{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T20:06:18Z","timestamp":1792613178997,"version":"4.5.0"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,6,8]],"date-time":"2017-06-08T00:00:00Z","timestamp":1496880000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Chinese crocodile lizard, Shinisaurus crocodilurus, is the only living representative of the monotypic family Shinisauridae under the order Squamata. It is an obligate semi-aquatic, viviparous, diurnal species restricted to specific portions of mountainous locations in southwestern China and northeastern Vietnam. However, in the past several decades, this species has undergone a rapid decrease in population size due to illegal poaching and habitat disruption, making this unique reptile species endangered and listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Appendix II since 1990. A proposal to uplist it to Appendix I was passed at the Convention on International Trade in Endangered Species of Wild Fauna and Flora Seventeenth meeting of the Conference of the Parties in 2016. To promote the conservation of this species, we sequenced the genome of a male Chinese crocodile lizard using a whole-genome shotgun strategy on the Illumina HiSeq 2000 platform. In total, we generated ~291 Gb of raw sequencing data (\u00d7149 depth) from 13 libraries with insert sizes ranging from 250 bp to 40 kb. After filtering for polymerase chain reaction\u2013duplicated and low-quality reads, ~137 Gb of clean data (\u00d770 depth) were obtained for genome assembly. We yielded a draft genome assembly with a total length of 2.24 Gb and an N50 scaffold size of 1.47 Mb. The assembled genome was predicted to contain 20 150 protein-coding genes and up to 1114 Mb (49.6%) of repetitive elements. The genomic resource of the Chinese crocodile lizard will contribute to deciphering the biology of this organism and provides an essential tool for conservation efforts. It also provides a valuable resource for future study of squamate evolution.<\/jats:p>","DOI":"10.1093\/gigascience\/gix041","type":"journal-article","created":{"date-parts":[[2017,6,8]],"date-time":"2017-06-08T00:59:05Z","timestamp":1496883545000},"source":"Crossref","is-referenced-by-count":23,"title":["Sequencing,\n                    <i>de novo<\/i>\n                    assembling, and annotating the genome of the endangered Chinese crocodile lizard\n                    <i>Shinisaurus crocodilurus<\/i>"],"prefix":"10.1093","volume":"6","author":[{"given":"Jian","family":"Gao","sequence":"first","affiliation":[{"name":"1BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China"},{"name":"2China National Genebank, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"3BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiye","family":"Li","sequence":"additional","affiliation":[{"name":"2China National Genebank, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"3BGI-Shenzhen, Shenzhen 518083, China"},{"name":"4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongji","family":"Wang","sequence":"additional","affiliation":[{"name":"2China National Genebank, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"3BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Zhou","sequence":"additional","affiliation":[{"name":"2China National Genebank, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"3BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Martelli","sequence":"additional","affiliation":[{"name":"6Veterinary Department, Ocean Park Hong Kong, Hong Kong SAR"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Li","sequence":"additional","affiliation":[{"name":"2China National Genebank, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"3BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zijun","family":"Xiong","sequence":"additional","affiliation":[{"name":"2China National Genebank, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"3BGI-Shenzhen, Shenzhen 518083, China"},{"name":"4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Wang","sequence":"additional","affiliation":[{"name":"3BGI-Shenzhen, Shenzhen 518083, China"},{"name":"7James D. Watson Institute of Genome Sciences, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanming","family":"Yang","sequence":"additional","affiliation":[{"name":"3BGI-Shenzhen, Shenzhen 518083, China"},{"name":"7James D. Watson Institute of Genome Sciences, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guojie","family":"Zhang","sequence":"additional","affiliation":[{"name":"2China National Genebank, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"3BGI-Shenzhen, Shenzhen 518083, China"},{"name":"4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China"},{"name":"8Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,6,8]]},"reference":[{"key":"2024111706510367100_bib1","first-page":"326","article-title":"Beitrage zur Lurch und Kriechtierfauna Kwangsi: Section 5, Eidechsen","volume":"1930","author":"Ahl","year":"1930","journal-title":"Sitzungsberichte der Gesellschaft der naturforschenden Freunde zu Berlin"},{"issue":"2","key":"2024111706510367100_bib2","first-page":"71","article-title":"Potential distribution and effectiveness of the protected area network for the crocodile lizard, Shinisaurus crocodilurus (Reptilia: Squamata: Sauria)","volume":"50","author":"van Schingen","year":"2014","journal-title":"Salamandra"},{"issue":"3","key":"2024111706510367100_bib3","doi-asserted-by":"crossref","first-page":"e91570","DOI":"10.1371\/journal.pone.0091570","article-title":"Genetic diversity and population demography of the Chinese crocodile lizard (Shinisaurus crocodilurus) in China","volume":"9","author":"Huang","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"2024111706510367100_bib4","first-page":"1","article-title":"The ossified braincase and cephalic osteoderms of Shinisaurus crocodilurus (Squamata, Shinisauridae)","volume":"8","author":"Bever","year":"2005","journal-title":"Palaeonto Electronica"},{"issue":"2","key":"2024111706510367100_bib5","doi-asserted-by":"crossref","first-page":"63","DOI":"10.32800\/abc.2008.31.2.0063","article-title":"Population and conservation strategies for the Chinese crocodile lizard (Shinisaurus crocodilurus) in China","volume":"31","author":"Huang","year":"2008","journal-title":"Anim Biodivers Conserv"},{"key":"2024111706510367100_bib6","article-title":"Shinisaurus crocodilurus","author":"Nguyen","year":"2014","journal-title":"The IUCN Red List of Threatened Species"},{"key":"2024111706510367100_bib7","first-page":"181","article-title":"A comparative study of crocodile lizards (Shinisaurus crocodilurus AHL, 1930) from Vietnam and China","volume-title":"Raffles Bull Zool","author":"Ziegler","year":"2008"},{"key":"2024111706510367100_bib8","article-title":"Convention on International trade in endangered species of wild fauna and flora","author":"Appendices I, II and III","year":"2011"},{"issue":"1","key":"2024111706510367100_bib9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2047-217X-1-18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","author":"Luo","year":"2012","journal-title":"Gigascience"},{"issue":"7279","key":"2024111706510367100_bib10","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/nature08696","article-title":"The sequence and de novo assembly of the giant panda genome","volume":"463","author":"Li","year":"2010","journal-title":"Nature"},{"issue":"1","key":"2024111706510367100_bib11","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s13742-016-0112-y","article-title":"Draft genome of the Chinese mitten crab, Eriocheir sinensis","volume":"5","author":"Song","year":"2016","journal-title":"Gigascience"},{"issue":"4","key":"2024111706510367100_bib12","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1101\/gr.2264004","article-title":"The Atlas Genome Assembly System","volume":"14","author":"Havlak","year":"2004","journal-title":"Genome Res"},{"issue":"19","key":"2024111706510367100_bib13","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Simao","year":"2015","journal-title":"Bioinformatics"},{"key":"2024111706510367100_bib14","article-title":"RepeatMasker","author":"Smit","year":"1996"},{"key":"2024111706510367100_bib15","volume-title":"RepeatModeler-1.0.5","author":"Smit","year":"2012"},{"issue":"Web Server issue","key":"2024111706510367100_bib16","doi-asserted-by":"crossref","first-page":"W265","DOI":"10.1093\/nar\/gkm286","article-title":"LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons","volume":"35","author":"Xu","year":"2007","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"2024111706510367100_bib17","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res"},{"issue":"51","key":"2024111706510367100_bib18","doi-asserted-by":"crossref","first-page":"20645","DOI":"10.1073\/pnas.1314475110","article-title":"The Burmese python genome reveals the molecular basis for extreme adaptation in snakes","volume":"110","author":"Castoe","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"51","key":"2024111706510367100_bib19","doi-asserted-by":"crossref","first-page":"20651","DOI":"10.1073\/pnas.1314702110","article-title":"The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system","volume":"110","author":"Vonk","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2024111706510367100_bib20","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13742-015-0085-2","article-title":"High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps","volume":"4","author":"Georges","year":"2015","journal-title":"Gigascience"},{"issue":"7366","key":"2024111706510367100_bib21","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nature10390","article-title":"The genome of the green anole lizard and a comparative analysis with birds and mammals","volume":"477","author":"Alf\u00f6ldi","year":"2011","journal-title":"Nature"},{"issue":"4","key":"2024111706510367100_bib22","first-page":"656","article-title":"BLAT\u2013the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"issue":"1","key":"2024111706510367100_bib23","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1101\/gr.082081.108","article-title":"GenBlastA: enabling BLAST to identify homologous gene sequences","volume":"19","author":"She","year":"2009","journal-title":"Genome Res"},{"issue":"5","key":"2024111706510367100_bib24","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1101\/gr.1865504","article-title":"GeneWise and Genomewise","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"issue":"Web Server issue","key":"2024111706510367100_bib25","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkl200","article-title":"AUGUSTUS: ab initio prediction of alternative transcripts","volume":"34","author":"Stanke","year":"2006","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2024111706510367100_bib26","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/s13742-016-0151-4","article-title":"Draft genome of the leopard gecko, Eublepharis macularius","volume":"5","author":"Xiong","year":"2016","journal-title":"Gigascience"},{"issue":"1","key":"2024111706510367100_bib27","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/nar\/28.1.45","article-title":"The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"2024111706510367100_bib28","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1093\/bioinformatics\/17.9.847","article-title":"InterProScan\u2013an integration platform for the signature-recognition methods in InterPro","volume":"17","author":"Zdobnov","year":"2001","journal-title":"Bioinformatics"},{"issue":"1","key":"2024111706510367100_bib29","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1093\/nar\/28.1.267","article-title":"ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons","volume":"28","author":"Corpet","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2024111706510367100_bib30","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1093\/nar\/gkg030","article-title":"PRINTS and its automatic supplement, prePRINTS","volume":"31","author":"Attwood","year":"2003","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"2024111706510367100_bib31","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam Protein Families Database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024111706510367100_bib32","doi-asserted-by":"crossref","first-page":"D302","DOI":"10.1093\/nar\/gkr931","article-title":"SMART 7: recent updates to the protein domain annotation resource","volume":"40","author":"Letunic","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2024111706510367100_bib33","first-page":"D204","article-title":"PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium","volume":"38","author":"Mi","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"2024111706510367100_bib34","doi-asserted-by":"crossref","first-page":"D161","DOI":"10.1093\/nar\/gkp885","article-title":"PROSITE, a protein domain database for functional characterization and annotation","volume":"38","author":"Sigrist","year":"2010","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2024111706510367100_bib35","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"issue":"1","key":"2024111706510367100_bib36","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"7076","key":"2024111706510367100_bib37","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1038\/nature04328","article-title":"Early evolution of the venom system in lizards and snakes","volume":"439","author":"Fry","year":"2006","journal-title":"Nature"},{"issue":"11","key":"2024111706510367100_bib38","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1074\/mcp.M110.001370","article-title":"Functional and structural diversification of the Anguimorpha lizard venom system","volume":"9","author":"Fry","year":"2010","journal-title":"Mol Cell Proteomics"},{"key":"2024111706510367100_bib39","unstructured":"Li Q, Wang Z, Zhou Y. The genome of the Chinese crocodile lizard; Shinisaurus crocodilurus. GigaScience Database2017. 10.5524\/100315."},{"issue":"6215","key":"2024111706510367100_bib40","doi-asserted-by":"crossref","first-page":"1254449","DOI":"10.1126\/science.1254449","article-title":"Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs","volume":"346","author":"Green","year":"2014","journal-title":"Science"},{"issue":"9","key":"2024111706510367100_bib41","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1038\/cr.2013.104","article-title":"Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator","volume":"23","author":"Wan","year":"2013","journal-title":"Cell Res"},{"issue":"7366","key":"2024111706510367100_bib42","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nature10390","article-title":"The genome of the green anole lizard and a comparative analysis with birds and mammals","volume":"477","author":"Alfoldi","year":"2011","journal-title":"Nature"},{"key":"2024111706510367100_bib43","first-page":"R28","article-title":"The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage","volume-title":"Genome Biol","author":"Minx","year":"2013"},{"issue":"6","key":"2024111706510367100_bib44","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/ng.2615","article-title":"The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan","volume":"45","author":"Wang","year":"2013","journal-title":"Nat Genet"},{"key":"2024111706510367100_bib45","doi-asserted-by":"crossref","first-page":"13107","DOI":"10.1038\/ncomms13107","article-title":"Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper","volume":"7","author":"Yin","year":"2016","journal-title":"Nat Commun"},{"key":"2024111706510367100_bib46","doi-asserted-by":"crossref","first-page":"10033","DOI":"10.1038\/ncomms10033","article-title":"Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration","volume":"6","author":"Liu","year":"2015","journal-title":"Nat Commun"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/6\/7\/gix041\/60710417\/gigascience_6_7_gix041.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/6\/7\/gix041\/60710417\/gigascience_6_7_gix041.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,17]],"date-time":"2024-11-17T01:51:24Z","timestamp":1731808284000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/gix041\/3862719"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,8]]},"references-count":46,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2017,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gigascience\/gix041","relation":{},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,7]]},"published":{"date-parts":[[2017,6,8]]},"article-number":"gix041"}}