Chen Jing, Yu Yaya, Kang Kui, Zhang Daowei
College of Basic Medical Science, Zunyi Medical University, Zunyi, China.
School of Biological and Agricultural Science and Technology, Zunyi Normal University, Zunyi, China.
PeerJ. 2020 Jun 9;8:e9320. doi: 10.7717/peerj.9320. eCollection 2020.
The white-backed planthopper is an economically important rice pest distributed throughout Asia. It damages rice crops by sucking phloem sap, resulting in stunted growth and plant virus transmission. We aimed to obtain the full-length transcriptome data of using PacBio single-molecule real-time (SMRT) sequencing. Total RNA extracted from at various developmental stages (egg, larval, and adult stages) was mixed and used to generate a full-length transcriptome for SMRT sequencing. Long non-coding RNA (lncRNA) identification, full-length coding sequence prediction, full-length non-chimeric (FLNC) read detection, simple sequence repeat (SSR) analysis, transcription factor detection, and transcript functional annotation were performed. A total of 12,514,449 subreads (15.64 Gbp, clean reads) were generated, including 630,447 circular consensus sequences and 388,348 FLNC reads. Transcript cluster analysis of the FLNC reads revealed 251,109 consensus reads including 29,700 high-quality reads. Additionally, 100,360 SSRs and 121,395 coding sequences were identified using SSR analysis and ANGEL software, respectively. Furthermore, 44,324 lncRNAs were annotated using four tools and 1,288 transcription factors were identified. In total, 95,495 transcripts were functionally annotated based on searches of seven different databases. To the best of our knowledge, this is the first study of the full-length transcriptome of the white-backed planthopper obtained using SMRT sequencing. The acquired transcriptome data can facilitate further studies on the ecological and viral-host interactions of this agricultural pest.
白背飞虱是一种在亚洲广泛分布的对经济有重要影响的水稻害虫。它通过吸食韧皮部汁液来损害水稻作物，导致生长发育受阻并传播植物病毒。我们旨在利用PacBio单分子实时（SMRT）测序获得[白背飞虱]的全长转录组数据。从[白背飞虱]不同发育阶段（卵、幼虫和成虫阶段）提取的总RNA混合后用于生成用于SMRT测序的全长转录组。进行了长链非编码RNA（lncRNA）鉴定、全长编码序列预测、全长非嵌合（FLNC）读段检测、简单序列重复（SSR）分析、转录因子检测以及转录本功能注释。共产生了12,514,449条子读段（15.64 Gbp，clean reads），包括630,447个环状一致序列和388,348个FLNC读段。对FLNC读段的转录本聚类分析揭示了251,109个一致读段，其中包括29,700个高质量读段。此外，分别使用SSR分析和ANGEL软件鉴定出100,360个SSR和121,395个编码序列。此外，使用四种工具注释了44,324个lncRNA，并鉴定出1,288个转录因子。基于对七个不同数据库的搜索，总共对95,495个转录本进行了功能注释。据我们所知，这是首次使用SMRT测序对白背飞虱全长转录组进行的研究。所获得的转录组数据有助于对这种农业害虫的生态和病毒-宿主相互作用进行进一步研究。
