Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton

作者:Wang, K (Wang, Kun)^{[ 1 ]} ; Wang, DH (Wang, Dehe)^{[ 1,2 ]} ; Zheng, XM (Zheng, Xiaomin)^{[ 1 ]} ; Qin, A (Qin, Ai)^{[ 1 ]} ; Zhou, J (Zhou, Jie)^{[ 1 ]} ; Guo, BY (Guo, Boyu)^{[ 1 ]} ; Chen, YJ (Chen, Yanjun)^{[ 1 ]} ; Wen, XP (Wen, Xingpeng)^{[ 3 ]} ; Ye, W (Ye, Wen)^{[ 4 ]} ; Zhou, Y (Zhou, Yu)^{[ 1,2,3 ]} ...更多内容

NATURE COMMUNICATIONS

卷: 10

文献号: 4714

DOI: 10.1038/s41467-019-12575-x

出版年: OCT 17 2019

文献类型:Article

摘要

Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes invarious aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.

关键词

KeyWords Plus:FUNCTIONAL CONSEQUENCES; GENOME SEQUENCE; GENE-EXPRESSION; START SITES; POLYADENYLATION; IDENTIFICATION; EVOLUTION; PROVIDES; PROTEIN; STRESS

通讯作者地址: Zhou, Y; Zhu, YX (通讯作者)

Wuhan Univ, Coll Life Sci, Wuhan 430072, Hubei, Peoples R China.

通讯作者地址: Zhou, Y (通讯作者)

Wuhan Univ, State Key Lab Virol, Wuhan 430072, Hubei, Peoples R China.

通讯作者地址: Zhou, Y; Zhu, YX (通讯作者)

Wuhan Univ, Inst Adv Studies, Wuhan 430072, Hubei, Peoples R China.

原文PDF地址：

https://www.nature.com/articles/s41467-019-12575-x