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<p>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.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年2月3日

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

摘要

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.