{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T05:47:29Z","timestamp":1788587249113,"version":"build-2803163510"},"posted":{"date-parts":[[2026,6,28]]},"group-title":"Evolutionary Biology","reference-count":101,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,6,28]],"date-time":"2026-06-28T00:00:00Z","timestamp":1782604800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["None"],"award-info":[{"award-number":["None"]}],"id":[{"id":"https:\/\/ror.org\/006w34k90","id-type":"ROR","asserted-by":"publisher"}]},{"award":["Balo-Simon Chair of Biological Science"],"award-info":[{"award-number":["Balo-Simon Chair of Biological Science"]}],"id":[{"id":"https:\/\/ror.org\/047s2c258","id-type":"ROR","asserted-by":"publisher"}]},{"award":["Viper Resource Grant at Texas A&M University-Kingsville (#P40OD010960-22)"],"award-info":[{"award-number":["Viper Resource Grant at Texas A&M University-Kingsville (#P40OD010960-22)"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,6,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Evolutionary innovation is a key driver of the colonization of new environments and the adaptive radiations of major groups. Novel traits typically evolve through the modification of pre-existing characters but the genetic paths underlying their origin have been challenging to trace, and the general requirements for and relative order of different kinds of gene mutations have been difficult to assess. Here, we trace the genomic origins of four procoagulant venom toxins (factor X, factor V, group I phospholipase A\n                  <jats:sub>\u2082<\/jats:sub>\n                  , and Kunitz-type toxins) that collectively underlie a novel, especially potent blood-clotting venom type in the recently evolved Australian brown snake and taipan clade. We discover evidence for a previously unknown fifth toxin, coagulation factor VII, and show that the toxins evolved through two distinct genetic paths. The factor X and factor V toxins evolved through the sequential\n                  <jats:italic>de novo<\/jats:italic>\n                  co-option of ancestral clotting factor proteins that entailed their heterotopic expression in the venom gland, the fixation of segmental duplications containing each locus, and subsequent gain-of-function mutations that rendered factor X and factor V constitutively active. In contrast, the phospholipase A\n                  <jats:sub>\u2082<\/jats:sub>\n                  and Kunitz-type toxins evolved by modifying the functions of neurotoxins that were part of the venom arsenal. Our findings support models in which innovative mutations in single-copy genes precede gene duplication in the evolution of novel proteins and offer a rare view into the genesis of a complex trait that has played a central role in a major adaptive radiation.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Significance Statement<\/jats:title>\n                  <jats:p>This study investigates how an entirely new blood-clotting venom type evolved during the recent radiation of Australia\u2019s iconic venomous snakes. We traced the key genetic events that occurred on the evolutionary path to one of the world\u2019s most potent venoms. We found that the novel venom activity evolved through the sequential co-option of multiple proteins of the snake\u2019s own blood-clotting system, followed by the modification of two venom neurotoxins into proteins with procoagulant activities. We suggest that these unique de novo gene co-options are seminal events that can unlock new ecological strategies, which in turn, may enable major adaptive radiations.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.06.23.733212","type":"posted-content","created":{"date-parts":[[2026,6,28]],"date-time":"2026-06-28T14:45:18Z","timestamp":1782657918000},"source":"Crossref","is-referenced-by-count":1,"title":["The genomic origins and evolutionary path to a key innovation in the world\u2019s most venomous snakes"],"prefix":"10.64898","author":[{"given":"Jory","family":"van Thiel","sequence":"first","affiliation":[{"name":"Howard Hughes Medical Institute and Department of Biology, University of Maryland, College Park, 20742, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noah L.","family":"Dowell","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute and Department of Biology, University of Maryland, College Park, 20742, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cara F.","family":"Smith","sequence":"additional","affiliation":[{"name":"Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elda E.","family":"Sanchez","sequence":"additional","affiliation":[{"name":"National Natural Toxins Research Center, Texas A&M University-Kingsville, Kingsville, 78363, United States of America"},{"name":"Department of Chemistry, Texas A&M University-Kingsville, Kingsville, 78363, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7839-5458","authenticated-orcid":false,"given":"Sean B.","family":"Carroll","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute and Department of Biology, University of Maryland, College Park, 20742, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026063015500770000_2026.06.23.733212v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.06.030"},{"key":"2026063015500770000_2026.06.23.733212v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2009.11.010"},{"key":"2026063015500770000_2026.06.23.733212v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nature07891"},{"key":"2026063015500770000_2026.06.23.733212v1.4","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0809668106"},{"key":"2026063015500770000_2026.06.23.733212v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/nature08896"},{"key":"2026063015500770000_2026.06.23.733212v1.6","doi-asserted-by":"publisher","DOI":"10.1126\/science.1208227"},{"key":"2026063015500770000_2026.06.23.733212v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2015.08.005"},{"key":"2026063015500770000_2026.06.23.733212v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2016.09.020"},{"key":"2026063015500770000_2026.06.23.733212v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.09.028"},{"key":"2026063015500770000_2026.06.23.733212v1.10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2108661119"},{"key":"2026063015500770000_2026.06.23.733212v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2023.03.003"},{"key":"2026063015500770000_2026.06.23.733212v1.12","doi-asserted-by":"crossref","unstructured":"J. W. Satterlee et al., Convergent evolution of plant prickles by repeated gene co-option over deep time. Science 385, eado1663 (2024).","DOI":"10.1126\/science.ado1663"},{"key":"2026063015500770000_2026.06.23.733212v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2024.08.042"},{"key":"2026063015500770000_2026.06.23.733212v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/bs.ctdb.2020.03.002"},{"key":"2026063015500770000_2026.06.23.733212v1.15","doi-asserted-by":"publisher","DOI":"10.1038\/nature03235"},{"key":"2026063015500770000_2026.06.23.733212v1.16","doi-asserted-by":"publisher","DOI":"10.1126\/science.1233749"},{"key":"2026063015500770000_2026.06.23.733212v1.17","doi-asserted-by":"crossref","unstructured":"S. Ohno , Evolution by gene duplication (Springer Science & Business Media, 1970).","DOI":"10.1007\/978-3-642-86659-3"},{"key":"2026063015500770000_2026.06.23.733212v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2482"},{"key":"2026063015500770000_2026.06.23.733212v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2808"},{"key":"2026063015500770000_2026.06.23.733212v1.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-026-00935-5"},{"key":"2026063015500770000_2026.06.23.733212v1.21","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.tree.2012.10.020","article-title":"Complex cocktails: the evolutionary novelty of venoms","volume":"28","year":"2013","journal-title":"Trends in Ecology & Evolution"},{"key":"2026063015500770000_2026.06.23.733212v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2016.07.038"},{"key":"2026063015500770000_2026.06.23.733212v1.23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1920011117"},{"key":"2026063015500770000_2026.06.23.733212v1.24","doi-asserted-by":"crossref","unstructured":"A. Barua , I. Koludarov , A. S. Mikheyev , Co-option of the same ancestral gene family gave rise to mammalian and reptilian toxins. BMC Biology 19, 268 (2021).","DOI":"10.1186\/s12915-021-01191-1"},{"key":"2026063015500770000_2026.06.23.733212v1.25","doi-asserted-by":"crossref","first-page":"4861","DOI":"10.1038\/s41467-023-40550-0","article-title":"Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily","volume":"14","year":"2023","journal-title":"Nature Communications"},{"key":"2026063015500770000_2026.06.23.733212v1.26","doi-asserted-by":"publisher","DOI":"10.3390\/genes13020217"},{"key":"2026063015500770000_2026.06.23.733212v1.27","doi-asserted-by":"publisher","DOI":"10.1655\/HERPMONOGRAPHS-D-16-00003"},{"key":"2026063015500770000_2026.06.23.733212v1.28","doi-asserted-by":"publisher","DOI":"10.1111\/j.1420-9101.2008.01525.x"},{"key":"2026063015500770000_2026.06.23.733212v1.29","doi-asserted-by":"crossref","first-page":"1896","DOI":"10.1038\/s41559-017-0355-8","article-title":"Phylogenetic evidence for mid-Cenozoic turnover of a diverse continental biota","volume":"1","year":"2017","journal-title":"Nature Ecology & Evolution"},{"key":"2026063015500770000_2026.06.23.733212v1.30","doi-asserted-by":"crossref","first-page":"9366","DOI":"10.1016\/S0021-9258(17)39373-0","article-title":"Purification and properties of a prothrombin activator from the venom of Notechis scutatus scutatus","volume":"260","year":"1985","journal-title":"Journal of Biological Chemistry"},{"key":"2026063015500770000_2026.06.23.733212v1.31","doi-asserted-by":"crossref","first-page":"13258","DOI":"10.1016\/S0021-9258(18)69299-3","article-title":"Prothrombin activation by an activator from the venom of Oxyuranus scutellatus (Taipan snake)","volume":"261","year":"1986","journal-title":"Journal of Biological Chemistry"},{"key":"2026063015500770000_2026.06.23.733212v1.32","doi-asserted-by":"publisher","DOI":"10.1042\/bj20020889"},{"key":"2026063015500770000_2026.06.23.733212v1.33","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1160\/TH04-03-0144","article-title":"The catalytic subunit of pseutarin C, a group C prothrombin activator from the venom of Pseudonaja textilis, is structurally similar to mammalian blood coagulation factor Xa","volume":"92","year":"2004","journal-title":"Thromb Haemost"},{"key":"2026063015500770000_2026.06.23.733212v1.34","first-page":"40","article-title":"Two parallel prothrombin activator systems in Australian rough-scaled snake","volume":"93","year":"2005","journal-title":"Tropidechis carinatus. Structural comparison of venom prothrombin activator with blood coagulation factor X"},{"key":"2026063015500770000_2026.06.23.733212v1.35","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1111\/j.1538-7836.2006.01969.x","article-title":"Molecular evolution caught in action: gene duplication and evolution of molecular isoforms of prothrombin activators in Pseudonaja textilis (brown snake)","volume":"4","year":"2006","journal-title":"Journal of Thrombosis and Haemostasis"},{"key":"2026063015500770000_2026.06.23.733212v1.36","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.toxlet.2019.08.014","article-title":"Clinical implications of convergent procoagulant toxicity and differential antivenom efficacy in Australian elapid snake venoms","volume":"316","year":"2019","journal-title":"Toxicology Letters"},{"key":"2026063015500770000_2026.06.23.733212v1.37","doi-asserted-by":"publisher","DOI":"10.3390\/toxins8110309"},{"key":"2026063015500770000_2026.06.23.733212v1.38","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2002-12-3839"},{"key":"2026063015500770000_2026.06.23.733212v1.39","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1160\/TH04-11-0707","article-title":"Gene duplication of coagulation factor V and origin of venom prothrombin activator in Pseudonaja textilis snake","volume":"93","year":"2005","journal-title":"Thromb Haemost"},{"key":"2026063015500770000_2026.06.23.733212v1.40","doi-asserted-by":"crossref","first-page":"10952","DOI":"10.1016\/S0021-9258(19)86616-4","article-title":"The contribution of bovine Factor V and Factor Va to the activity of prothrombinase","volume":"254","year":"1979","journal-title":"Journal of Biological Chemistry"},{"key":"2026063015500770000_2026.06.23.733212v1.41","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.abb.2003.09.045","article-title":"Group IB phospholipase A2 from Pseudonaja textilis","volume":"421","year":"2004","journal-title":"Archives of Biochemistry and Biophysics"},{"key":"2026063015500770000_2026.06.23.733212v1.42","doi-asserted-by":"crossref","unstructured":"P. P. Masci et al., Textilinins from Pseudonaja textilis textilis. Characterization of two plasmin inhibitors that reduce bleeding in an animal model. Blood Coagulation & Fibrinolysis 11 (2000).","DOI":"10.1097\/00001721-200006000-00011"},{"key":"2026063015500770000_2026.06.23.733212v1.43","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2141.2002.03878.x"},{"key":"2026063015500770000_2026.06.23.733212v1.44","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.biochi.2011.08.003","article-title":"Identification and characterisation of Kunitz-type plasma kallikrein inhibitors unique to Oxyuranus sp. snake venoms","volume":"94","year":"2012","journal-title":"Biochimie"},{"key":"2026063015500770000_2026.06.23.733212v1.45","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/0041-0101(79)90245-9","article-title":"The lethality in mice of dangerous Australian and other snake venom","volume":"17","year":"1979","journal-title":"Toxicon"},{"key":"2026063015500770000_2026.06.23.733212v1.46","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi181"},{"key":"2026063015500770000_2026.06.23.733212v1.47","doi-asserted-by":"publisher","DOI":"10.1016\/0268-960X(94)90007-8"},{"key":"2026063015500770000_2026.06.23.733212v1.48","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1055\/s-0040-1715441","article-title":"Evolutionary Adaptations in Pseudonaja Textilis Venom Factor X Induce Zymogen Activity and Resistance to the Intrinsic Tenase Complex","volume":"120","year":"2020","journal-title":"Thromb Haemost"},{"key":"2026063015500770000_2026.06.23.733212v1.49","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0216148"},{"key":"2026063015500770000_2026.06.23.733212v1.50","unstructured":"D. Verhoef et al., Evolutionary conservation of regulatory B-domain elements in blood coagulation factor V in snakes. Lessons from snake venom: New insights into the structural and functional aspects of factor V and factor X, 25 (2021)."},{"key":"2026063015500770000_2026.06.23.733212v1.51","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2009-02-202663"},{"key":"2026063015500770000_2026.06.23.733212v1.52","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/0167-4838(93)90217-F","article-title":"Studies on the subunit structure of textilotoxin, a potent presynaptic neurotoxin from the venom of the Australian common brown snake (Pseudonaja textilis). 3. The complete amino-acid sequences of all the subunits","volume":"1161","year":"1993","journal-title":"Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology"},{"key":"2026063015500770000_2026.06.23.733212v1.53","doi-asserted-by":"publisher","DOI":"10.1111\/j.1432-1033.1976.tb10833.x"},{"key":"2026063015500770000_2026.06.23.733212v1.54","doi-asserted-by":"publisher","DOI":"10.1016\/0041-0101(72)90066-9"},{"key":"2026063015500770000_2026.06.23.733212v1.55","doi-asserted-by":"publisher","DOI":"10.1006\/abbi.1995.1257"},{"key":"2026063015500770000_2026.06.23.733212v1.56","doi-asserted-by":"publisher","DOI":"10.1093\/jb\/mvg187"},{"key":"2026063015500770000_2026.06.23.733212v1.57","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/S0026-895X(25)09435-0","article-title":"Potassium channel blockade by the B subunit of beta-bungarotoxin","volume":"38","year":"1990","journal-title":"Molecular Pharmacology"},{"key":"2026063015500770000_2026.06.23.733212v1.58","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/139.1.421"},{"key":"2026063015500770000_2026.06.23.733212v1.59","doi-asserted-by":"publisher","DOI":"10.1007\/s10709-008-9311-5"},{"key":"2026063015500770000_2026.06.23.733212v1.60","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0707158104"},{"key":"2026063015500770000_2026.06.23.733212v1.61","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.1994.0058"},{"key":"2026063015500770000_2026.06.23.733212v1.62","doi-asserted-by":"publisher","DOI":"10.1126\/science.252.5009.1078"},{"key":"2026063015500770000_2026.06.23.733212v1.63","doi-asserted-by":"publisher","DOI":"10.1038\/nature06151"},{"key":"2026063015500770000_2026.06.23.733212v1.64","doi-asserted-by":"publisher","DOI":"10.1038\/nature07092"},{"key":"2026063015500770000_2026.06.23.733212v1.65","doi-asserted-by":"publisher","DOI":"10.1126\/science.1226521"},{"key":"2026063015500770000_2026.06.23.733212v1.66","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.11.043"},{"key":"2026063015500770000_2026.06.23.733212v1.67","doi-asserted-by":"crossref","unstructured":"A. M. Rice , A. McLysaght , Dosage-sensitive genes in evolution and disease. BMC Biology 15, 78 (2017).","DOI":"10.1186\/s12915-017-0418-y"},{"key":"2026063015500770000_2026.06.23.733212v1.68","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.105.048058"},{"key":"2026063015500770000_2026.06.23.733212v1.69","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.117.202655"},{"key":"2026063015500770000_2026.06.23.733212v1.70","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2017.05.032"},{"key":"2026063015500770000_2026.06.23.733212v1.71","doi-asserted-by":"crossref","first-page":"e83966","DOI":"10.7554\/eLife.83966","article-title":"The evolution and structure of snake venom phosphodiesterase (svPDE) highlight its importance in venom actions","volume":"12","year":"2023","journal-title":"eLife"},{"key":"2026063015500770000_2026.06.23.733212v1.72","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2015159118"},{"key":"2026063015500770000_2026.06.23.733212v1.73","doi-asserted-by":"publisher","DOI":"10.1038\/nature10607"},{"key":"2026063015500770000_2026.06.23.733212v1.74","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3522"},{"key":"2026063015500770000_2026.06.23.733212v1.75","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.273.39.25393"},{"key":"2026063015500770000_2026.06.23.733212v1.76","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/jbt.21538","article-title":"BF9, the First Functionally Characterized Snake Toxin Peptide with Kunitz-Type Protease and Potassium Channel Inhibiting Properties","volume":"28","year":"2014","journal-title":"Journal of Biochemical and Molecular Toxicology"},{"key":"2026063015500770000_2026.06.23.733212v1.77","doi-asserted-by":"publisher","DOI":"10.1126\/science.aam5979"},{"key":"2026063015500770000_2026.06.23.733212v1.78","unstructured":"J. B. Losos , Improbable destinies: Fate, chance, and the future of evolution (Penguin, 2018)."},{"key":"2026063015500770000_2026.06.23.733212v1.79","doi-asserted-by":"crossref","unstructured":"B. Xie et al., Dynamic genetic differentiation drives the widespread structural and functional convergent evolution of snake venom proteinaceous toxins. BMC Biology 20, 4 (2022).","DOI":"10.1186\/s12915-021-01208-9"},{"key":"2026063015500770000_2026.06.23.733212v1.80","doi-asserted-by":"publisher","DOI":"10.1101\/gr.240952.118"},{"key":"2026063015500770000_2026.06.23.733212v1.81","doi-asserted-by":"crossref","unstructured":"G. Mochales-Ria\u00f1o et al., Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii). GigaScience 14, giaf030 (2025).","DOI":"10.1093\/gigascience\/giaf030"},{"key":"2026063015500770000_2026.06.23.733212v1.82","doi-asserted-by":"crossref","unstructured":"A. J. Mason et al., Molecular mechanisms underlying early functional divergence in snake venom inferred from the genomes of two pitviper lineages. BMC Biology 23, 366 (2025).","DOI":"10.1186\/s12915-025-02465-8"},{"key":"2026063015500770000_2026.06.23.733212v1.83","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1111\/j.1432-1033.1983.tb07481.x","article-title":"Serine Proteinase Inhibitors from Vipera ammodytes Venom","volume":"133","year":"1983","journal-title":"European Journal of Biochemistry"},{"key":"2026063015500770000_2026.06.23.733212v1.84","doi-asserted-by":"crossref","unstructured":"A.-C. Cheng , I.-H. Tsai , Functional characterization of a slow and tight-binding inhibitor of plasmin isolated from Russell\u2019s viper venom. Biochimica et Biophysica Acta (BBA) - General Subjects 1840, 153\u2013159 (2014).","DOI":"10.1016\/j.bbagen.2013.08.019"},{"key":"2026063015500770000_2026.06.23.733212v1.85","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0054104"},{"key":"2026063015500770000_2026.06.23.733212v1.86","doi-asserted-by":"crossref","unstructured":"S. Nurk et al., HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Research 30, 1291\u20131305.","DOI":"10.1101\/gr.263566.120"},{"key":"2026063015500770000_2026.06.23.733212v1.87","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","year":"2021","journal-title":"Nature Methods"},{"key":"2026063015500770000_2026.06.23.733212v1.88","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"2026063015500770000_2026.06.23.733212v1.89","doi-asserted-by":"crossref","unstructured":"I. H. Rossetto , A. J. Ludington , B. F. Sim\u00f5es , N. Van Cao , K. L. Sanders , Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes. Genome Biology and Evolution 16 (2024).","DOI":"10.1093\/gbe\/evae150"},{"key":"2026063015500770000_2026.06.23.733212v1.90","doi-asserted-by":"crossref","unstructured":"A. J. Ludington , J. M. Hammond , J. Breen , I. W. Deveson , K. L. Sanders , New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biology 21, 284 (2023).","DOI":"10.1186\/s12915-023-01772-2"},{"key":"2026063015500770000_2026.06.23.733212v1.91","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1093\/jhered\/esac048","article-title":"Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae)","volume":"113","year":"2022","journal-title":"Journal of Heredity"},{"key":"2026063015500770000_2026.06.23.733212v1.92","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"2026063015500770000_2026.06.23.733212v1.93","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu531"},{"key":"2026063015500770000_2026.06.23.733212v1.94","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"2026063015500770000_2026.06.23.733212v1.95","doi-asserted-by":"crossref","unstructured":"B. Li , C. N. Dewey , RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).","DOI":"10.1186\/1471-2105-12-323"},{"key":"2026063015500770000_2026.06.23.733212v1.96","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","year":"2012","journal-title":"Nature Methods"},{"key":"2026063015500770000_2026.06.23.733212v1.97","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry\u2013based proteomics","volume":"14","year":"2017","journal-title":"Nature Methods"},{"key":"2026063015500770000_2026.06.23.733212v1.98","doi-asserted-by":"crossref","first-page":"4065","DOI":"10.1038\/s41467-020-17921-y","article-title":"Identification of modified peptides using localization-aware open search","volume":"11","year":"2020","journal-title":"Nature Communications"},{"key":"2026063015500770000_2026.06.23.733212v1.99","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh340"},{"key":"2026063015500770000_2026.06.23.733212v1.100","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/sys029"},{"key":"2026063015500770000_2026.06.23.733212v1.101","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3519"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.06.23.733212","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T22:50:32Z","timestamp":1782859832000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.06.23.733212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,28]]},"references-count":101,"URL":"https:\/\/doi.org\/10.64898\/2026.06.23.733212","relation":{},"subject":[],"published":{"date-parts":[[2026,6,28]]},"subtype":"preprint"}}