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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2020
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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. |
format | Online Article Text |
id | pubmed-7292024 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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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