SMRT sequencing of full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt).
SMRT sequencing of full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt).
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跳甲虫 Agasicles hygrophila（Selman 和 Vogt）全长转录组的 SMRT 测序
DOI：
10.1038/s41598-018-20181-y
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发表时间：
2018-02-02
影响因子：
4.6
通讯作者：
Ma R
中科院分区：
文献类型：
--
作者：
Jia D;Wang Y;Liu Y;Hu J;Guo Y;Gao L;Ma R
本研究的目的是利用单分子实时荧光（SMRT）测序技术获得嗜湿扁甲（Agasicles hygrophila，Selman和沃格特）的全长转录组。A.收获包括卵、幼虫、蛹和成虫在内的嗜湿草履虫，用于分离总RNA。将混合的样品用于SMRT测序以产生全长转录组。基于获得的转录组数据，选择性剪接事件，简单序列重复（SSR）分析，编码序列预测，转录本功能注释，和lncRNA预测。生成了总共9.45 Gb的干净读段，包括335，045个插入片段（ROI）读段和158，085个全长非嵌合（FLNC）读段。FLNC读段的转录本聚类分析鉴定了40，004种共有亚型，包括31，015种高质量亚型。删除冗余读数后，获得了28，982份转录本。共预测了145个选择性剪接事件。此外，根据SSR分析鉴定了12，753个SSR和16，205个编码序列。此外，在8个功能数据库中注释了24，031个转录本，预测了4，198个lncRNA。这是第一个对A.喜湿植物本研究获得的转录组有助于进一步探索A.并揭示这种昆虫与生态系统之间的相互作用。
This study was aimed at generating the full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt) using single-molecule real-time (SMRT) sequencing. Four developmental stages of A. hygrophila, including eggs, larvae, pupae, and adults were harvested for isolating total RNA. The mixed samples were used for SMRT sequencing to generate the full-length transcriptome. Based on the obtained transcriptome data, alternative splicing event, simple sequence repeat (SSR) analysis, coding sequence prediction, transcript functional annotation, and lncRNA prediction were performed. Total 9.45 Gb of clean reads were generated, including 335,045 reads of insert (ROI) and 158,085 full-length non-chimeric (FLNC) reads. Transcript clustering analysis of FLNC reads identified 40,004 consensus isoforms, including 31,015 high-quality ones. After removing redundant reads, 28,982 transcripts were obtained. Total 145 alternative splicing events were predicted. Additionally, 12,753 SSRs and 16,205 coding sequences were identified based on SSR analysis. Furthermore, 24,031 transcripts were annotated in eight functional databases, and 4,198 lncRNAs were predicted. This is the first study to perform SMRT sequencing of the full-length transcriptome of A. hygrophila. The obtained transcriptome may facilitate further exploration of the genetic data of A. hygrophila and uncover the interactions between this insect and the ecosystem.
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