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Journal article
A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity
Nature genetics, Vol.57, pp.441-450
2025
PMID: 39901014
Abstract
A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry.
Details
- Title
- A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity
- Authors/Creators
- Wenbin Guo - James Hutton InstituteMiriam Schreiber - James Hutton InstituteVanda B Marosi - Technical University of MunichPaolo Bagnaresi - CREA Research Centre for Olive, Fruit and Citrus Crops, Forlì, ItalyMorten Egevang Jørgensen - Carlsberg LaboratoryKatarzyna B Braune - Carlsberg LaboratoryKen Chalmers - The University of AdelaideBrett Chapman - Murdoch UniversityViet Dang - Murdoch UniversityChristoph Dockter - Carlsberg LaboratoryAnne Fiebig - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Geoffrey B Fincher - The University of AdelaideAgostino Fricano - Genomics (United Kingdom)John Fuller - James Hutton InstituteAllison Haaning - University of MinnesotaGeorg Haberer - Helmholtz Zentrum MünchenAxel Himmelbach - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Murukarthick Jayakodi - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Yong Jia - Murdoch UniversityNadia Kamal - Helmholtz Zentrum MünchenPeter Langridge - The University of AdelaideChengdao Li - Murdoch UniversityQiongxian Lu - Carlsberg LaboratoryThomas Lux - Helmholtz Zentrum MünchenMartin Mascher - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Klaus F X Mayer - Plant (United States)Nicola McCallum - James Hutton InstituteLinda Milne - James Hutton InstituteGary J Muehlbauer - University of MinnesotaMartin T S Nielsen - Carlsberg LaboratorySudharsan Padmarasu - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Pai Rosager Pedas - Carlsberg LaboratoryKlaus Pillen - Martin Luther University Halle-WittenbergCurtis Pozniak - University of SaskatchewanMagnus W Rasmussen - Carlsberg LaboratoryKazuhiro Sato - Kazusa DNA Research InstituteThomas Schmutzer - Martin Luther University Halle-WittenbergUwe Scholz - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Danuta Schüler - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Hana Šimková - Czech Academy of Sciences, Institute of Experimental BotanyBirgitte Skadhauge - Carlsberg LaboratoryNils Stein - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Nina W Thomsen - Carlsberg LaboratoryCynthia Voss - Carlsberg LaboratoryPenghao Wang - Murdoch UniversityRonja Wonneberger - James Hutton InstituteXiao-Qi Zhang - Murdoch UniversityGuoping Zhang - Zhejiang UniversityLuigi Cattivelli - Genomics (United Kingdom)Manuel Spannagl - Helmholtz Zentrum MünchenMicha Bayer - James Hutton InstituteCraig Simpson - James Hutton InstituteRunxuan Zhang - James Hutton InstituteRobbie Waugh - University of Dundee
- Publication Details
- Nature genetics, Vol.57, pp.441-450
- Publisher
- Springer Nature; BERLIN
- Number of pages
- 29
- Grant note
- BB/X018636/1 / RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) CTAG2 / Genome Canada (Génome Canada) BB/S020160/1 / RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) CF15-0236 / Carlsbergfondet (Carlsberg Foundation) UMU1806-002RTX / Grains Research and Development Corporation (Grains Research & Development Corporation) CF15-0672 / Carlsbergfondet (Carlsberg Foundation) ERA-CAPS BB/S004610/1 / RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) ERA-CAPS project 1844331 / National Science Foundation (NSF) KJHI-B1-2 / Rural and Environment Science and Analytical Services Division (Scottish Government's Rural and Environment Science and Analytical Services Division) CF15-0476 / Carlsbergfondet (Carlsberg Foundation)
- Identifiers
- 991005737833007891
- Copyright
- © 2025. The Author(s).
- Murdoch Affiliation
- Centre for Crop and Food Innovation; School of Medical, Molecular and Forensic Sciences
- Language
- English
- Resource Type
- Journal article
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