biostudies-literatureWhite BSwiss National Science FoundationBiotechnology and Biological Sciences Research Council8538https://www.ebi.ac.uk/biostudies/studies/S-EPMC12501010biostudies-literatureUnknown16(1)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-speNature communicationsDe novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome.PMC12501010BB/CCG1720/1212551BB/M011216/1BB/X011003/1BBX011089/1310030Simmonds JBose ULux TClark MHucl PJHimmelbach AMcCartney CASese JChalmers KCostamagna ACKaithakottil GHalstead-Nussloch GBudak HKoo DHDuncan SColmer JWright JBorrill PColgrave MLAccinelli GGRamirez-Gonzalez RHHatakeyama MSwarbreck DMuehlbauer GClavijo BShimizu KKJoynson RDelorean EKolodziej MCPoland JKeller BPozniak CJTsuji HFu BXJuhasz AMcKenzie NHenderson SSharpe AGByrns BKuo TStein NGharbi KMascher MLangridge PJuliana PTanaka TMelonek JCloutier SPaape THall AGardner KAWhite BSiri JNKawaura KLegg EJPozniak CHaerty WPoland JAMonat CBevan MLegg EEns JTameshige TPercival-Alwyn LBharti ACoombes BSmall IKrattinger SGWu JRees HCatchpole LMayer KFXLang DBharti AKWicker TFiebig AKobayashi FSingh RBarker TGundlach H10+ Wheat Genome ProjectFradgley NSteuernagel BFosker CTibbets JNaamati GBan TIrish NNabeka YGutierrez-Gonzalez JWalkowiak SGao LDeek JFobert PKagale SDistelfeld AGutwin CMurata KFritz AKWiebe KCockram JHeavens DWard SNasuda SSpannagl MKrasileva KHanda HN'Diaye ACopetti DKlymiuk VRusholme-Pilcher RChapman HThambugala DVenturini LAquino COkada MShimizu-Inatsugi RHaberer GUauy CScholz UKoh CSKanamori HBrinton JNilsen KKassa MTPadmarasu SKeeble-Gagnere GBandi VfalseDe novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome.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-spe2025-01-01T00:00:00Z2025 Oct2026-06-04T06:20:20.309Z2026-05-06T03:13:08.399ZS-EPMC125010104105303710.1038/s41467-025-64046-1