 ) show surprisingly well-conserved karyotypes. This suggests that the Vampyroteuthis genome provides another example where TE-driven genome expansion was decoupled from an increase in genome rearrangements. Future studies of both epigenetic states and genome topology in this species should provide fruitful insight into the role of TE accumulation in the maintenance of ancestral genomic configuration in animal genomes. To further investigate the role of chromosomal fusion events onto putative regulatory landscapes as reflected by conserved non-coding element (CNE) preservation, we have conducted whole genome alignments between Vampyroteuthis and other coleoid cephalopods (Methods). We found that the conservation of non-coding regions was higher between Vampyroteuthis and Decapodiformes (over 7.1 Mb aligned sequences) compared to Vampyroteuthis and Octopus (2.5 Mb total alignment, Figure 4a ). The decrease in the overall alignment length is particularly visible in Argonauta and Octopus . This pattern, while correlated with the genome size, is also corroborated by the overall repeat composition of the Vampyroteuthis genome, with long interspersed nuclear elements (LINEs) comprising a major part of the genome (14.12%) and short interspersed nuclear elements (SINEs) less than 1% ( Supplemental table 4 ). This is similar to other Decapodiformes genomes and in contrast to the SINE-dominated octopod genomes 19 , indicating Vampyroteuthis ’s higher propensity to retain ancestral non-coding features. Download figure Open in new tab Figure 4. Conserved non-coding element complement in coleoid genomes. (a) Vampyroteuthis -centered whole genome alignments show the total content (in alignment numbers) of coding and non-coding alignments. (b) Ribbon diagram showing location of homologous alignments of coding (red, CDS) and non-coding (green) regions between Doryteuthis chromosomes (top) to Vampyroteuthis (middle) and Octopus vulgaris (bottom) for the complex FWM shown in Figures 2 and 3 (pink and blue colors). Zoom-in on a middle portion of O. vulgaris chromosome 2 (Ovu2) is highlighted below (NCBI genome browser) with gene track of annotation and conservation of both coding and non-coding elements derived from one homologous Vampyroteuthis contig and its pre-octopodiform unmixed state on two chromosomes Dpe29 and Dpe23 (pink color). Two Vampyroteuthis contigs homologous to Dpe09 and Dpe08, on the other hand, remain unmixed and their homologs undergo FWM only in octopods (lila color). Using chromosomal homologies inferred from gene-level comparisons ( Figures 2 and 3 ), we traced their CNE complement evolution on the derived octopod chromosomes. Vampyroteuthis homologs of unfused Doryteuthis chromosomes (Dpe09 and Dpe08) remain unmixed as separate units, whereas Vampyroteuthis contigs that correspond to the predicted octopodiform FWM events show substantial mixing of both coding and non-coding elements (Dpe29 and Dpe23, Figure 4b ). All these contigs map to a set of O. vulgaris chromosomes, resulting in a high degree of mixing of gene loci and their putative regulatory sites. From this observation, we can infer that a large portion of the regulatory landscapes on modern O. vulgaris chromosomes has a complex evolutionary origin, shaped by FWM events combining segments derived from distinct chromosomal units in the ancestral octopodiform lineage. Discussion Our findings show that the decapodiform-like karyotype represents the ancestral state of coleoids and support the basal position of Vampyroteuthis within Octopodiformes. This conclusion aligns well with paleontological data and insights regarding cephalopod bauplan evolution. Stem coleoid species from the Paleozoic, such as Gordoniconus and Bactrites , exhibit internal shells, streamlined morphologies, and ten arms, long before the appearance of the oldest vampyropods in the Jurassic, such as Teudopsis and Vampyronassa . Interestingly, Vampyroteuthis also possesses two long feeding filaments, thought to be vestigial arms, indicating a possible morphological affinity to the 10-armed decapodiform. The retention of parts of the decapodiform-like chromosomal architecture in Vampyroteuthis , along with the extensive chromosomal rearrangements observed in octopods, provides genomic evidence supporting the transition from decapodiform-like ancestors to Octopodiformes. Our analyses also indicate a surge of inter-chromosomal translocations at the base of the octopods, potentially facilitated by demographic shifts or genomic instability. These ACCRE-like inter-chromosomal translocations, possibly stabilized by the notably large genome sizes in coleoids, may have driven morphological innovations and regulatory complexity. For instance, the specialization of arms into feeding tentacles in squids and the reduction of arms in octopuses likely result from modifications in gene regulation and its chromosomal context, and not gene content. Similarly, the presence of shell matrix protein-coding genes in shell-less octopods suggests that regulatory changes, rather than structural ones 33 , 40 , facilitated shell degeneration. Fossil record and molecular data provide a temporal framework to time of these innovations ( Figure 1a ), including the accumulation of chromosomal rearrangements and their impacts on phenotypic evolution in the octopod lineage. Taken together, our findings have important implications for understanding the directionality of chromosomal evolution in the animal kingdom, its long-term impact on the emergence of novel putative regulatory regions, and, eventually, morphological innovations. Further attempts to obtain a chromosomal-scale assembly of Vampyroteuthis will help to determine the exact karyotypic changes that occurred at the base of Octopodiformes. Materials and Methods Samples The genomes of a single juvenile Vampyroteuthis of unknown sex, caught in Suruga Bay by T/V Hokuto of Tokai University, and a single Argonauta hians adult female caught as bycatch in fixed nets set along the coasts of Oki Island, Shimane Prefecture, Japan (36°17′20.6″ ″N 133°12′46.4″″E), were sequenced. The eggcase of sequenced A. hians specimen was deposited in the University Museum, the University of Tokyo (UMUT RM34224). Sample preparations Whole-genome shotgun sequencing was performed using PacBio and Illumina sequencing platforms. Genomic DNA was extracted from the muscles (whole body) of Vampyroteuthis and the ovary of A. hians using a Genomic-tip Kit (QIAGEN, Hilden, Germany) and then sheared into fragments (size: 15 kb to 20 kb) with a g-tube device (Covaris Inc., MA, USA). PacBio HiFi libraries for Vampyroteuthis and A. hians were prepared using a SMRTbell Prep Kit 3.0 (Pacific Bioscience, CA, USA) according to the manufacturer’s instructions, and were size-selected using the SageELF system (Saga Science, MA, USA). Seventeen SMRT cells for Vampyroteuthis libraries and two SMRT cells for A. hians libraries were sequenced on the PacBio Sequel II/IIe systems with Binding Kit 3.2 and Sequencing Kit 2.0 (30 hours collection times). The consensus (HiFi) reads were generated from raw full-pass subreads using the DeepConsensus v1.1.0 program 41 with default parameter settings. For Illumina sequencing, genomic DNA was fragmented to an average size of 500 bp using the Focused-ultrasonicator M220 (Covaris Inc., MA. USA). Paired-end libraries were constructed with a TruSeq DNA PCR-Free Library Prep kit (Illumina, CA, USA) and size-selected on an agarose gel with a Zymoclean Large Fragment DNA Recovery Kit (Zymo Research, CA. USA). The final libraries were sequenced on a NovaSeq 6000 system (Illumina, San Diego, CA, USA) with 2 × 150 bp read length. Total RNA was extracted from three Vampyroteuthis tissues (brain, buccal mass, and eyes) and four A. hians tissues (brain, eyes, heart, and embryo) using E.Z.N.A. Mollusc RNA kit (Omega Bio-Tek, GA. USA) and a Nucleospin RNA clean-up XS (TaKaRa, Japan). We obtained the tissues from the same individuals to the genome DNA. The RNA-seq libraries were constructed using an Illumina Stranded mRNA Prep, Ligation (Illumina, San Diego, CA, USA) following the manufacturer’s protocol. Sequencing was conducted on the NovaSeq 6000 system with 2 x 100 bp read length. Library concentration and qualities were assessed using Qubit 4 Fluorometer (Thermo Fisher Scientific, MA, USA), the 2100 Bioanalyzer system (Agilent Technologies, CA, USA), and 7900HT Fast Real-Time PCR System (Thermo Fisher Scientific, MA, USA). Genome sequencing and informatics In total, 571,504,779,822 bp HiFi reads were obtained by PacBio Sequel II/IIe for Vampyroteuthis . The total sequencing depth was approximately 40X, and the average read length was 16.3 kb. 1,303,449,174,900 bp of clean data were acquired through illumina NovaSeq6000 (PE500) short reads. We analyzed the whole genome by Hifiasm 42 , 43 , followed by purge_dups 44 . The details of the assembly, repeat modelling, and annotation are presented in the supplementary material. Genome assembly of A. hians was conducted by Hifiasm using standard parameters. Hi-C libraries for scaffolding were constructed using Dovetail Omni-C Kits (Cantata Bio, CA, USA), and were sequenced on an Illumina MiSeq system. The Hi-C reads were mapped to the contigs and filtered using Juicer v1.6 45 . Scaffolding was performed with 3D-DNA v180419 46 . The resulting scaffolds were manually inspected and refined using Juicebox v1.11.08 47 . Orthology and syntenic analysis For consistency in orthology handling, we mapped Doryteuthis pealeii and Octopus vulgaris peptides to all genomes using miniprot 0.12 48 using-gff option as an output. In total, 30,432 D. pealeii and 25,682 O. vulgaris genes were mapped. Custom scripts were used to parse the mapping results and convert them into pairwise synteny files (.psynt) for each species pair (available on the repository link below). Each .psynt file contains information on mutual best orthologs as well as their genomic locations in two species. Only contigs with 15 or more orthologous genes were used. Dotplots were made using a custom R (version 4.2.2) script psyntPlot.R using published procedures 49 . Significance of chromosomal homologies was tested using Fisher’s exact test, and associations of adjusted p-value (Bonferroni correction) of 0.05 are shown as black colored dots. Clustering of contigs or chromosomes on dotplots was done either by predefined order of chromosomes ( Figure 2 ) to enable multi-species comparisons, or via Euclidean distance measure on the number of shared orthologs and ward.D2 clustering in R. Statistical analysis of mixing was done with TraMineR 2.2-11 package in R 48 . Whole genome alignments were done on hard-masked genomes (RepeatModeler 2.0.6 and RepeatMasker 4.1.8) with blastn 2.16.0+ using the following parameters: -task megablast-perc_identity 0-template_length 16 -penalty -2 - word_size 11-evalue 1-template_type coding_and_optimal 50 . Transdecoder 5.7.1 was used to predict open reading frames on conserved aligned sequences (TransDecoder.LongOrfs-m10 parameter was used) and classify alignments into coding vs non-coding regions, in addition to available gene annotation overlap. Only alignments of 50 or more base pairs were reported. All dotplots for every figure and their supporting data can be generated by running the prepInput.sh and plot_figures.R scripts on the repository. Grants Genome sequencings of Vampyroteuthis sp. and A . hians were supported by JSPS KAKENHI Grant Number JP22H04925 (Platform for Advanced Genome Science). M.A.Y. was partially supported by Takeda Science Foundation Life Science Research Grants FY 2023, and KAKENHI Grants-in-aid for Basic Research (No. 22K06340) awarded to M.A.Y. and D.H.E.S. M.A.Y. also thank the Faculty of Life and Environmental Sciences at Shimane University for the financial support for publishing this report. D.H.E.S. was partially supported by KAKENHI Grants-in-aid for Basic Research (19K12424 and 23K11511), Takeda Science Foundation for Life Sciences Research Grant FY 2022, and the National Institute of Technology GEAR 5.0 Project for Agriculture, Forestry, and Fisheries to support KH’s position in Setiamarga lab. K.H. was partially supported by Sasakawa Scientific Research Grant FY 2024 from the Japan Science Society and JST SPRING GX grant (No. 23A360), both of which are fellowships for graduate students. O.S. was supported by the European Research Council’s Horizon 2020: European Union Research and Innovation Programme, grant No. 945026. The computational results of this work have been achieved using the Life Science Compute Cluster (LiSC) of the University of Vienna. Author contributions This work is a result of an equal collaboration among three labs led by three Principal Investigators (the corresponding authors: M.A.Y., D.H.E.S. and O.S.), all giving their shares equally toward the completion of this project. M.A.Y., D.H.E.S. and O.S. designed and led the study; M.A.Y., A. T., H. T., and H. N. contributed to the genome sequencing and data deposit; E.T., K.K., T. K., K. H., H. M., M. T., and H. N. conducted the bioinformatical work; M.A.Y., D.H.E.S. and O.S. produced the first draft of the manuscript. All authors contributed to the final manuscript. Declaration of interests The authors declare no competing interests. Supplemental information Figures S1–S8, Table S1-S4 Acknowledgments We thank Noriyoshi Sato (Tokai University) for providing Vampyroteuthis samples. We also thank all members of the Simakov lab (University of Vienna), in particular Thea Rogers and Darrin Schultz, for invaluable discussions and comments on the manuscript. D.H.E.S. and K.H. would like to thank Nanami Tochino (Setiamarga Lab at NIT Wakayama), for her assistance on the phylogeny/timetree inference. Funder Information Declared Japan Society for the Promotion of Science, https://ror.org/00hhkn466 , JP22H04925 , 22K06340 , 19K12424 , 23K11511 Takeda Science Foundation for Life Sciences Research the National Institute of Technology GEAR 5.0 Project for Agriculture, Forestry, and Fisheries Japan Science and Technology Agency, https://ror.org/00097mb19 , 23A360 European Research Council , 945026 Footnotes ↵ 1 This work is a result of an equal collaboration of three Principal Investigators, all giving their shares equally toward the completion of this project. Title and abstract updated; Significance statements have been added; Supplemental files updated. References 1. ↵ R. Hanlon , J. Messenger , Cephalopod Behaviour , 2 nd Ed. ( Cambridge University Press , 2018 ). 2. ↵ A. R. Tanner , et al. , Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution . Proc. Biol. Sci . 284 ( 2017 ). 3. ↵ B. Kröger , J. Vinther , D. Fuchs , Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules: Extant cephalopods are younger than previously realised and were under major selection to become agile, shell-less predators . Bioessays 33 , 602 – 613 ( 2011 ). OpenUrl CrossRef PubMed Web of Science 4. ↵ T. Clements , C. Colleary , K. De Baets , J. Vinther , Buoyancy mechanisms limit preservation of coleoid cephalopod soft tissues in Mesozoic Lagerstätten . Palaeontology 60 , 1 – 14 ( 2017 ). OpenUrl CrossRef 5. ↵ P. Amodio , et al. , Shell Loss in Cephalopods: Trigger for, or By-Product of, the Evolution of Intelligence? A Reply to Mollo et al. Trends Ecol. Evol . 34 , 690 – 692 ( 2019 ). OpenUrl CrossRef PubMed 6. ↵ D. A. López-Córdova , et al. , Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns . Mol. Phylogenet. Evol . 166 , 107331 ( 2022 ). 7. R. E. Young , M. Vecchione , D. T. Donovan , The evolution of coleoid cephalopods and their present biodiversity and ecology . S. Afr. J. Mar. Sci./S.-Afr. Tydskr. Seewet . 20 , 393 – 420 ( 1998 ). OpenUrl 8. ↵ M. J. Benton , F. Wu , Triassic Revolution . Front. Earth Sci . 10 , 899541 ( 2022 ). 9. ↵ P. Amodio , S. Shigeno , L. Ostojić , “ Evolution of Intelligence in Cephalopods ” in eLS , ( Wiley , 2020 ), pp. 77 – 84 . 10. J. A. Mather , M. J. Kuba , The cephalopod specialties: complex nervous system, learning, and cognition . Can. J. Zool . 91 , 431 – 449 ( 2013 ). OpenUrl CrossRef Web of Science 11. A. K. Schnell , P. Amodio , M. Boeckle , N. S. Clayton , How intelligent is a cephalopod? Lessons from comparative cognition: How intelligent is a cephalopod? Biol. Rev. Camb. Philos. Soc . 96 , 162 – 178 ( 2021 ). OpenUrl CrossRef 12. ↵ R. Jaitly , et al. , The evolution of predator avoidance in cephalopods: A case of brain over brawn? Front. Mar. Sci . 9 , 909192 ( 2022 ). 13. ↵ M. Belcaid , et al. , Symbiotic organs shaped by distinct modes of genome evolution in cephalopods . Proc. Natl. Acad. Sci. U. S. A . 116 , 3030 – 3035 ( 2019 ). OpenUrl Abstract / FREE Full Text 14. ↵ C. B. Albertin , et al. , The octopus genome and the evolution of cephalopod neural and morphological novelties . Nature 524 , 220 – 224 ( 2015 ). OpenUrl CrossRef PubMed 15. ↵ C. B. Albertin , et al. , Genome and transcriptome mechanisms driving cephalopod evolution . Nat. Commun . 13 , 2427 ( 2022 ). 16. Y. Zhang , et al. , The genome of Nautilus pompilius illuminates eye evolution and biomineralization . Nature Ecology & Evolution 1 – 12 ( 2021 ). doi: 10.1038/s41559-021-01448-6 . OpenUrl CrossRef PubMed 17. ↵ Z. Huang , et al. , Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving “living fossil.” Mol. Ecol. Resour . 22 , 15 – 27 ( 2022 ). OpenUrl PubMed 18. ↵ H. Schmidbaur , et al. , Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization . Nat. Commun . 13 , 2172 ( 2022 ). 19. ↵ A. Marino , A. Kizenko , W. Y. Wong , F. Ghiselli , O. Simakov , Repeat age decomposition informs an ancient set of repeats associated with coleoid cephalopod divergence . Front. Genet . 13 , 793734 ( 2022 ). 20. ↵ R. Styfhals , et al. , Cell type diversity in a developing octopus brain . Nat. Commun . 13 , 7392 ( 2022 ). 21. ↵ E. A. Ritschard , R. R. Fitak , O. Simakov , S. Johnsen , Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction . Proc. Biol. Sci . 286 , 20182929 ( 2019 ). 22. ↵ O. Simakov , et al. , Deeply conserved synteny and the evolution of metazoan chromosomes . Science Advances 8 , eabi5884 ( 2022 ). 23. ↵ M. Košťák , et al. , Fossil evidence for vampire squid inhabiting oxygen-depleted ocean zones since at least the Oligocene . Commun Biol 4 , 216 ( 2021 ). 24. ↵ A. J. Rowe , et al. , Exceptional soft-tissue preservation of Jurassic Vampyronassa rhodanica provides new insights on the evolution and palaeoecology of vampyroteuthids . Sci. Rep . 12 , 8292 ( 2022 ). 25. ↵ A. V. Golikov , et al. , The first global deep-sea stable isotope assessment reveals the unique trophic ecology of Vampire Squid Vampyroteuthis infernalis (Cephalopoda) . Sci. Rep . 9 , 19099 ( 2019 ). 26. ↵ J. Schlögl , M. Košt’ák , M. Hyžný , First record of a gladius-bearing coleoid Teudopsis bollensis Voltz (Cephalopoda, Coleoidea) in the Toarcian of the Western Carpathians (Slovakia) . Palaontol. Z . 86 , 367 – 375 ( 2012 ). OpenUrl 27. ↵ D. Fuchs , H. Keupp , G. Schweigert , First record of a complete arm crown of the Early Jurassic coleoid Loligosepia (Cephalopoda) . Palaontol. Z . 87 , 431 – 435 ( 2013 ). OpenUrl 28. ↵ D. Fuchs , R. Weis , B. Thuy , Simoniteuthis, a new vampyromorph coleoid with prey in its arms from the Early Jurassic of Luxembourg . Research Square ( 2023 ). 29. ↵ Y. Iba , et al. , Belemnite extinction and the origin of modern cephalopods 35 m.y. prior to the Cretaceous−Paleogene event . Geology 39 , 483 – 486 ( 2011 ). OpenUrl Abstract / FREE Full Text 30. ↵ K. Tanabe , A. Misaki , Y. Hikida , T. Nishimura , New records of coleoid cephalopod jaws from the Upper Cretaceous of Hokkaido, Japan, and their paleobiogeographic and evolutionary implications . Cretac. Res . 70 , 128 – 141 ( 2017 ). OpenUrl CrossRef 31. ↵ C. B. Albertin , O. Simakov , Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties . Annu Rev Anim Biosci 8 , 71 – 90 ( 2020 ). OpenUrl CrossRef PubMed 32. ↵ D. H. E. Setiamarga , et al. , Hydrophilic Shell Matrix Proteins of Nautilus pompilius and the identification of a core set of Conchiferan domains . Genes (Basel ) 12 , 1925 ( 2021 ). 33. ↵ M. A. Yoshida , et al. , Gene recruitments and dismissals in the argonaut genome provide insights into pelagic lifestyle adaptation and shell-like eggcase reacquisition . Genome Biol. Evol . ( 2022 ). doi: 10.1093/gbe/evac140 . OpenUrl CrossRef 34. C. B. Albertin , et al. , The octopus genome and the evolution of cephalopod neural and morphological novelties . Nature 524 , 220 – 224 ( 2015 ). OpenUrl CrossRef PubMed 35. ↵ D. T. Schultz , et al. , Ancient gene linkages support ctenophores as sister to other animals . Nature 618 , 110 – 117 ( 2023 ). OpenUrl CrossRef PubMed 36. ↵ A. Mackintosh , R. Vila , S. H. Martin , D. Setter , K. Lohse , Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies . Mol. Ecol . ( 2023 ). doi: 10.1111/mec.17146 . OpenUrl CrossRef 37. ↵ G. Ritschard , Measuring the nature of individual sequences . Sociol. Methods Res . 52 , 2016 – 2049 ( 2023 ). OpenUrl CrossRef 38. ↵ G. C. Coffing , et al. , Cephalopod Sex Determination and its Ancient Evolutionary Origin Revealed by Chromosome-level Assembly of the California Two-Spot Octopus . bioRxiv 2024 .02.21.581452 ( 2024 ). 39. ↵ A. Meyer , et al. , Giant lungfish genome elucidates the conquest of land by vertebrates . Nature 590 , 284 – 289 ( 2021 ). OpenUrl CrossRef PubMed 40. ↵ K. Hirota , et al. , Comparative proteomics of the shell matrix proteins of Nautilus pompilius and the conchiferans provide insights into mollusk shell evolution at the molecular level . Mar. Biol . 170 , 106 ( 2023 ). 41. ↵ G. Baid , et al. , DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer . Nat. Biotechnol . 41 , 232 – 238 ( 2023 ). OpenUrl PubMed 42. ↵ H. Cheng , G. T. Concepcion , X. Feng , H. Zhang , H. Li , Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm . Nat. Methods 18 , 170 – 175 ( 2021 ). OpenUrl CrossRef PubMed 43. ↵ H. Cheng , et al. , Haplotype-resolved assembly of diploid genomes without parental data . Nat. Biotechnol . 40 , 1332 – 1335 ( 2022 ). OpenUrl CrossRef PubMed 44. ↵ D. Guan , et al. , Identifying and removing haplotypic duplication in primary genome assemblies . Bioinformatics 36 , 2896 – 2898 ( 2020 ). OpenUrl CrossRef PubMed 45. ↵ N. C. Durand , et al. , Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments . Cell Syst . 3 , 95 – 98 ( 2016 ). OpenUrl CrossRef PubMed 46. ↵ O. Dudchenko , et al. , De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds . Science 356 , 92 – 95 ( 2017 ). OpenUrl Abstract / FREE Full Text 47. ↵ N. C. Durand , et al. , Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom . Cell Syst . 3 , 99 – 101 ( 2016 ). OpenUrl CrossRef PubMed 48. ↵ H. Li , Protein-to-genome alignment with miniprot . Bioinformatics 39 ( 2023 ). 49. ↵ A. Gabadinho , G. Ritschard , N. S. Müller , M. Studer , Analyzing and visualizing state sequences inRwithTraMineR . J. Stat. Softw . 40 , 1 – 37 ( 2011 ). OpenUrl CrossRef PubMed 50. ↵ O. Simakov , et al. , Hemichordate genomes and deuterostome origins . Nature 527 , 459 – 465 ( 2015 ). OpenUrl CrossRef PubMed View the discussion thread. Back to top Previous Next Posted July 07, 2025. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes Masa-aki Yoshida , Emese Tóth , Koto Kon-Nanjo , Tetsuo Kon , Kazuki Hirota , Atsushi Toyoda , Hidehiro Toh , Hideyuki Miyazawa , Makoto Terauchi , Hideki Noguchi , Davin H. E. Setiamarga , Oleg Simakov bioRxiv 2025.05.16.652989; doi: https://doi.org/10.1101/2025.05.16.652989 Share This Article: Copy Citation Tools Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes Masa-aki Yoshida , Emese Tóth , Koto Kon-Nanjo , Tetsuo Kon , Kazuki Hirota , Atsushi Toyoda , Hidehiro Toh , Hideyuki Miyazawa , Makoto Terauchi , Hideki Noguchi , Davin H. E. Setiamarga , Oleg Simakov bioRxiv 2025.05.16.652989; doi: https://doi.org/10.1101/2025.05.16.652989 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 Genomics Subject Areas All Articles Animal Behavior and Cognition (7636) Biochemistry (17704) Bioengineering (13898) Bioinformatics (41967) Biophysics (21460) Cancer Biology (18599) Cell Biology (25525) Clinical Trials (138) Developmental Biology (13384) Ecology (19909) Epidemiology (2067) Evolutionary Biology (24326) Genetics (15613) Genomics (22512) Immunology (17740) Microbiology (40423) Molecular Biology (17191) Neuroscience (88645) Paleontology (667) Pathology (2835) Pharmacology and Toxicology (4825) Physiology (7646) Plant Biology (15158) Scientific Communication and Education (2046) Synthetic Biology (4302) Systems Biology (9825) Zoology (2271)