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Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation.
Plant Physiology ( IF 6.5 ) Pub Date : 2019-12-19 , DOI: 10.1104/pp.19.00430
Mo-Xian Chen 1, 2 , Fu-Yuan Zhu 3 , Bei Gao 4 , Kai-Long Ma 5 , Youjun Zhang 6, 7 , Alisdair R Fernie 6, 7 , Xi Chen 8 , Lei Dai 9 , Neng-Hui Ye 4 , Xue Zhang 9 , Yuan Tian 1 , Di Zhang 4 , Shi Xiao 9 , Jianhua Zhang 10 , Ying-Gao Liu 1
Affiliation  

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, 906,456 transcript isoforms were identified, and 72.9% of the genes can generate splicing isoforms. A total of 706,075 posttranscriptional events were subsequently categorized into 10 subtypes, demonstrating the interdependence of posttranscriptional 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.

中文翻译:

基于全长转录本的水稻蛋白质组学改进了其基因组和蛋白质组注释。

水稻(Oryza sativa)分子育种近年来受到了广泛关注,但是不正确的基因组注释阻碍了其进展和对水稻基因组的功能研究。在这项研究中,我们应用了基于单分子长读RNA测序(lrRNA_seq)的蛋白质组学,以揭示水稻转录组的复杂性及其编码能力。出乎意料的是,由lrRNA_seq鉴定的基因座中约有60%与天然反义转录本(NAT)相关。NAT基因的高密度基因组排列表明它们在基因表达的多方面控制中的潜在作用。另外,已经观察到大量融合和基因间的转录物。此外,鉴定了906,456个转录亚型,并且72.9%的基因可以产生剪接亚型。总共706 随后将075个转录后事件分为10个亚型,证明了有助于转录组多样性的转录后机制的相互依赖性。并行的短读RNA测序表明lrRNA_seq具有较高的识别较长转录本的能力。另外,鉴定出属于9706种蛋白/蛋白质组的190,000多种独特肽,扩大了水稻蛋白质组的多样性。我们的发现表明,水稻转录组的基因组组织,转录组多样性和编码潜力比以前预期的要复杂得多。并行的短读RNA测序表明lrRNA_seq具有较高的识别较长转录本的能力。另外,鉴定出属于9706种蛋白/蛋白质组的190,000多种独特肽,扩大了水稻蛋白质组的多样性。我们的发现表明,水稻转录组的基因组组织,转录组多样性和编码潜力比以前预期的要复杂得多。并行的短读RNA测序表明lrRNA_seq具有较高的识别较长转录本的能力。另外,鉴定出属于9706种蛋白/蛋白质组的190,000多种独特肽,扩大了水稻蛋白质组的多样性。我们的发现表明,水稻转录组的基因组组织,转录组多样性和编码潜力比以前预期的要复杂得多。
更新日期:2020-03-03
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