Publications and Media

@article{WOS:001411678300001,

title = {A barley pan-transcriptome reveals layers of genotype-dependent  transcriptional complexity},

author = {Wenbin Guo and Miriam Schreiber and Vanda B. Marosi and Paolo Bagnaresi and Morten Egevang Jorgensen and Katarzyna B. Braune and Ken Chalmers and Brett Chapman and Viet Dang and Christoph Dockter and Anne Fiebig and Geoffrey B. Fincher and Agostino Fricano and John Fuller and Allison Haaning and Georg Haberer and Axel Himmelbach and Murukarthick Jayakodi and Yong Jia and Nadia Kamal and Peter Langridge and Chengdao Li and Qiongxian Lu and Thomas Lux and Martin Mascher and Klaus F. X. Mayer and Nicola Mccallum and Linda Milne and Gary J. Muehlbauer and Martin T. S. Nielsen and Sudharsan Padmarasu and Pai Rosager Pedas and Klaus Pillen and Curtis Pozniak and Magnus W. Rasmussen and Kazuhiro Sato and Thomas Schmutzer and Uwe Scholz and Danuta Schueler and Hana Simkova and Birgitte Skadhauge and Nils Stein and Nina W. Thomsen and Cynthia Voss and Penghao Wang and Ronja Wonneberger and Xiao-Qi Zhang and Guoping Zhang and Luigi Cattivelli and Manuel Spannagl and Micha Bayer and Craig Simpson and Runxuan Zhang and Robbie Waugh},

doi = {10.1038/s41588-024-02069-y},

issn = {1061-4036},

year  = {2025},

date = {2025-02-01},

urldate = {2025-02-01},

journal = {NATURE GENETICS},

volume = {57},

number = {2},

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.},

keywords = {Gene expression, Pan-genome, Pan-transcriptome, Plant genetics, RNA sequencing},

pubstate = {published},

tppubtype = {article}

}