PuSH - Publication Server of Helmholtz Zentrum München

Guo, W.* ; Schreiber, M.* ; Marosi, V.B. ; Bagnaresi, P.* ; Jørgensen, M.E.* ; Braune, K.B.* ; Chalmers, K.* ; Chapman, B.* ; Dang, V.D.* ; Dockter, C.* ; Fiebig, A.* ; Fincher, G.B.* ; Fricano, A.* ; Fuller, J.* ; Haaning, A.* ; Haberer, G. ; Himmelbach, A.* ; Jayakodi, M.* ; Jia, Y.* ; Kamal, N. ; Langridge, P.* ; Li, C.* ; Lu, Q.* ; Lux, T. ; Mascher, M.* ; Mayer, K.F.X. ; McCallum, N.* ; Milne, L.* ; Muehlbauer, G.J.* ; Nielsen, M.T.S.* ; Padmarasu, S.* ; Pedas, P.R.* ; Pillen, K.* ; Pozniak, C.* ; Rasmussen, M.W.* ; Sato, K.* ; Schmutzer, T.* ; Scholz, U.* ; Schuler, D.* ; Šimková, H.* ; Skadhauge, B.* ; Stein, N.* ; Thomsen, N.W.* ; Voss, C.* ; Wang, P.* ; Wonneberger, R.* ; Zhang, X.Q.* ; Zhang, G.* ; Cattivelli, L.* ; Spannagl, M. ; Bayer, M.* ; Simpson, C.* ; Zhang, R.* ; Waugh, R.*

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.

Nat. Genet. 57, 441-450 (2025)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
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.
Altmetric
Additional Metrics?
[➜Log in]
Edit extra informations Login
Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Expression; Quality; Annotation; Mutation; Datasets; Binding
ISSN (print) / ISBN 1061-4036
e-ISSN 1546-1718
Journal Nature Genetics
Quellenangaben Volume: 57, Issue: 2, Pages: 441-450 Article Number: , Supplement: ,
Publisher Nature Publishing Group
Publishing Place New York, NY
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)
Grants Zhejiang University-CNSF
Helmholtz Center Munich-BMBF
ERA-CAPS
BBSRC project
University of Dundee-the Scottish Government RESAS project
Institute of Experimental Botany of the Czech Academy of Sciences-ERDF project
Martin-Luther-University Halle-Wittenberg-DFG
University of Minnesota-NSF ERA-CAPS project
BMBF project
Carlsberg Research Laboratory-Carlsberg Foundation
Rural and Environment Science and Analytical Services Division (Scottish Government's Rural and Environment Science and Analytical Services Division)