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Full-length codling moth transcriptome atlas revealed by single-molecule real-time sequencing

文献类型： 外文期刊

作者： Xing, Longsheng 1 ; Wu, Qiang 1 ; Xi, Yu 1 ; Huang, Cong 1 ; Liu, Wanxue 2 ; Wan, Fanghao 1 ; Qian, Wanqiang 1 ;

作者机构： 1.Chinese Acad Agr Sci, Minist Agr, Agr Genom Inst Shenzhen, Genome Anal Lab,Guangdong Lab Lingnan Modern Agr, Shenzhen 518120, Peoples R China

2.Chinese Acad Agr Sci, Inst Plant Protect, State Key Lab Biol Plant Dis & Insect Pests, Beijing 100193, Peoples R China

关键词： Full-length transcriptome; Alternative splicing; Fusion gene; Cydia pomonella; IsoSeq

期刊名称：GENOMICS （ 影响因子：4.31； 五年影响因子：4.38 ）

ISSN： 0888-7543

年卷期： 2022 年 114 卷 2 期

页码：

收录情况： SCI

摘要： Over the past decade, second-generation sequencing (SGS) has been widely used to elucidate the transcriptome across many organisms. However, the full-length (FL) transcripts and alternative splice (AS) isoforms could not be confidently and accurately defined with SGS. Pacific biosciences (PacBio) single-molecule real-time sequencing was conducted to obtain FL transcriptome data in the codling moth. In total, 25,940 high-quality FL isoforms were obtained and clustered to 14,099 nonredundant clusters. Interestingly, nearly 90% of nonredundant PacBio transcripts were novel compared to reference genes. Among them, 3389 transcripts potentially represented novel genes. Additionally, a large number of AS events were discovered, and most of the splice junctions in the PacBio isoforms could be supported by short reads in public datasets. Furthermore, 952 FL lncRNAs and 81 fusion transcripts were identified and validated using RT-PCR analysis. Overall, an atlas of FL transcripts was obtained in the codling moth, which will help provide further insights into the complexity of the transcriptome and facilitate improving genome annotations and functional studies in this insect

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