{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T20:30:29Z","timestamp":1793478629909,"version":"4.5.0"},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T00:00:00Z","timestamp":1782691200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T00:00:00Z","timestamp":1782691200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Biochem Genet"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1007\/s10528-026-11421-2","type":"journal-article","created":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T05:04:40Z","timestamp":1782709480000},"page":"8079-8095","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Chromosome-Level Genome Assembly of the Sea Urchin Glyptocidaris crenularis and Sex Chromosome Identification"],"prefix":"10.1007","volume":"64","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0439-6431","authenticated-orcid":false,"given":"Quanchao","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanlong","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufeng","family":"Zhai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojing","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hena","family":"Ji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rongrong","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zenglei","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,29]]},"reference":[{"issue":"1","key":"11421_CR1","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1016\/j.gene.2007.10.005","volume":"407","author":"I Boutet","year":"2008","unstructured":"Boutet I, Moraga D, Marinovic L, Obreque J, Chavez-Crooker P (2008) Characterization of reproduction-specific genes in a marine bivalve mollusc: Influence of maturation stage and sex on mRNA expression. Gene 407(1):130\u2013138. https:\/\/doi.org\/10.1016\/j.gene.2007.10.005","journal-title":"Gene"},{"issue":"1","key":"11421_CR2","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59\u201360. https:\/\/doi.org\/10.1038\/nmeth.3176","journal-title":"Nat Methods"},{"issue":"28","key":"11421_CR3","doi-asserted-by":"publisher","first-page":"18790","DOI":"10.1074\/jbc.M109.005702","volume":"284","author":"MO Castro","year":"2009","unstructured":"Castro MO, Pomin VH, Santos LL, Vilela-Silva ACES, Hirohashi N, Pol-Fachin L, Verli H, Mour\u00e3o PAS (2009) A Unique 2-Sulfated \u03b2-Galactan from the Egg Jelly of the Sea Urchin Glyptocidaris crenularis. J Biol Chem 284(28):18790\u201318800. https:\/\/doi.org\/10.1074\/jbc.M109.005702","journal-title":"J Biol Chem"},{"key":"11421_CR4","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0410s05","author":"N Chen","year":"2004","unstructured":"Chen N (2004) Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences. Curr Protoc Bioinformatics. https:\/\/doi.org\/10.1002\/0471250953.bi0410s05","journal-title":"Curr Protoc Bioinformatics"},{"issue":"17","key":"11421_CR5","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884\u2013i890. https:\/\/doi.org\/10.1093\/bioinformatics\/bty560","journal-title":"Bioinformatics"},{"key":"11421_CR6","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","author":"P Danecek","year":"2021","unstructured":"Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H (2021) Twelve years of SAMtools and BCFtools. GigaScience. https:\/\/doi.org\/10.1093\/gigascience\/giab008","journal-title":"GigaScience"},{"key":"11421_CR7","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evad093","author":"PL Davidson","year":"2023","unstructured":"Davidson PL, Lessios HA, Wray GA, McMillan WO, Prada C (2023) Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter, a Model for Speciation in the Sea. Genome Biol Evol. https:\/\/doi.org\/10.1093\/gbe\/evad093","journal-title":"Genome Biol Evol"},{"key":"11421_CR8","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/j.chemosphere.2015.01.045","volume":"128","author":"G Ding","year":"2015","unstructured":"Ding G, Wang L, Zhang J, Wei Y, Wei L, Li Y, Shao M, Xiong D (2015) Toxicity and DNA methylation changes induced by perfluorooctane sulfonate (PFOS) in sea urchin Glyptocidaris crenularis. Chemosphere 128:225\u2013230. https:\/\/doi.org\/10.1016\/j.chemosphere.2015.01.045","journal-title":"Chemosphere"},{"issue":"6333","key":"11421_CR9","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.aal3327","volume":"356","author":"O Dudchenko","year":"2017","unstructured":"Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL (2017) De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356(6333):92\u201395. https:\/\/doi.org\/10.1126\/science.aal3327","journal-title":"Science"},{"key":"11421_CR10","doi-asserted-by":"publisher","DOI":"10.1101\/254797","author":"O Dudchenko","year":"2018","unstructured":"Dudchenko O, Shamim MS, Batra SS, Durand NC, Musial NT, Mostofa R, Pham M, Glenn St Hilaire B, Yao W, Stamenova E, Hoeger M, Nyquist SK, Korchina V, Pletch K, Flanagan JP, Tomaszewicz A, McAloose D, P\u00e9rez Estrada C, Novak BJ, Omer AD, Aiden EL (2018) The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv. https:\/\/doi.org\/10.1101\/254797","journal-title":"bioRxiv"},{"issue":"1","key":"11421_CR11","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL (2016a) Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst 3(1):99\u2013101. https:\/\/doi.org\/10.1016\/j.cels.2015.07.012","journal-title":"Cell Syst"},{"issue":"1","key":"11421_CR12","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, Aiden EL (2016b) Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst 3(1):95\u201398. https:\/\/doi.org\/10.1016\/j.cels.2016.07.002","journal-title":"Cell Syst"},{"issue":"1","key":"11421_CR13","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20(1):238. https:\/\/doi.org\/10.1186\/s13059-019-1832-y","journal-title":"Genome Biol"},{"issue":"17","key":"11421_CR14","doi-asserted-by":"publisher","first-page":"9451","DOI":"10.1073\/pnas.1921046117","volume":"117","author":"JM Flynn","year":"2020","unstructured":"Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF (2020) RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A 117(17):9451\u20139457. https:\/\/doi.org\/10.1073\/pnas.1921046117","journal-title":"Proc Natl Acad Sci U S A"},{"key":"11421_CR15","unstructured":"Gabriel L, Hoff K, Bruna T, Lomsadze A, Borodovsky M, Stanke M (2023) The BRAKER3 Genome Annotation Pipeline"},{"key":"11421_CR16","doi-asserted-by":"publisher","DOI":"10.1093\/dnares\/dsae020","author":"C Gali\u00e0-Camps","year":"2024","unstructured":"Gali\u00e0-Camps C, Carreras C, Pascual M, Greve C, Schell T, Turon X, Palac\u00edn C, P\u00e9rez-Portela R, Wangensteen OS, Pegueroles C (2024) Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758). DNA Res. https:\/\/doi.org\/10.1093\/dnares\/dsae020","journal-title":"DNA Res"},{"issue":"9","key":"11421_CR17","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","volume":"36","author":"D Guan","year":"2020","unstructured":"Guan D, McCarthy SA, Wood J, Howe K, Wang Y, Durbin R (2020) Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36(9):2896\u20132898. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa025","journal-title":"Bioinformatics"},{"issue":"3","key":"11421_CR18","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1007\/s10126-022-10127-x","volume":"24","author":"WZ Guan","year":"2022","unstructured":"Guan WZ, Jiang K, Lai XL, Dong YT, Qiu GF (2022) Comprehensive Transcriptome Analysis of Gonadal and Somatic Tissues for Identification of Sex-Related Genes in the Largemouth Bass Micropterus salmoides. Mar Biotechnol 24(3):588\u2013598. https:\/\/doi.org\/10.1007\/s10126-022-10127-x","journal-title":"Mar Biotechnol"},{"key":"11421_CR19","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2021.756530","author":"Y-L Han","year":"2021","unstructured":"Han Y-L, Sun Z-H, Chang S, Wen B, Song J, Zuo R-T, Chang Y-Q (2021) Application of SNP in Genetic Sex Identification and Effect of Estradiol on Gene Expression of Sex-Related Genes in Strongylocentrotus intermedius. Front Endocrinol. https:\/\/doi.org\/10.3389\/fendo.2021.756530","journal-title":"Front Endocrinol"},{"key":"11421_CR20","doi-asserted-by":"crossref","unstructured":"Hui JH-L, Chan T-F, Chan LL, Cheung SG, Chi CC, Fang JKH, Gait\u00e1n\u2010Espitia JD, Lau SCK, Sung YH, Wong CKC, Yip KYL, Wei Y, So WL, Nong W, Chui APY, Fong THW, Yip HY (2024) Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778). GigaByte 2024","DOI":"10.46471\/gigabyte.121"},{"issue":"14","key":"11421_CR21","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059\u20133066. https:\/\/doi.org\/10.1093\/nar\/gkf436","journal-title":"Nucleic Acids Res"},{"key":"11421_CR22","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evac144","author":"RN Ketchum","year":"2022","unstructured":"Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, Reitzel AM (2022) A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes. Genome Biol Evol. https:\/\/doi.org\/10.1093\/gbe\/evac144","journal-title":"Genome Biol Evol"},{"issue":"4","key":"11421_CR23","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","volume":"12","author":"D Kim","year":"2015","unstructured":"Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357\u2013360. https:\/\/doi.org\/10.1038\/nmeth.3317","journal-title":"Nat Methods"},{"issue":"3","key":"11421_CR24","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1111\/dgd.12429","volume":"60","author":"S Kinjo","year":"2018","unstructured":"Kinjo S, Kiyomoto M, Yamamoto T, Ikeo K, Yaguchi S (2018) HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus. Dev Growth Differ 60(3):174\u2013182. https:\/\/doi.org\/10.1111\/dgd.12429","journal-title":"Dev Growth Differ"},{"issue":"5","key":"11421_CR25","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA (2019) Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37(5):540\u2013546. https:\/\/doi.org\/10.1038\/s41587-019-0072-8","journal-title":"Nat Biotechnol"},{"issue":"7","key":"11421_CR26","doi-asserted-by":"publisher","first-page":"1812","DOI":"10.1093\/molbev\/msx116","volume":"34","author":"S Kumar","year":"2017","unstructured":"Kumar S, Stecher G, Suleski M, Hedges SB (2017) TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. Mol Biol Evol 34(7):1812\u20131819. https:\/\/doi.org\/10.1093\/molbev\/msx116","journal-title":"Mol Biol Evol"},{"issue":"D1","key":"11421_CR27","doi-asserted-by":"publisher","first-page":"D445","DOI":"10.1093\/nar\/gkac998","volume":"51","author":"D Kuznetsov","year":"2022","unstructured":"Kuznetsov D, Tegenfeldt F, Manni M, Seppey M, Berkeley M, Kriventseva EV, Zdobnov EM (2022) OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res 51(D1):D445\u2013D451. https:\/\/doi.org\/10.1093\/nar\/gkac998","journal-title":"Nucleic Acids Res"},{"key":"11421_CR28","unstructured":"Kyoko S (1987). Chromosome Numbers in 8 Japanese Species of Sea Urchins : Genetics. Zoological Science"},{"issue":"4","key":"11421_CR29","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1007\/s10126-016-9706-8","volume":"18","author":"Y Li","year":"2016","unstructured":"Li Y, Zhang L, Sun Y, Ma X, Wang J, Li R, Zhang M, Wang S, Hu X, Bao Z (2016) Transcriptome sequencing and comparative analysis of ovary and testis identifies potential key sex-related genes and pathways in scallop Patinopecten yessoensis. Mar Biotechnol 18(4):453\u2013465. https:\/\/doi.org\/10.1007\/s10126-016-9706-8","journal-title":"Mar Biotechnol"},{"issue":"1","key":"11421_CR30","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1007\/s00438-025-02276-0","volume":"300","author":"Z Li","year":"2025","unstructured":"Li Z, Tang X, Liu X, Huo J, Guo Y, Yang Y (2025) Deciphering gonadal transcriptome reveals circRNA-miRNA-mRNA regulatory network involved in sex differentiation and gametogenesis of Apostichopus japonicus. Mol Genet Genomics 300(1):70. https:\/\/doi.org\/10.1007\/s00438-025-02276-0","journal-title":"Mol Genet Genomics"},{"issue":"2","key":"11421_CR31","doi-asserted-by":"publisher","first-page":"206","DOI":"10.5483\/bmbrep.2005.38.2.206","volume":"38","author":"B Liu","year":"2005","unstructured":"Liu B, Liu S, He S, Zhao Y, Hu H, Wang Z (2005) Cloning and expression analysis of gonadogenesis-associated gene SPATA4 from rainbow trout (Oncorhynchus mykiss). BMB Rep 38(2):206\u2013210. https:\/\/doi.org\/10.5483\/bmbrep.2005.38.2.206","journal-title":"BMB Rep"},{"issue":"1","key":"11421_CR32","doi-asserted-by":"publisher","first-page":"1382","DOI":"10.1038\/s41597-024-04255-3","volume":"11","author":"Y Liu","year":"2024","unstructured":"Liu Y, Chen T, Ma B, Yin J, Ren C, Jiang X, Wang Y, Pan W, Huang J, Yu S, Luo P (2024) A chromosome-level genome assembly of tropical purple sea urchin Heliocidaris crassispina. Sci Data 11(1):1382. https:\/\/doi.org\/10.1038\/s41597-024-04255-3","journal-title":"Sci Data"},{"issue":"12","key":"11421_CR33","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550. https:\/\/doi.org\/10.1186\/s13059-014-0550-8","journal-title":"Genome Biol"},{"issue":"5","key":"11421_CR34","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.955","volume":"25","author":"TM Lowe","year":"1997","unstructured":"Lowe TM, Eddy SR (1997) tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Res 25(5):955\u2013964. https:\/\/doi.org\/10.1093\/nar\/25.5.955","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"11421_CR35","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1007\/s00343-014-3106-6","volume":"32","author":"S Luo","year":"2014","unstructured":"Luo S, Tian X, Zhao C, Zhou H, Zhang W, Feng W, Chang Y (2014) Phenotypic correlations of somatic and gonad traits of sea urchins Glyptocidaris crenularis in two sampled periods: first insight into its breeding and aquaculture. Chin J Oceanol Limnol 32(2):344\u2013348. https:\/\/doi.org\/10.1007\/s00343-014-3106-6","journal-title":"Chin J Oceanol Limnol"},{"issue":"10","key":"11421_CR36","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","volume":"38","author":"M Manni","year":"2021","unstructured":"Manni M, Berkeley MR, Seppey M, Sim\u00e3o FA, Zdobnov EM (2021) BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol 38(10):4647\u20134654. https:\/\/doi.org\/10.1093\/molbev\/msab199","journal-title":"Mol Biol Evol"},{"issue":"6","key":"11421_CR37","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","volume":"27","author":"G Mar\u00e7ais","year":"2011","unstructured":"Mar\u00e7ais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764\u2013770. https:\/\/doi.org\/10.1093\/bioinformatics\/btr011","journal-title":"Bioinformatics"},{"key":"11421_CR38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cbd.2014.01.001","volume":"10","author":"X Mi","year":"2014","unstructured":"Mi X, Wei Z, Zhou Z, Liu X (2014) Identification and profiling of sex-biased microRNAs from sea urchin Strongylocentrotus nudus gonad by Solexa deep sequencing. Comp Biochem Physiol D Genomics Proteomics 10:1\u20138. https:\/\/doi.org\/10.1016\/j.cbd.2014.01.001","journal-title":"Comp Biochem Physiol D Genomics Proteomics"},{"issue":"5","key":"11421_CR39","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol 37(5):1530\u20131534. https:\/\/doi.org\/10.1093\/molbev\/msaa015","journal-title":"Mol Biol Evol"},{"issue":"1","key":"11421_CR40","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1186\/s12862-018-1300-4","volume":"18","author":"N Mongiardino Koch","year":"2018","unstructured":"Mongiardino Koch N, Coppard SE, Lessios HA, Briggs DEG, Mooi R, Rouse GW (2018) A phylogenomic resolution of the sea urchin tree of life. BMC Evol Biol 18(1):189. https:\/\/doi.org\/10.1186\/s12862-018-1300-4","journal-title":"BMC Evol Biol"},{"issue":"1","key":"11421_CR41","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s12915-021-01154-6","volume":"19","author":"MP Nallasivan","year":"2021","unstructured":"Nallasivan MP, Haussmann IU, Civetta A, Soller M (2021) Channel nuclear pore protein 54 directs sexual differentiation and neuronal wiring of female reproductive behaviors in Drosophila. BMC Biol 19(1):226. https:\/\/doi.org\/10.1186\/s12915-021-01154-6","journal-title":"BMC Biol"},{"issue":"22","key":"11421_CR42","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","volume":"29","author":"EP Nawrocki","year":"2013","unstructured":"Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29(22):2933\u20132935. https:\/\/doi.org\/10.1093\/bioinformatics\/btt509","journal-title":"Bioinformatics"},{"key":"11421_CR43","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2024.114021","author":"JM Polinski","year":"2024","unstructured":"Polinski JM, Castellano KR, Buckley KM, Bodnar AG (2024) Genomic signatures of exceptional longevity and negligible aging in the long-lived red sea urchin. Cell Rep. https:\/\/doi.org\/10.1016\/j.celrep.2024.114021","journal-title":"Cell Rep"},{"key":"11421_CR44","unstructured":"Qi L, Jie W, Yuan W (2024) Triphenyltin induced oxidative damage in sea urchin Glyptocidaris crenularis, Proc.SPIE. p 132791G"},{"key":"11421_CR45","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2025","unstructured":"R Core Team (2025) R: A Language and Environment for Statistical Computing. Austria, Vienna"},{"issue":"5801","key":"11421_CR46","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1126\/science.1133609","volume":"314","author":"E Sodergren","year":"2006","unstructured":"Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Belle\u00cc R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevie\u00ccre A-M, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron K-F, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallbo\u00cco\u00cck F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su Y-H, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc VR, Duloquin L, Flytzanis C, Gache C, Lapraz FO, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Ro\u00cc\u02c6ttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu S-Y, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu L-L, Thorn R, Wright R (2006) The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science 314(5801):941\u2013952. https:\/\/doi.org\/10.1126\/science.1133609","journal-title":"Science"},{"issue":"2","key":"11421_CR47","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1080\/07924259.2017.1287780","volume":"61","author":"S Song","year":"2017","unstructured":"Song S, Yu H, Li Q (2017) Genome survey and characterization of reproduction-related genes in the Pacific oyster. Invertebr Reprod Dev 61(2):97\u2013109. https:\/\/doi.org\/10.1080\/07924259.2017.1287780","journal-title":"Invertebr Reprod Dev"},{"key":"11421_CR48","doi-asserted-by":"publisher","first-page":"102137","DOI":"10.1016\/j.aqrep.2024.102137","volume":"36","author":"WY Su","year":"2024","unstructured":"Su WY, Meng WH, Kong LN, Chang S, Zhang J, Chang YQ, Sun ZH (2024) Characterization and sexual dimorphic expression of cytochrome P450 genes in gonads of the sea urchin (Mesocentrotus nudus). Aquacult Rep 36:102137. https:\/\/doi.org\/10.1016\/j.aqrep.2024.102137","journal-title":"Aquacult Rep"},{"issue":"4","key":"11421_CR49","doi-asserted-by":"publisher","first-page":"e211","DOI":"10.1002\/imt2.211","volume":"3","author":"H Tang","year":"2024","unstructured":"Tang H, Krishnakumar V, Zeng X, Xu Z, Taranto A, Lomas JS, Zhang Y, Huang Y, Wang Y, Yim WC, Zhang J, Zhang X (2024) JCVI: a versatile toolkit for comparative genomics analysis. iMeta 3(4):e211. https:\/\/doi.org\/10.1002\/imt2.211","journal-title":"iMeta"},{"issue":"2","key":"11421_CR50","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1111\/1755-0998.13273","volume":"21","author":"W Tao","year":"2021","unstructured":"Tao W, Xu L, Zhao L, Zhu Z, Wu X, Min Q, Wang D, Zhou Q (2021) High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes. Mol Ecol Resour 21(2):543\u2013560. https:\/\/doi.org\/10.1111\/1755-0998.13273","journal-title":"Mol Ecol Resour"},{"issue":"40","key":"11421_CR51","first-page":"613","volume":"23","author":"T Uehara","year":"1991","unstructured":"Uehara T, Shingaki M, Taira K, Arakaki Y, Nakatomi H (1991) Chromosome studies in eleven Okinawan species of sea urchins, with special reference to four species of the Indo-Pacific Echinometra. ChemInform 23(40):613\u2013620","journal-title":"ChemInform"},{"issue":"14","key":"11421_CR52","doi-asserted-by":"publisher","first-page":"2202","DOI":"10.1093\/bioinformatics\/btx153","volume":"33","author":"GW Vurture","year":"2017","unstructured":"Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC (2017) GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33(14):2202\u20132204. https:\/\/doi.org\/10.1093\/bioinformatics\/btx153","journal-title":"Bioinformatics"},{"issue":"11","key":"11421_CR53","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM (2014) Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9(11):e112963. https:\/\/doi.org\/10.1371\/journal.pone.0112963","journal-title":"PLoS ONE"},{"issue":"4","key":"11421_CR54","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1007\/s10126-025-10499-w","volume":"27","author":"Q Wang","year":"2025","unstructured":"Wang Q, Wang Y, Dong Z, Wang Y, Li X (2025) Chromosome-level Assembly of the Genome of Mesocentrotus nudus Reveals a Sex-Linked Region on Chromosome 7. Mar Biotechnol 27(4):117. https:\/\/doi.org\/10.1007\/s10126-025-10499-w","journal-title":"Mar Biotechnol"},{"key":"11421_CR55","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evab061","author":"JF Warner","year":"2021","unstructured":"Warner JF, Lord JW, Schreiter SA, Nesbit KT, Hamdoun A, Lyons DC (2021) Chromosomal-level genome assembly of the painted sea urchin Lytechinus pictus: a genetically enabled model system for cell biology and embryonic development. Genome Biol Evol. https:\/\/doi.org\/10.1093\/gbe\/evab061","journal-title":"Genome Biol Evol"},{"key":"11421_CR56","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evae237","author":"JF Warner","year":"2024","unstructured":"Warner JF, Range RC, Fenner J, Ka C, Waits DS, Boddy K, David KT, Mahon AR, Halanych KM (2024) Chromosomal-level genome assembly of the Antarctic sea urchin Sterechinus neumayeri: a model for Antarctic invertebrate biology. Genome Biol Evol. https:\/\/doi.org\/10.1093\/gbe\/evae237","journal-title":"Genome Biol Evol"},{"issue":"8","key":"11421_CR57","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang Z (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol 24(8):1586\u20131591. https:\/\/doi.org\/10.1093\/molbev\/msm088","journal-title":"Mol Biol Evol"},{"key":"11421_CR58","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.31.465852","author":"Y Zhang","year":"2021","unstructured":"Zhang Y, Wang J, Lv M, Gao H, Meng L, Yunga A, Seim I, Zhang H, Liu S, Zhang L, Liu X, Xu X, Yang H, Consortium MK, Fan G (2021) Diversity, function and evolution of marine invertebrate genomes. bioRxiv. https:\/\/doi.org\/10.1101\/2021.10.31.465852","journal-title":"bioRxiv"},{"issue":"1","key":"11421_CR59","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1038\/s41597-024-03733-y","volume":"11","author":"J Zhang","year":"2024","unstructured":"Zhang J, Guo Y, Su J, Yu G, Ma Z, Qin C (2024) The first high-quality genome assembly and annotation of Anthocidaris crassispina. Sci Data 11(1):866. https:\/\/doi.org\/10.1038\/s41597-024-03733-y","journal-title":"Sci Data"}],"container-title":["Biochemical Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10528-026-11421-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10528-026-11421-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10528-026-11421-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T20:02:50Z","timestamp":1793476970000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10528-026-11421-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,29]]},"references-count":59,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["11421"],"URL":"https:\/\/doi.org\/10.1007\/s10528-026-11421-2","relation":{},"ISSN":["0006-2928","1573-4927"],"issn-type":[{"value":"0006-2928","type":"print"},{"value":"1573-4927","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,29]]},"assertion":[{"value":"12 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}}]}}