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

  1. Guo, Wenbin ORCID logo
  2. Schreiber, Miriam ORCID logo
  3. Marosi, Vanda Beata ORCID logo
  4. Bagnaresi, Paolo ORCID logo
  5. Jørgensen, Morten Egevang ORCID logo
  6. Braune, Katarzyna B
  7. Chalmers, Ken
  8. Chapman, Brett ORCID logo
  9. Dang, Viet ORCID logo
  10. Dockter, Christoph ORCID logo
  11. Fiebig, Anne ORCID logo
  12. Fincher, Geoffrey B
  13. Fricano, Agostino
  14. Fuller, John
  15. Haaning, Allison
  16. Haberer, Georg ORCID logo
  17. Himmelbach, Axel ORCID logo
  18. Jayakodi, Murukarthick ORCID logo
  19. JIA, YONG ORCID logo
  20. Kamal, Nadia ORCID logo
  21. Langridge, Peter ORCID logo
  22. Li, Chengdao ORCID logo
  23. Lu, Qiongxian ORCID logo
  24. Lux, Thomas ORCID logo
  25. Mascher, Martin ORCID logo
  26. Mayer, Klaus ORCID logo
  27. McCallum, Nicola ORCID logo
  28. Milne, Linda
  29. Muehlbauer, Gary ORCID logo
  30. Nielsen, Martin T S
  31. Padmarasu, Sudharsan ORCID logo
  32. Pedas, Pai Rosager
  33. Pillen, Klaus ORCID logo
  34. Pozniak, Curtis ORCID logo
  35. Rasmussen, Magnus ORCID logo
  36. Sato, Kazuhiro ORCID logo
  37. Schmutzer, Thomas ORCID logo
  38. Scholz, Uwe ORCID logo
  39. Schüler, Danuta ORCID logo
  40. Šimková, Hana ORCID logo
  41. Skadhauge, Birgitte ORCID logo
  42. Stein, Nils ORCID logo
  43. Thomsen, Nina W
  44. Voss, Cynthia
  45. Wang, Penghao
  46. Wonneberger, Ronja
  47. Zhang, Xiao-Qi
  48. Zhang, Guoping
  49. cattivelli, luigi ORCID logo
  50. Spannagl, Manuel ORCID logo
  51. Bayer, Micha ORCID logo
  52. Simpson, Craig ORCID logo
  53. Zhang, Runxuan ORCID logo
  54. Waugh, Robbie ORCID logo

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1000 Titel
  • A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity
1000 Autor/in
  1. Guo, Wenbin |
  2. Schreiber, Miriam |
  3. Marosi, Vanda Beata |
  4. Bagnaresi, Paolo |
  5. Jørgensen, Morten Egevang |
  6. Braune, Katarzyna B |
  7. Chalmers, Ken |
  8. Chapman, Brett |
  9. Dang, Viet |
  10. Dockter, Christoph |
  11. Fiebig, Anne |
  12. Fincher, Geoffrey B |
  13. Fricano, Agostino |
  14. Fuller, John |
  15. Haaning, Allison |
  16. Haberer, Georg |
  17. Himmelbach, Axel |
  18. Jayakodi, Murukarthick |
  19. JIA, YONG |
  20. Kamal, Nadia |
  21. Langridge, Peter |
  22. Li, Chengdao |
  23. Lu, Qiongxian |
  24. Lux, Thomas |
  25. Mascher, Martin |
  26. Mayer, Klaus |
  27. McCallum, Nicola |
  28. Milne, Linda |
  29. Muehlbauer, Gary |
  30. Nielsen, Martin T S |
  31. Padmarasu, Sudharsan |
  32. Pedas, Pai Rosager |
  33. Pillen, Klaus |
  34. Pozniak, Curtis |
  35. Rasmussen, Magnus |
  36. Sato, Kazuhiro |
  37. Schmutzer, Thomas |
  38. Scholz, Uwe |
  39. Schüler, Danuta |
  40. Šimková, Hana |
  41. Skadhauge, Birgitte |
  42. Stein, Nils |
  43. Thomsen, Nina W |
  44. Voss, Cynthia |
  45. Wang, Penghao |
  46. Wonneberger, Ronja |
  47. Zhang, Xiao-Qi |
  48. Zhang, Guoping |
  49. cattivelli, luigi |
  50. Spannagl, Manuel |
  51. Bayer, Micha |
  52. Simpson, Craig |
  53. Zhang, Runxuan |
  54. Waugh, Robbie |
1000 Erscheinungsjahr 2025
1000 LeibnizOpen
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2025-02-03
1000 Erschienen in
1000 Quellenangabe
  • 57(2):441-450
1000 FRL-Sammlung
1000 Lizenz
1000 Verlagsversion
  • https://dx.doi.org/10.1038/s41588-024-02069-y |
  • https://pmc.ncbi.nlm.nih.gov/articles/PMC11821519/ |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • 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.
1000 Sacherschließung
lokal plant genetics
lokal gene expression
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://orcid.org/0000-0002-1829-6044|https://orcid.org/0000-0002-3732-8822|https://orcid.org/0000-0002-1444-2972|https://orcid.org/0000-0001-8466-4805|https://orcid.org/0000-0001-6503-0495|https://frl.publisso.de/adhoc/uri/QnJhdW5lLCBLYXRhcnp5bmEgQiA=|https://frl.publisso.de/adhoc/uri/Q2hhbG1lcnMsIEtlbg==|https://orcid.org/0000-0003-4484-2253|https://orcid.org/0000-0001-6408-6323|https://orcid.org/0000-0001-5923-3667|https://orcid.org/0000-0003-3159-3593|https://frl.publisso.de/adhoc/uri/RmluY2hlciwgR2VvZmZyZXkgQiAgIA==|https://frl.publisso.de/adhoc/uri/RnJpY2FubywgQWdvc3Rpbm8g|https://frl.publisso.de/adhoc/uri/RnVsbGVyLCBKb2hu|https://frl.publisso.de/adhoc/uri/SGFhbmluZywgQWxsaXNvbg==|https://orcid.org/0000-0002-6612-6939|https://orcid.org/0000-0001-7338-0946|https://orcid.org/0000-0003-2951-0541|https://orcid.org/0000-0002-0394-3966|https://orcid.org/0000-0002-3258-4130|https://orcid.org/0000-0001-9494-400X|https://orcid.org/0000-0002-9653-2700|https://orcid.org/0000-0002-1358-2623|https://orcid.org/0000-0002-5543-1911|https://orcid.org/0000-0001-6373-6013|https://orcid.org/0000-0001-6484-1077|https://orcid.org/0000-0002-9438-1697|https://frl.publisso.de/adhoc/uri/TWlsbmUsIExpbmRh|https://orcid.org/0000-0001-9320-2629|https://frl.publisso.de/adhoc/uri/TmllbHNlbiwgTWFydGluIFQgUyA=|https://orcid.org/0000-0003-3125-3695|https://frl.publisso.de/adhoc/uri/UGVkYXMsIFBhaSBSb3NhZ2VyICA=|https://orcid.org/0000-0003-4646-6351|https://orcid.org/0000-0002-7536-3856|https://orcid.org/0000-0001-6720-8832|https://orcid.org/0000-0001-8818-5203|https://orcid.org/0000-0003-1073-6719|https://orcid.org/0000-0001-6113-3518|https://orcid.org/0000-0003-4277-9879|https://orcid.org/0000-0003-4159-7619|https://orcid.org/0000-0001-7317-4376|https://orcid.org/0000-0003-3011-8731|https://frl.publisso.de/adhoc/uri/VGhvbXNlbiwgTmluYSBXIA==|https://frl.publisso.de/adhoc/uri/Vm9zcywgQ3ludGhpYQ==|https://frl.publisso.de/adhoc/uri/V2FuZywgUGVuZ2hhbyAg|https://frl.publisso.de/adhoc/uri/V29ubmViZXJnZXIsIFJvbmph|https://frl.publisso.de/adhoc/uri/WmhhbmcsIFhpYW8tUWkg|https://frl.publisso.de/adhoc/uri/WmhhbmcsIEd1b3BpbmcgIA==|https://orcid.org/0000-0002-6067-4600|https://orcid.org/0000-0003-0701-7035|https://orcid.org/0000-0003-0041-3115|https://orcid.org/0000-0002-1723-1492|https://orcid.org/0000-0001-7558-765X|https://orcid.org/0000-0003-1045-3065
1000 Label
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  11. Zhejiang University |
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