Single-molecule real-time transcript sequencing of developing cotton anthers facilitates genome annotation and fertility restoration candidate gene discovery
Single-molecule real-time transcript sequencing of developing cotton anthers facilitates genome annotation and fertility restoration candidate gene discovery
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棉花花药发育中的单分子实时转录测序有助于基因组注释和育性恢复候选基因的发现
DOI：
10.1016/j.ygeno.2021.11.014
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发表时间：
2021-11-18
期刊：
影响因子：
4.4
通讯作者：
Wu, Jianyong
中科院分区：
文献类型：
--
作者：
Li, Ting;Zhang, Xuexian;Wu, Jianyong
杂种优势是指杂种中观察到的优越表型。细胞质雄性不育系统在棉花杂种优势利用中起着重要作用。然而，CMS-D2的整体基因表达模式及其与恢复基因Rf1的相互作用尚不清楚。本文采用PacBio单分子实时测序技术对CMS-D2恢复系花药进行了全长转录本测序。结合PacBio SMRT长读异构体和Illumina RNA-seq数据，共获得44,338个位点的107,066个异构体，其中包括新基因的10,086个新异构体和已知基因的66,419个新异构体。共有56,572个选择性剪接（AS）事件，1146个lncrna， 61个融合转录物和10,466个基因表现出选择性聚腺苷化（APA），并进一步鉴定出60,995个具有预测开放阅读框（orf）的新亚型。此外，选择恢复系中特异性表达的基因，并通过qRTPCR进行验证。这些发现为陆地棉基因组注释和转录组研究提供了基础，并有助于揭示Rf1与CMS-D2细胞质相互作用的分子机制。
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.