{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["White B"],"funding":["Swiss National Science Foundation","Biotechnology and Biological Sciences Research Council"],"pagination":["8538"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12501010"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["16(1)"],"pubmed_abstract":["Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Using the de novo annotations we identify cultivar-specific genes and define the core and dispensable genomes. Expression analysis across cultivars and tissues reveals conservation in expression between a large core set of homeologous genes, in addition to widespread changes in subgenome homeolog expression bias between cultivars and cultivar-spe"],"journal":["Nature communications"],"pubmed_title":["De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome."],"pmcid":["PMC12501010"],"funding_grant_id":["BB/CCG1720/1","212551","BB/M011216/1","BB/X011003/1","BBX011089/1","310030"],"pubmed_authors":["Simmonds J","Bose U","Lux T","Clark M","Hucl PJ","Himmelbach A","McCartney CA","Sese J","Chalmers K","Costamagna AC","Kaithakottil G","Halstead-Nussloch G","Budak H","Koo DH","Duncan S","Colmer J","Wright J","Borrill P","Colgrave ML","Accinelli GG","Ramirez-Gonzalez RH","Hatakeyama M","Swarbreck D","Muehlbauer G","Clavijo B","Shimizu KK","Joynson R","Delorean E","Kolodziej MC","Poland J","Keller B","Pozniak CJ","Tsuji H","Fu BX","Juhasz A","McKenzie N","Henderson S","Sharpe AG","Byrns B","Kuo T","Stein N","Gharbi K","Mascher M","Langridge P","Juliana P","Tanaka T","Melonek J","Cloutier S","Paape T","Hall A","Gardner KA","White B","Siri JN","Kawaura K","Legg EJ","Pozniak C","Haerty W","Poland JA","Monat C","Bevan M","Legg E","Ens J","Tameshige T","Percival-Alwyn L","Bharti A","Coombes B","Small I","Krattinger SG","Wu J","Rees H","Catchpole L","Mayer KFX","Lang D","Bharti AK","Wicker T","Fiebig A","Kobayashi F","Singh R","Barker T","Gundlach H","10+ Wheat Genome Project","Fradgley N","Steuernagel B","Fosker C","Tibbets J","Naamati G","Ban T","Irish N","Nabeka Y","Gutierrez-Gonzalez J","Walkowiak S","Gao L","Deek J","Fobert P","Kagale S","Distelfeld A","Gutwin C","Murata K","Fritz AK","Wiebe K","Cockram J","Heavens D","Ward S","Nasuda S","Spannagl M","Krasileva K","Handa H","N'Diaye A","Copetti D","Klymiuk V","Rusholme-Pilcher R","Chapman H","Thambugala D","Venturini L","Aquino C","Okada M","Shimizu-Inatsugi R","Haberer G","Uauy C","Scholz U","Koh CS","Kanamori H","Brinton J","Nilsen K","Kassa MT","Padmarasu S","Keeble-Gagnere G","Bandi V"],"additional_accession":[]},"is_claimable":false,"name":"De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome.","description":"Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Using the de novo annotations we identify cultivar-specific genes and define the core and dispensable genomes. Expression analysis across cultivars and tissues reveals conservation in expression between a large core set of homeologous genes, in addition to widespread changes in subgenome homeolog expression bias between cultivars and cultivar-spe","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Oct","modification":"2026-06-04T06:20:20.309Z","creation":"2026-05-06T03:13:08.399Z"},"accession":"S-EPMC12501010","cross_references":{"pubmed":["41053037"],"doi":["10.1038/s41467-025-64046-1"]}}