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

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 PacB...

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Autores principales: Chen, Jing, Yu, Yaya, Kang, Kui, Zhang, Daowei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292024/
https://www.ncbi.nlm.nih.gov/pubmed/32551204
http://dx.doi.org/10.7717/peerj.9320
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author Chen, Jing
Yu, Yaya
Kang, Kui
Zhang, Daowei
author_facet Chen, Jing
Yu, Yaya
Kang, Kui
Zhang, Daowei
author_sort Chen, Jing
collection PubMed
description 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.
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spelling pubmed-72920242020-06-17 SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera Chen, Jing Yu, Yaya Kang, Kui Zhang, Daowei PeerJ Agricultural Science 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. PeerJ Inc. 2020-06-09 /pmc/articles/PMC7292024/ /pubmed/32551204 http://dx.doi.org/10.7717/peerj.9320 Text en ©2020 Chen et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Agricultural Science
Chen, Jing
Yu, Yaya
Kang, Kui
Zhang, Daowei
SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera
title SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera
title_full SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera
title_fullStr SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera
title_full_unstemmed SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera
title_short SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera
title_sort smrt sequencing of the full-length transcriptome of the white-backed planthopper sogatella furcifera
topic Agricultural Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292024/
https://www.ncbi.nlm.nih.gov/pubmed/32551204
http://dx.doi.org/10.7717/peerj.9320
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