{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T19:47:24Z","timestamp":1785872844053,"version":"3.56.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T00:00:00Z","timestamp":1715644800000},"content-version":"vor","delay-in-days":546,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,11,15]],"date-time":"2022-11-15T00:00:00Z","timestamp":1668470400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,11,8]],"date-time":"2022-11-08T00:00:00Z","timestamp":1667865600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2018YFC1706601"],"award-info":[{"award-number":["2018YFC1706601"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province of China","doi-asserted-by":"crossref","award":["C2017012"],"award-info":[{"award-number":["C2017012"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"publisher","award":["C2017012"],"award-info":[{"award-number":["C2017012"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFC1706601"],"award-info":[{"award-number":["2018YFC1706601"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2023,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.<\/jats:p>","DOI":"10.1016\/j.gpb.2022.11.001","type":"journal-article","created":{"date-parts":[[2022,11,15]],"date-time":"2022-11-15T01:55:36Z","timestamp":1668477336000},"page":"470-482","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":14,"title":["Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution"],"prefix":"10.1093","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4115-7533","authenticated-orcid":false,"given":"Ruobing","family":"Han","sequence":"first","affiliation":[{"name":"College of Wildlife and Protected Area, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6487-7520","authenticated-orcid":false,"given":"Lei","family":"Han","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7499-8817","authenticated-orcid":false,"given":"Xunwu","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7959-0482","authenticated-orcid":false,"given":"Qianghui","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5407-9047","authenticated-orcid":false,"given":"Yanling","family":"Xia","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8284-0449","authenticated-orcid":false,"given":"Heping","family":"Li","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,15]]},"reference":[{"key":"2024051404172853900_b0005","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4613-8966-8","article-title":"Horns, pronghorns, and antlers","author":"Bubenik","year":"1990"},{"key":"2024051404172853900_b0010","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.biocel.2014.07.007","article-title":"Deer antler - a novel model for studying organ regeneration in mammals","volume":"56","author":"Li","year":"2014","journal-title":"Int J Biochem Cell Biol"},{"key":"2024051404172853900_b0015","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1105\/tpc.022087","article-title":"Allelic variation of gene expression in maize hybrids","volume":"16","author":"Guo","year":"2004","journal-title":"Plant Cell"},{"key":"2024051404172853900_b0020","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/ng992","article-title":"Detection of regulatory variation in mouse genes","volume":"32","author":"Cowles","year":"2002","journal-title":"Nat Genet"},{"key":"2024051404172853900_b0025","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1126\/science.1072545","article-title":"Allelic variation in human gene expression","volume":"297","author":"Yan","year":"2002","journal-title":"Science"},{"key":"2024051404172853900_b0030","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/s41586-021-03535-x","article-title":"Evolutionary and biomedical insights from a marmoset diploid genome assembly","volume":"594","author":"Yang","year":"2021","journal-title":"Nature"},{"key":"2024051404172853900_b0035","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/s41587-020-0711-0","article-title":"Chromosome-scale, haplotype-resolved assembly of human genomes","volume":"39","author":"Garg","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2024051404172853900_b0040","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1023\/A:1018466107822","article-title":"A reappraisal of the tandem fusion theory of karyotype evolution in the Indian muntjac using chromosome painting","volume":"5","author":"Yang","year":"1997","journal-title":"Chromosome Res"},{"key":"2024051404172853900_b0045","doi-asserted-by":"crossref","first-page":"6858","DOI":"10.1038\/s41467-021-27091-0","article-title":"Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer","volume":"12","author":"Yin","year":"2021","journal-title":"Nat Commun"},{"key":"2024051404172853900_b0050","first-page":"65","article-title":"Advances on the chromosome of cervid in China","volume":"39","author":"Yu","year":"2012","journal-title":"China Animal Husbandary Veterinary Med"},{"key":"2024051404172853900_b0055","first-page":"61","article-title":"Research progress in Cervidae\u2019s chromosome","volume":"42","author":"Tang","year":"2020","journal-title":"Special Wild Econ Animal Plant Res"},{"key":"2024051404172853900_b0060","doi-asserted-by":"crossref","first-page":"237","DOI":"10.2174\/157488809789057446","article-title":"Adult stem cells and mammalian epimorphic regeneration - insights from studying annual renewal of deer antlers","volume":"4","author":"Li","year":"2009","journal-title":"Curr Stem Cell Res Ther"},{"key":"2024051404172853900_b0065","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/s41597-020-0537-0","article-title":"Chromosome-level genome assembly of Tarim red deer, Cervus elaphus yarkandensis","volume":"7","author":"Ba","year":"2020","journal-title":"Sci Data"},{"key":"2024051404172853900_b0070","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1071\/AN10195","article-title":"Relationships between rank-related behaviour, antler cycle timing and antler growth in deer: behavioural aspects","volume":"51","author":"Barto\u0161","year":"2011","journal-title":"Anim Prod Sci"},{"key":"2024051404172853900_b0075","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1038\/s41588-020-00723-9","article-title":"Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication","volume":"52","author":"Sun","year":"2020","journal-title":"Nat Genet"},{"key":"2024051404172853900_b0080","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","author":"Cheng","year":"2021","journal-title":"Nat Methods"},{"key":"2024051404172853900_b0085","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.gpb.2022.05.008","article-title":"The first high-quality reference genome of sika deer provides insights for high-tannin adaptation","volume":"21","author":"Xing","year":"2023","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024051404172853900_b0090","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1038\/nbt.4318","article-title":"A reference standard for genome biology","volume":"36","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024051404172853900_b0095","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1186\/s12864-019-5785-z","article-title":"Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus","volume":"20","author":"Hu","year":"2019","journal-title":"BMC Genomics"},{"key":"2024051404172853900_b0100","first-page":"168","article-title":"On the geological distribution, taxonomic status of species and evolutionary history of sika deer in China","volume":"20","author":"Guo","year":"2000","journal-title":"Acta Theriol Sinica"},{"key":"2024051404172853900_b0105","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/j.jep.2012.12.008","article-title":"Deer antler base as a traditional Chinese medicine: a review of its traditional uses, chemistry and pharmacology","volume":"145","author":"Wu","year":"2013","journal-title":"J Ethnopharmacol"},{"key":"2024051404172853900_b0110","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1021\/acs.jproteome.1c00003","article-title":"Bioactive molecular discovery using deer antlers as a model of mammalian regeneration","volume":"20","author":"Dong","year":"2021","journal-title":"J Proteome Res"},{"key":"2024051404172853900_b0115","doi-asserted-by":"crossref","first-page":"eaav6335","DOI":"10.1126\/science.aav6335","article-title":"Genetic basis of ruminant headgear and rapid antler regeneration","volume":"364","author":"Wang","year":"2019","journal-title":"Science"},{"key":"2024051404172853900_b0120","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1271\/bbb.110774","article-title":"Relationship between ATM and ribosomal protein S6 revealed by the chemical inhibition of Ser\/Thr protein phosphatase type 1","volume":"76","author":"Li","year":"2012","journal-title":"Biosci Biotechnol Biochem"},{"key":"2024051404172853900_b0125","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.canlet.2014.08.045","article-title":"Downregulation of ribosomal protein S6 inhibits the growth of non-small cell lung cancer by inducing cell cycle arrest, rather than apoptosis","volume":"354","author":"Chen","year":"2014","journal-title":"Cancer Lett"},{"key":"2024051404172853900_b0130","doi-asserted-by":"crossref","first-page":"3755","DOI":"10.1021\/acs.jmedchem.7b00574","article-title":"Modulators of 14-3-3 protein\u2013protein interactions","volume":"61","author":"Stevers","year":"2018","journal-title":"J Med Chem"},{"key":"2024051404172853900_b0135","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.semcancer.2006.03.005","article-title":"14-3-3 proteins: a historic overview","volume":"16","author":"Aitken","year":"2006","journal-title":"Semin Cancer Biol"},{"key":"2024051404172853900_b0140","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.cell.2007.06.034","article-title":"PP2A: unveiling a reluctant tumor suppressor","volume":"130","author":"Mumby","year":"2007","journal-title":"Cell"},{"key":"2024051404172853900_b0145","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.mrfmmm.2011.08.004","article-title":"Identification and functional analyses of polymorphism haplotypes of protein phosphatase 2A-A\u03b1 gene promoter","volume":"716","author":"Lin","year":"2011","journal-title":"Mutat Res"},{"key":"2024051404172853900_b0150","first-page":"113","article-title":"PPP2R1A mutation is a rare event in ovarian carcinoma across histological subtypes","volume":"33","author":"Rahman","year":"2013","journal-title":"Anticancer Res"},{"key":"2024051404172853900_b0155","article-title":"Mutational analysis of the ppp2r1a and ppp2r1b genes in Chinese patients with ovarian cancer. A Master thesis","author":"Li","year":"2014","journal-title":"Nanchang University"},{"key":"2024051404172853900_b0160","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1210\/er.2006-0017","article-title":"RET as a diagnostic and therapeutic target in sporadic and hereditary endocrine tumors","volume":"27","author":"De Groot","year":"2006","journal-title":"Endocr Rev"},{"key":"2024051404172853900_b0165","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.mce.2010.01.012","article-title":"Molecular genetics and phenomics of RET mutations: impact on prognosis of MTC","volume":"322","author":"Frank-Raue","year":"2010","journal-title":"Mol Cell Endocrinol"},{"key":"2024051404172853900_b0170","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1016\/S0168-9525(01)02420-9","article-title":"The RET receptor: function in development and dysfunction in congenital malformation","volume":"17","author":"Mani\u00e9","year":"2001","journal-title":"Trends Genet"},{"key":"2024051404172853900_b0175","doi-asserted-by":"crossref","first-page":"giac028","DOI":"10.1093\/gigascience\/giac028","article-title":"The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features","volume":"11","author":"Qi","year":"2022","journal-title":"Gigascience"},{"key":"2024051404172853900_b0180","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.3389\/fgene.2019.01403","article-title":"Whole transcriptome analysis of mesenchyme tissue in sika deer antler revealed the ceRNAs regulatory network associated with antler development","volume":"10","author":"Han","year":"2020","journal-title":"Front Genet"},{"key":"2024051404172853900_b0185","doi-asserted-by":"crossref","first-page":"148","DOI":"10.3389\/fgene.2017.00148","article-title":"The necessity of diploid genome sequencing to unravel the genetic component of complex phenotypes","volume":"8","author":"Fernando","year":"2017","journal-title":"Front Genet"},{"key":"2024051404172853900_b0190","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1038\/s41467-020-15848-y","article-title":"Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle","volume":"11","author":"Low","year":"2020","journal-title":"Nat Commun"},{"key":"2024051404172853900_b0195","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/s41438-021-00599-8","article-title":"Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger","volume":"8","author":"Cheng","year":"2021","journal-title":"Hortic Res"},{"key":"2024051404172853900_b0200","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/s13258-019-00911-w","article-title":"Molecular evidence for adaptive evolution of olfactory-related genes in cervids","volume":"42","author":"Ba","year":"2020","journal-title":"Genes Genomics"},{"key":"2024051404172853900_b0205","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1038\/s41598-020-79779-w","article-title":"Anti-tumour activity of deer growing antlers and its potential applications in the treatment of malignant gliomas","volume":"11","author":"Chonco","year":"2021","journal-title":"Sci Rep"},{"key":"2024051404172853900_b0210","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/s10735-019-09853-9","article-title":"Identification of interactive molecules between antler stem cells and dermal papilla cells using an in vitro co-culture system","volume":"51","author":"Sun","year":"2020","journal-title":"J Mol Histol"},{"key":"2024051404172853900_b0215","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/j.ijbiomac.2019.08.164","article-title":"Sika deer antler protein against acetaminophen-induced nephrotoxicity by activating Nrf2 and inhibition FoxO1 via PI3K\/Akt signaling","volume":"141","author":"Ruan","year":"2019","journal-title":"Int J Biol Macromol"},{"key":"2024051404172853900_b0220","doi-asserted-by":"crossref","first-page":"1778","DOI":"10.3390\/ijms17111778","article-title":"iTRAQ-based quantitative proteomic analysis of the potentiated and dormant antler stem cells","volume":"17","author":"Dong","year":"2016","journal-title":"Int J Mol Sci"},{"key":"2024051404172853900_b0225","doi-asserted-by":"crossref","first-page":"e7299","DOI":"10.7717\/peerj.7299","article-title":"Comparative proteomics analysis reveals the difference during antler regeneration stage between red deer and sika deer","volume":"7","author":"Su","year":"2019","journal-title":"PeerJ"},{"key":"2024051404172853900_b0230","doi-asserted-by":"crossref","first-page":"eaav6312","DOI":"10.1126\/science.aav6312","article-title":"Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus)","volume":"364","author":"Lin","year":"2019","journal-title":"Science"},{"key":"2024051404172853900_b0235","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"key":"2024051404172853900_b0240","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"key":"2024051404172853900_b0245","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A universal SNP and small-indel variant caller using deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024051404172853900_b0250","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1101\/gr.213462.116","article-title":"HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies","volume":"27","author":"Edge","year":"2017","journal-title":"Genome Res"},{"key":"2024051404172853900_b0255","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1089\/cmb.2014.0157","article-title":"WhatsHap: weighted haplotype assembly for future-generation sequencing reads","volume":"22","author":"Patterson","year":"2015","journal-title":"J Comput Biol"},{"key":"2024051404172853900_b0260","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2024051404172853900_b0265","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies","volume":"36","author":"Guan","year":"2020","journal-title":"Bioinformatics"},{"key":"2024051404172853900_b0270","doi-asserted-by":"crossref","first-page":"W309","DOI":"10.1093\/nar\/gkh379","article-title":"AUGUSTUS: a web server for gene finding in eukaryotes","volume":"32","author":"Stanke","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2024051404172853900_b0275","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2105-5-59","article-title":"Gene finding in novel genomes","volume":"5","author":"Korf","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2024051404172853900_b0280","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"},{"key":"2024051404172853900_b0285","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"},{"key":"2024051404172853900_b0290","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024051404172853900_b0295","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/978-1-61779-603-6_2","article-title":"Using and understanding RepeatMasker","volume":"859","author":"Tempel","year":"2012","journal-title":"Methods Mol Biol"},{"key":"2024051404172853900_b0300","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkj118","article-title":"TreeFam: a curated database of phylogenetic trees of animal gene families","volume":"34","author":"Li","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2024051404172853900_b0305","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1093\/bioinformatics\/btl097","article-title":"CAFE: a computational tool for the study of gene family evolution","volume":"22","author":"Bie","year":"2006","journal-title":"Bioinformatics"},{"key":"2024051404172853900_b0310","doi-asserted-by":"crossref","first-page":"2723","DOI":"10.1093\/molbev\/mst179","article-title":"PAMLX: a graphical user interface for PAML","volume":"30","author":"Xu","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2024051404172853900_b0315","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/nature10231","article-title":"Inference of human population history from individual whole-genome sequences","volume":"475","author":"Li","year":"2011","journal-title":"Nature"},{"key":"2024051404172853900_b0320","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"2024051404172853900_b0325","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1002\/em.21943","article-title":"Structural variation mutagenesis of the human genome: impact on disease and evolution","volume":"56","author":"Lupski","year":"2015","journal-title":"Environ Mol Mutagen"},{"key":"2024051404172853900_b0330","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.tig.2016.07.002","article-title":"Sequencing structural variants in cancer for precision therapeutics","volume":"32","author":"Macintyre","year":"2016","journal-title":"Trends Genet"},{"key":"2024051404172853900_b0335","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1101\/gr.142646.112","article-title":"Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing","volume":"23","author":"Zichner","year":"2013","journal-title":"Genome Res"},{"key":"2024051404172853900_b0340","doi-asserted-by":"crossref","first-page":"4712","DOI":"10.1111\/mec.14134","article-title":"Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin","volume":"26","author":"Dennenmoser","year":"2017","journal-title":"Mol Ecol"},{"key":"2024051404172853900_b0345","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2504 human genomes","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"},{"key":"2024051404172853900_b0350","doi-asserted-by":"crossref","first-page":"14061","DOI":"10.1038\/ncomms14061","article-title":"Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast","volume":"8","author":"Jeffares","year":"2017","journal-title":"Nat Commun"},{"key":"2024051404172853900_b0355","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Yupeng","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2024051404172853900_b0360","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/s41592-018-0001-7","article-title":"Accurate detection of complex structural variations using single-molecule sequencing","volume":"15","author":"Sedlazeck","year":"2018","journal-title":"Nat Methods"},{"key":"2024051404172853900_b0365","doi-asserted-by":"crossref","first-page":"550","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":"2024051404172853900_b0370","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1093\/bioinformatics\/btw369","article-title":"Assemblytics: a web analytics tool for the detection of variants from an assembly","volume":"32","author":"Nattestad","year":"2016","journal-title":"Bioinformatics"},{"key":"2024051404172853900_b0375","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The Genome Sequence Archive Family: toward explosive data growth and diverse data types","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024051404172853900_b0380","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/j.gpb.2021.04.001","article-title":"Genome Warehouse: a public repository housing genome-scale data","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022922001413?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022922001413?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/21\/3\/470\/57590275\/gpb_21_3_470.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/21\/3\/470\/57590275\/gpb_21_3_470.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T05:42:21Z","timestamp":1715665341000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/21\/3\/470\/7588913"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,15]]},"references-count":76,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,6,1]]}},"URL":"https:\/\/doi.org\/10.1016\/j.gpb.2022.11.001","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,6]]},"published":{"date-parts":[[2022,11,15]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution","name":"articletitle","label":"Article Title"},{"value":"Genomics, Proteomics & Bioinformatics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.gpb.2022.11.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Authors. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences \/ China National Center for Bioinformation and Genetics Society of China.","name":"copyright","label":"Copyright"}]}}