English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  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.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/21.11116/0000-0005-6C41-9 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-F4B7-9
Genre: Journal Article

Files

show Files

Locators

show
hide
Locator:
Link (Any fulltext)
Description:
-

Creators

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

Content

show
hide
Free keywords: -
 Abstract: 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.

Details

show
hide
Language(s): eng - English
 Dates: 2020
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1104/pp.19.00430
BibTex Citekey: Chenpp.00430.2019
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Plant Physiology
  Other : Plant Physiol.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Bethesda, Md. : American Society of Plant Biologists
Pages: - Volume / Issue: 182 (3) Sequence Number: - Start / End Page: 1510 - 1526 Identifier: ISSN: 0032-0889
CoNE: https://pure.mpg.de/cone/journals/resource/991042744294438