SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera.

Jing Chen,Yaya Yu,Kui Kang,Daowei Zhang

doi:10.7717/peerj.9320

Jing Chen, Yaya Yu + Show 2 more

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https://doi.org/10.7717/peerj.9320

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Journal: PeerJ	Publication Date: Jun 9, 2020
Citations: 10	License type: CC BY 4.0

Affiliation: Zunyi Medical University, Zunyi Normal College

Abstract

The white-backed planthopper Sogatella furcifera 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 S. furcifera using PacBio single-molecule real-time (SMRT) sequencing. Total RNA extracted from S. furcifera 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.

Highlights

The white-backed planthopper (WBPH) Sogatella furcifera (Hemiptera: Delphacidae) is an economically destructive rice pest distributed throughout Asia (Ma et al, 2017; Matsumura et al, 2014)
The WBPH transcriptome was sequenced using the Pacific Biosciences (PacBio) Sequel platform from a pooled RNA sample of S. furcifera obtained at different developmental stages, to accurately capture full-length transcript isoforms (BioSample accession: SAMN12612920)
RNA was isolated from pooled samples and the complementary DNA (cDNA) was classified as fractions of full-length transcripts up to 4 kb

Summary

Introduction

The white-backed planthopper (WBPH) Sogatella furcifera (Hemiptera: Delphacidae) is an economically destructive rice pest distributed throughout Asia (Ma et al, 2017; Matsumura et al, 2014). S. furcifera has a great ability to spread, causing widespread damage to crops (Wang et al, 2012). S. furcifera mainly affects crops in two ways, by sucking phloem sap and causing growth delay (Zhou et al, 2013); in severe cases, it causes ‘hopper burn’ (Lei et al, 2014; Wang et al, 2017). S. furcifera transmits plant viruses such as southern rice black-streaked dwarf virus (SRBSDV), rice ragged stunt virus (RRSV), and rice grassy stunt virus (RGSV) (Chen et al, 2018; He et al, 2016; Zhou et al, 2013). SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera.

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