Single-molecule real-time transcript sequencing of developing cotton anthers facilitates genome annotation and fertility restoration candidate gene discovery

文献类型： 外文期刊

第一作者： Li, Ting

作者： Li, Ting;Zhang, Yongjie;Wu, Jianyong;Zhang, Xuexian;Guo, Liping;Qi, Tingxiang;Tang, Huini;Wang, Hailin;Qiao, Xiuqin;Zhang, Meng;Zhang, Bingbing;Feng, Juanjuan;Zuo, Zhidan;Xing, Chaozhu

作者机构：

关键词： Upland cotton; CMS-D2; SMRT sequencing; Full-length transcriptome; AS; Rf1

期刊名称：GENOMICS （ 影响因子：5.736； 五年影响因子：4.939 ）

ISSN： 0888-7543

年卷期： 2021 年 113 卷 6 期

页码：

收录情况： SCI

摘要： Heterosis refers to the superior phenotypes observed in hybrids. Cytoplasmic male sterility (CMS) system plays an important role in cotton heterosis utilization. However, the global gene expression patterns of CMS-D2 and its interaction with the restorer gene Rf1 remain unclear. Here, the full-length transcript sequencing was performed in anthers of the CMS-D2 restorer line using PacBio single-molecule real-time sequencing technology. Combining PacBio SMRT long-read isoforms and Illumina RNA-seq data, 107,066 isoforms from 44,338 loci were obtained, including 10,086 novel isoforms of novel genes and 66,419 new isoforms of known genes. Totally 56,572 alternative splicing (AS) events, 1146 lncRNAs, 61 fusion transcripts and 10,466 genes exhibited alternative polyadenylation (APA), and 60,995 novel isoforms with predicted open reading frames (ORFs) were further identified. Furthermore, the specifically expressed genes in restorer line were selected and confirmed by qRTPCR. These findings provide a basis for upland cotton genome annotation and transcriptome research, and will help to reveal the molecular mechanism of interaction between Rf1 and CMS-D2 cytoplasm.

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