{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T10:14:27Z","timestamp":1756894467263,"version":"3.41.2"},"reference-count":63,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T00:00:00Z","timestamp":1611792000000},"content-version":"vor","delay-in-days":27,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31772238"],"award-info":[{"award-number":["31772238"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2020QNA6024"],"award-info":[{"award-number":["2020QNA6024"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LZ18C060001"],"award-info":[{"award-number":["LZ18C060001"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Sex determination and the regulation of sexual dimorphism are among the most fascinating topics in modern biology. As the most species-rich group of sexually reproducing organisms on Earth, insects have multiple sex determination systems. Though sex chromosomes and sex-biased genes are well-studied in dozens of insects, their gene sequences are scattered in various databases. Moreover, a shortage of annotation hinders the deep mining of these data. Here, we collected the chromosome-level sex chromosome data of 49 insect species, including 34 X chromosomes, 15 Z chromosomes, 5 W chromosomes and 2 Y chromosomes. We also obtained Y-linked contigs of four insects species\u2014Anopheles gambiae, Drosophila innubila, Drosophila yakuba and Tribolium castaneum. The unannotated chromosome-level sex chromosomes were annotated using a standard pipeline, yielding a total of 123\u2009030 protein-coding genes, 2\u2009159\u2009427 repeat sequences, 894 miRNAs, 1574 rRNAs, 5105 tRNAs, 395 snoRNAs (small nucleolar RNA), 54 snRNAs (small nuclear RNA) and 5959 other ncRNAs (non-coding RNA). In addition, 36\u2009781 sex-biased genes were identified by analyzing 62 RNA-seq (RNA sequencing) datasets. Together with 5707 sex-biased genes from the Drosophila genus collected from the Sex-Associated Gene Database, we obtained a total of 42\u2009488 sex-biased genes from 13 insect species. All these data were deposited into InSexBase, a new user-friendly database of insect sex chromosomes and sex-biased genes.<\/jats:p>\n               <jats:p>Database URL: http:\/\/www.insect-genome.com\/Sexdb\/.<\/jats:p>","DOI":"10.1093\/database\/baab001","type":"journal-article","created":{"date-parts":[[2021,1,6]],"date-time":"2021-01-06T21:27:05Z","timestamp":1609968425000},"source":"Crossref","is-referenced-by-count":6,"title":["InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects"],"prefix":"10.1093","volume":"2021","author":[{"given":"X i","family":"Chen","sequence":"first","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Mei","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengyao","family":"Chen","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dong","family":"Jing","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yumin","family":"He","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feiling","family":"Liu","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kang","family":"He","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4234-4218","authenticated-orcid":false,"given":"Fei","family":"Li","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,1,28]]},"reference":[{"key":"2021012815251837900_R1","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1111\/j.1558-5646.1984.tb00388.x","article-title":"Evolution of sex determining mechanisms: a review of fact and theory","volume":"38","author":"Feener","year":"1984","journal-title":"Evolution"},{"key":"2021012815251837900_R2","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1534\/genetics.110.117697","article-title":"The birds and the bees and the flowers and the trees: lessons from genetic mapping of sex determination in plants and animals","volume":"186","author":"Charlesworth","year":"2010","journal-title":"Genetics"},{"key":"2021012815251837900_R3","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1387\/ijdb.072396ls","article-title":"Sex-determining mechanisms in insects","volume":"52","author":"Sanchez","year":"2008","journal-title":"Int. J. Dev. Biol."},{"key":"2021012815251837900_R4","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1038\/nature13315","article-title":"A single female-specific piRNA is the primary determiner of sex in the silkworm","volume":"509","author":"Kiuchi","year":"2014","journal-title":"Nature"},{"key":"2021012815251837900_R5","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1534\/genetics.110.121202","article-title":"Evolution of the Drosophila feminizing switch gene Sex-lethal","volume":"186","author":"Cline","year":"2010","journal-title":"Genetics"},{"key":"2021012815251837900_R6","doi-asserted-by":"crossref","first-page":"E2114","DOI":"10.1073\/pnas.1525164113","article-title":"Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes","volume":"113","author":"Hall","year":"2016","journal-title":"Proc. Nat. Acad. Sci."},{"key":"2021012815251837900_R7","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/j.tig.2009.04.002","article-title":"Origin and evolution of Y chromosomes: Drosophila tales","volume":"25","author":"Bernardo Carvalho","year":"2009","journal-title":"Trends Genet."},{"key":"2021012815251837900_R8","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1093\/molbev\/mss010","article-title":"Sex chromosomes evolved from independent ancestral linkage groups in winged insects","volume":"29","author":"Pease","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"2021012815251837900_R9","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1126\/science.1225385","article-title":"Sex-specific adaptation drives early sex chromosome evolution in Drosophila","volume":"337","author":"Zhou","year":"2012","journal-title":"Science"},{"key":"2021012815251837900_R10","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001711","article-title":"The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation","volume":"11","author":"Zhou","year":"2013","journal-title":"PLoS Biol."},{"key":"2021012815251837900_R11","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1038\/s41587-020-0508-1","article-title":"A male-biased sex-distorter gene drive for the human malaria vector Anopheles gambiae","volume":"38","author":"Simoni","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"2021012815251837900_R12","first-page":"62","article-title":"An X-ray mutation in the silkworm (in Japanese with English summary)","volume":"16","author":"Hashimoto","year":"1948","journal-title":"J. Sericult. Sci. Jpn."},{"key":"2021012815251837900_R13","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1086\/510214","article-title":"The evolution of condition-dependent sexual dimorphism","volume":"169","author":"Bonduriansky","year":"2007","journal-title":"Am. Nat."},{"key":"2021012815251837900_R14","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1101\/gr.217216.116","article-title":"Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes","volume":"27","author":"Papa","year":"2017","journal-title":"Genome Res."},{"key":"2021012815251837900_R15","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1038\/s41559-017-0314-4","article-title":"Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest","volume":"1","author":"Cheng","year":"2017","journal-title":"Nat. Ecol. Evol."},{"key":"2021012815251837900_R16","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1111\/1755-0998.12966","article-title":"A high-quality chromosome-level genome assembly of a generalist herbivore, Trichoplusia ni","volume":"19","author":"Chen","year":"2019","journal-title":"Mol. Ecol. Resour."},{"key":"2021012815251837900_R17","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.ibmb.2019.02.002","article-title":"High-quality genome assembly of the silkworm, Bombyx mori","volume":"107","author":"Kawamoto","year":"2019","journal-title":"Insect Biochem. Mol. Biol."},{"key":"2021012815251837900_R18","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-12175-9","article-title":"A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance","volume":"10","author":"Wan","year":"2019","journal-title":"Nat. Commun."},{"key":"2021012815251837900_R19","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/1755-0998.13078","article-title":"A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis","volume":"20","author":"Ma","year":"2020","journal-title":"Mol. Ecol. Resour."},{"key":"2021012815251837900_R20","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1111\/1755-0998.13182","article-title":"The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion","volume":"20","author":"Xiao","year":"2020","journal-title":"Mol. Ecol. Resour."},{"key":"2021012815251837900_R21","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1111\/1755-0998.13206","article-title":"A chromosome-level genome assembly of the parasitoid wasp Pteromalus puparum","volume":"20","author":"Ye","year":"2020","journal-title":"Mol. Ecol. Resour."},{"key":"2021012815251837900_R22","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1534\/genetics.108.099994","article-title":"The silkworm Z chromosome is enriched in testis-specific genes","volume":"182","author":"Arunkumar","year":"2009","journal-title":"Genetics"},{"key":"2021012815251837900_R23","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-12-296","article-title":"A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae","volume":"12","author":"Baker","year":"2011","journal-title":"BMC Genom."},{"key":"2021012815251837900_R24","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1001121","article-title":"Comparative genomic hybridization (CGH) reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis)","volume":"6","author":"Baker","year":"2010","journal-title":"PLoS Genet."},{"key":"2021012815251837900_R25","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1038\/nature09172","article-title":"Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition","volume":"466","author":"Bellott","year":"2010","journal-title":"Nature"},{"key":"2021012815251837900_R26","doi-asserted-by":"crossref","first-page":"R192","DOI":"10.1016\/j.cub.2005.03.005","article-title":"Female-biased gene expression in the malaria mosquito Anopheles gambiae","volume":"15","author":"Hahn","year":"2005","journal-title":"Curr. Biol."},{"key":"2021012815251837900_R27","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1126\/science.1079190","article-title":"Paucity of genes on the Drosophila X chromosome showing male-biased expression","volume":"299","author":"Parisi","year":"2003","journal-title":"Science"},{"key":"2021012815251837900_R28","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1093\/gbe\/evq024","article-title":"Hyperexpression of the X chromosome in both sexes results in extensive female bias of X-linked genes in the flour beetle","volume":"2","author":"Prince","year":"2010","journal-title":"Genome. Biol. Evol."},{"key":"2021012815251837900_R29","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.tig.2005.03.005","article-title":"Sexual dimorphism in mammalian gene expression","volume":"21","author":"Rinn","year":"2005","journal-title":"Trends Genet."},{"key":"2021012815251837900_R30","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1007\/s00239-006-0022-1","article-title":"Nonrandom representation of sex-biased genes on chicken Z chromosome","volume":"63","author":"Storchova","year":"2006","journal-title":"J. Mol. Evol."},{"key":"2021012815251837900_R31","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/nature06330","article-title":"Demasculinization of X chromosomes in the Drosophila genus","volume":"450","author":"Sturgill","year":"2007","journal-title":"Nature"},{"key":"2021012815251837900_R32","doi-asserted-by":"crossref","first-page":"2357","DOI":"10.1093\/molbev\/msaa095","article-title":"The aphid X chromosome is a dangerous place for functionally important genes: diverse evolution of hemipteran genomes based on chromosome-level assemblies","volume":"37","author":"Li","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"2021012815251837900_R33","doi-asserted-by":"crossref","first-page":"D835","DOI":"10.1093\/nar\/gky1040","article-title":"SAGD: a comprehensive sex-associated gene database from transcriptomes","volume":"47","author":"Shi","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021012815251837900_R34","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2021012815251837900_R35","doi-asserted-by":"crossref","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase Update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mob. 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Mol. Biol."},{"key":"2021012815251837900_R40","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1093\/bioinformatics\/btp157","article-title":"Infernal 1.0: inference of RNA alignments","volume":"25","author":"Nawrocki","year":"2009","journal-title":"Bioinformatics"},{"key":"2021012815251837900_R41","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2021012815251837900_R42","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinform."},{"key":"2021012815251837900_R43","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"2021012815251837900_R44","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1093\/jhered\/esx063","article-title":"New insights into the evolution of the W chromosome in Lepidoptera","volume":"108","author":"Dalikova","year":"2017","journal-title":"J. Hered."},{"key":"2021012815251837900_R45","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s00412-006-0086-0","article-title":"Probing the W chromosome of the codling moth, Cydia pomonella, with sequences from microdissected sex chromatin","volume":"116","author":"Fukova","year":"2007","journal-title":"Chromosoma"},{"key":"2021012815251837900_R46","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1139\/g03-003","article-title":"Moth sex chromatin probed by comparative genomic hybridization (CGH)","volume":"46","author":"Sahara","year":"2003","journal-title":"Genome"},{"key":"2021012815251837900_R47","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/nrg3366","article-title":"Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration","volume":"14","author":"Bachtrog","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"2021012815251837900_R48","article-title":"Erratum: Sex-chromosome evolution: recent progress and the influence of male and female heterogamety","volume":"12","author":"Ellegren","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2021012815251837900_R49","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1093\/jhered\/esw047","article-title":"Sex determination, sex chromosomes, and karyotype evolution in insects","volume":"108","author":"Blackmon","year":"2017","journal-title":"J. Hered."},{"key":"2021012815251837900_R50","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/nature12235","article-title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","volume":"499","author":"Vicoso","year":"2013","journal-title":"Nature"},{"key":"2021012815251837900_R51","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1002078","article-title":"Numerous transitions of sex chromosomes in Diptera","volume":"13","author":"Vicoso","year":"2015","journal-title":"PLoS Biol."},{"key":"2021012815251837900_R52","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1126\/science.132.3443.1887","article-title":"An inherited male-producing factor in Aedes aegypti","volume":"132","author":"Craig","year":"1960","journal-title":"Science"},{"key":"2021012815251837900_R53","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1534\/genetics.110.118794","article-title":"Retrogenes reveal the direction of sex-chromosome evolution in mosquitoes","volume":"186","author":"Toups","year":"2010","journal-title":"Genetics"},{"key":"2021012815251837900_R54","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1649\/0010-065X-69.1.174","article-title":"Coleoptera karyotype database","volume":"69","author":"Blackmon","year":"2015","journal-title":"Coleopt. Bull."},{"key":"2021012815251837900_R55","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1093\/genetics\/119.4.829","article-title":"Evidence that sisterless-a and sisterless-b are two of several discrete \u201cnumerator elements\u201d of the X\/A sex determination signal in Drosophila that switch Sxl between two alternative stable expression states","volume":"119","author":"Cline","year":"1988","journal-title":"Genetics"},{"key":"2021012815251837900_R56","doi-asserted-by":"crossref","first-page":"2176","DOI":"10.1101\/gad.5.12a.2176","article-title":"The Drosophila segmentation gene runt acts as a position-specific numerator element necessary for the uniform expression of the sex-determining gene Sex-lethal","volume":"5","author":"Duffy","year":"1991","journal-title":"Genes Dev."},{"key":"2021012815251837900_R57","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1016\/S1097-2765(00)80451-7","article-title":"The JAK\/STAT signaling pathway is required for the initial choice of sexual identity in Drosophila melanogaster","volume":"5","author":"Jinks","year":"2000","journal-title":"Mol. 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