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  Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation

Chen, M.-X., Zhu, F.-Y., Gao, B., Ma, K.-L., Zhang, Y., Fernie, A. R., et al. (2020). Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Plant Physiology, 182(3), 1510-1526. doi:10.1104/pp.19.00430.

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Chen, Mo-Xian1, Autor
Zhu, Fu-Yuan1, Autor
Gao, Bei1, Autor
Ma, Kai-Long1, Autor
Zhang, YJ2, Autor           
Fernie, A. R.2, Autor           
Chen, Xi1, Autor
Dai, Lei1, Autor
Ye, Neng-Hui1, Autor
Zhang, Xue1, Autor
Tian, Yuan1, Autor
Zhang, Di1, Autor
Xiao, Shi1, Autor
Zhang, Jianhua1, Autor
Liu, Ying-Gao1, Autor
Affiliations:
1External Organizations, ou_persistent22              
2Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753339              

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 Zusammenfassung: Rice (Oryza sativa) molecular breeding has gained considerable attention in recent years but inaccurate genome annotation hampers its progress and functional studies of the rice genome. In this study, we applied single-molecule long-read RNA sequencing (lrRNA_seq)-based proteogenomics to reveal the complexity of the rice transcriptome and its coding abilities. Surprisingly, approximately 60% of loci identified by lrRNA_seq are associated with natural antisense transcripts (NATs). The high-density genomic arrangement of NAT genes suggests their potential roles in the multifaceted control of gene expression. In addition, a large number of fusion and intergenic transcripts have been observed. Furthermore, a total of 906,456 transcript isoforms were identified, and 72.9% of the genes can generate splicing isoforms. 706,075 post-transcriptional events were subsequently categorized into ten subtypes, demonstrating the interdependence of post-transcriptional mechanisms that contribute to transcriptome diversity. Parallel short-read RNA sequencing indicated that lrRNA_seq has a superior capacity for the identification of longer transcripts. In addition, over 190,000 unique peptides belonging to 9,706 proteoforms/protein groups were identified, expanding the diversity of the rice proteome. Our findings indicate that the genome organization, transcriptome diversity, and coding potential of the rice transcriptome are far more complex than previously anticipated.

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Sprache(n): eng - English
 Datum: 2020
 Publikationsstatus: Erschienen
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 Identifikatoren: DOI: 10.1104/pp.19.00430
BibTex Citekey: Chenpp.00430.2019
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Titel: Plant Physiology
  Andere : Plant Physiol.
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: Bethesda, Md. : American Society of Plant Biologists
Seiten: - Band / Heft: 182 (3) Artikelnummer: - Start- / Endseite: 1510 - 1526 Identifikator: ISSN: 0032-0889
CoNE: https://pure.mpg.de/cone/journals/resource/991042744294438