{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T22:44:56Z","timestamp":1784933096944,"version":"3.55.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,12,28]],"date-time":"2019-12-28T00:00:00Z","timestamp":1577491200000},"content-version":"vor","delay-in-days":27,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31702334"],"award-info":[{"award-number":["31702334"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31730098"],"award-info":[{"award-number":["31730098"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31430088"],"award-info":[{"award-number":["31430088"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Research and Development Program of Hunan Province","award":["2018NK2072"],"award-info":[{"award-number":["2018NK2072"]}]},{"DOI":"10.13039\/501100010038","name":"Earmarked Fund for China Agriculture Research System","doi-asserted-by":"publisher","award":["CARS-45"],"award-info":[{"award-number":["CARS-45"]}],"id":[{"id":"10.13039\/501100010038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Research and Development Project of Hunan Province","award":["2016NK2128"],"award-info":[{"award-number":["2016NK2128"]}]},{"name":"Key Research and Development Program of Hunan Province","award":["2018NK2072"],"award-info":[{"award-number":["2018NK2072"]}]},{"name":"Hunan Provincial Natural Science and Technology Major Project","award":["2017NK1031"],"award-info":[{"award-number":["2017NK1031"]}]},{"name":"Cooperative Innovation Center of Engineering"},{"name":"New Products for Developmental Biology of Hunan Province","award":["20134486"],"award-info":[{"award-number":["20134486"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Hybridization and polyploidy are pervasive evolutionary features of flowering plants and frequent among some animal groups, such as fish. These processes always lead to novel genotypes and various phenotypes, including growth heterosis. However, its genetic basis in lower vertebrate is still poorly understood. Here, we conducted transcriptome-level analyses of the allopolyploid complex of Carassius auratus red var. (R) (\u2640) \u00d7 Cyprinus carpio L. (C) (\u2642), including the allodiploid and allotetraploid with symmetric subgenomes, and the two allotriploids with asymmetric subgenomes. The gradual changes of gene silencing and novel gene expression suggested the weakening of the constraint of polymorphic expression in genotypic changes. Then, analyses of the direction and magnitude of homoeolog expression exhibited various asymmetric expression patterns, which supported that R incomplete dominance and dosage compensation were co-regulated in the two triploids. Under these effects, various magnitudes of R-homoeolog expression bias were observed in growth-regulated genes, suggesting that they might contribute to growth heterosis in the two triploids. The determination of R incomplete dominance and dosage compensation, which might be led by asymmetric subgenomes and multiple sets of homologous chromosomes, explained why various expression patterns were shaped and their potential contribution to growth heterosis in the two triploids.<\/jats:p>","DOI":"10.1093\/dnares\/dsz026","type":"journal-article","created":{"date-parts":[[2019,12,24]],"date-time":"2019-12-24T12:09:34Z","timestamp":1577189374000},"page":"485-494","source":"Crossref","is-referenced-by-count":16,"title":["Combined effects of dosage compensation and incomplete dominance on gene expression in triploid cyprinids"],"prefix":"10.1093","volume":"26","author":[{"given":"Li","family":"Ren","sequence":"first","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojing","family":"Yan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liu","family":"Cao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaming","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueyin","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jialin","family":"Cui","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaojun","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China"},{"name":"College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,12,27]]},"reference":[{"key":"2020012903570467000_dsz026-B1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/ng1705","article-title":"Dosage compensation of the active X chromosome in mammals","volume":"38","author":"Nguyen","year":"2006","journal-title":"Nat. Genet"},{"key":"2020012903570467000_dsz026-B2","doi-asserted-by":"crossref","first-page":"15020","DOI":"10.1038\/nplants.2015.20","article-title":"Heterosis: the genetic basis of hybrid vigour","volume":"1","author":"Birchler","year":"2015","journal-title":"Nat. Plants"},{"key":"2020012903570467000_dsz026-B3","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1007\/s00425-008-0765-6","article-title":"Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog","volume":"228","author":"Degenhardt","year":"2008","journal-title":"Planta"},{"key":"2020012903570467000_dsz026-B4","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1016\/j.cub.2008.07.096","article-title":"Dosage compensation by gene-copy silencing in a triploid hybrid fish","volume":"18","author":"Pala","year":"2008","journal-title":"Curr. Biol"},{"key":"2020012903570467000_dsz026-B5","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s12864-016-3424-5","article-title":"Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish","volume":"18","author":"Ren","year":"2017","journal-title":"BMC Genomics"},{"key":"2020012903570467000_dsz026-B6","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1146\/annurev.genet.39.073003.094210","article-title":"Chromatin remodeling in dosage compensation","volume":"39","author":"Lucchesi","year":"2005","journal-title":"Annu. Rev. Genet"},{"key":"2020012903570467000_dsz026-B7","first-page":"1","author":"Man-Sai","year":"2016"},{"key":"2020012903570467000_dsz026-B8","doi-asserted-by":"crossref","first-page":"6258","DOI":"10.1038\/ncomms7258","article-title":"Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis","volume":"6","author":"Huang","year":"2015","journal-title":"Nat. Commun"},{"key":"2020012903570467000_dsz026-B9","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1073\/pnas.1221966110","article-title":"Genomic dosage effects on heterosis in triploid maize","volume":"110","author":"Yao","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2020012903570467000_dsz026-B10","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1080\/10020070612330152","article-title":"A new type of triploid crucian crap-red crucian carp (female) \u00d7 allotetraploid (male)","volume":"16","author":"Shen","year":"2006","journal-title":"Prog. Nat. Sci"},{"key":"2020012903570467000_dsz026-B11","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1073\/pnas.1512955113","article-title":"Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish \u00d7 common carp cross","volume":"113","author":"Liu","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2020012903570467000_dsz026-B12","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1007\/s11427-009-0079-3","article-title":"Biological characteristics of an improved triploid crucian carp","volume":"52","author":"Chen","year":"2009","journal-title":"Sci. China C Life Sci"},{"key":"2020012903570467000_dsz026-B13","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.ygcen.2012.06.006","article-title":"Elevated expressions of GH\/IGF axis genes in triploid crucian carp","volume":"178","author":"Zhong","year":"2012","journal-title":"Gen. Comp. Endocrinol"},{"key":"2020012903570467000_dsz026-B14","doi-asserted-by":"crossref","first-page":"13679","DOI":"10.1038\/s41598-017-14084-7","article-title":"Analyzing homoeolog expression provides insights into the rediploidization event in gynogenetic hybrids of Carassius auratus red var. \u00d7 Cyprinus carpio","volume":"7","author":"Ren","year":"2017","journal-title":"Sci. Rep"},{"key":"2020012903570467000_dsz026-B15","doi-asserted-by":"crossref","first-page":"27040","DOI":"10.1038\/srep27040","article-title":"Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae","volume":"6","author":"Ren","year":"2016","journal-title":"Sci. Rep"},{"key":"2020012903570467000_dsz026-B16","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.1371\/journal.pgen.0030021","article-title":"A screen for recessive speciation genes expressed in the gametes of F1 hybrid yeast","volume":"3","author":"Greig","year":"2007","journal-title":"PLoS Genet"},{"key":"2020012903570467000_dsz026-B17","doi-asserted-by":"crossref","first-page":"e1007019","DOI":"10.1371\/journal.pgen.1007019","article-title":"Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize","volume":"13","author":"Yang","year":"2017","journal-title":"PLoS Genet"},{"key":"2020012903570467000_dsz026-B18","doi-asserted-by":"crossref","first-page":"R1089","DOI":"10.1016\/j.cub.2018.06.041","article-title":"Heterosis in plants","volume":"28","author":"Hochholdinger","year":"2018","journal-title":"Curr. Biol"},{"key":"2020012903570467000_dsz026-B19","doi-asserted-by":"crossref","first-page":"1878","DOI":"10.1105\/tpc.114.124388","article-title":"mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat","volume":"26","author":"Li","year":"2014","journal-title":"Plant Cell"},{"key":"2020012903570467000_dsz026-B20","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.anireprosci.2014.09.012","article-title":"The fertility of the hybrid lineage derived from female Megalobrama amblycephala \u00d7 male Culter alburnus","volume":"151","author":"Xiao","year":"2014","journal-title":"Anim. Reprod. Sci"},{"key":"2020012903570467000_dsz026-B21","first-page":"871","article-title":"FastQC: a quality control tool for high throughput sequence data","volume":"35","author":"Andrews","year":"2010","journal-title":"Bioinformatics"},{"key":"2020012903570467000_dsz026-B22","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":"2020012903570467000_dsz026-B23","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1038\/ng.3098","article-title":"Genome sequence and genetic diversity of the common carp, Cyprinus carpio","volume":"46","author":"Xu","year":"2014","journal-title":"Nat. Genet"},{"key":"2020012903570467000_dsz026-B24","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2020012903570467000_dsz026-B25","author":"Harris","year":"2007"},{"key":"2020012903570467000_dsz026-B26","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2020012903570467000_dsz026-B27","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1093\/molbev\/mst114","article-title":"Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast","volume":"30","author":"Schaefke","year":"2013","journal-title":"Mol. Biol. Evol"},{"key":"2020012903570467000_dsz026-B28","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1101\/gr.102491.109","article-title":"Regulatory divergence in Drosophila revealed by mRNA-seq","volume":"20","author":"McManus","year":"2010","journal-title":"Genome Res"},{"key":"2020012903570467000_dsz026-B29","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/ng1032","article-title":"Microarray data normalization and transformation","volume":"32","author":"Quackenbush","year":"2002","journal-title":"Nat. Genet"},{"key":"2020012903570467000_dsz026-B30","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/S0044-8486(00)00451-8","article-title":"The formation of tetraploid stocks of red crucian carp \u00d7 common carp hybrids as an effect of interspecific hybridization","volume":"192","author":"Liu","year":"2001","journal-title":"Aquaculture"},{"key":"2020012903570467000_dsz026-B31","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1007\/s11427-010-0057-9","article-title":"Distant hybridization leads to different ploidy fishes","volume":"53","author":"Liu","year":"2010","journal-title":"Sci. China Life Sci"},{"key":"2020012903570467000_dsz026-B32","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1534\/genetics.107.071373","article-title":"The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance","volume":"176","author":"Liu","year":"2007","journal-title":"Genetics"},{"key":"2020012903570467000_dsz026-B33","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.pbi.2013.03.009","article-title":"Heterosis in elite hybrid rice: speculation on the genetic and biochemical mechanisms","volume":"16","author":"Goff","year":"2013","journal-title":"Curr. Opin. Plant Biol"},{"key":"2020012903570467000_dsz026-B34","doi-asserted-by":"crossref","first-page":"534","DOI":"10.3389\/fpls.2019.00534","article-title":"Fine-tuning the expression of duplicate genes by translational regulation in arabidopsis and maize","volume":"10","author":"Wang","year":"2019","journal-title":"Front. Plant Sci"},{"key":"2020012903570467000_dsz026-B35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1749-6632.2011.06384.x","article-title":"Genome and gene duplications and gene expression divergence: a view from plants","volume":"1256","author":"Wang","year":"2012","journal-title":"Ann. N. Y. Acad. Sci"},{"key":"2020012903570467000_dsz026-B36","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.pbi.2012.01.007","article-title":"Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility","volume":"15","author":"Ng","year":"2012","journal-title":"Curr. Opin. Plant Biol"},{"key":"2020012903570467000_dsz026-B37","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1093\/genetics\/31.2.195","article-title":"Mosaic dominance in the inheritance of color patterns in the lady-bird beetle, Harmonia axyridis","volume":"31","author":"Tan","year":"1946","journal-title":"Genetics"},{"key":"2020012903570467000_dsz026-B38","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.1105\/tpc.110.076133","article-title":"Heterosis","volume":"22","author":"Birchler","year":"2010","journal-title":"Plant Cell"},{"key":"2020012903570467000_dsz026-B39","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.tig.2006.12.006","article-title":"Heterosis: revisiting the magic","volume":"23","author":"Lippman","year":"2007","journal-title":"Trends Genet"},{"key":"2020012903570467000_dsz026-B40","doi-asserted-by":"crossref","first-page":"21124","DOI":"10.1038\/srep21124","article-title":"Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster","volume":"6","author":"Wu","year":"2016","journal-title":"Sci. Rep"},{"key":"2020012903570467000_dsz026-B41","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.aquaculture.2015.09.004","article-title":"Salmonid heterosis for resistance to amoebic gill disease (AGD)","volume":"451","author":"Maynard","year":"2016","journal-title":"Aquaculture"}],"container-title":["DNA Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/dnaresearch\/advance-article-pdf\/doi\/10.1093\/dnares\/dsz026\/31904922\/dsz026.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/dnaresearch\/article-pdf\/26\/6\/485\/32217932\/dsz026.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/dnaresearch\/article-pdf\/26\/6\/485\/32217932\/dsz026.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,9]],"date-time":"2022-10-09T09:17:01Z","timestamp":1665307021000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/dnaresearch\/article\/26\/6\/485\/5688746"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12,1]]},"references-count":41,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2019,12,27]]},"published-print":{"date-parts":[[2019,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/dnares\/dsz026","relation":{},"ISSN":["1340-2838","1756-1663"],"issn-type":[{"value":"1340-2838","type":"print"},{"value":"1756-1663","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,12]]},"published":{"date-parts":[[2019,12,1]]}}}