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Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)

BACKGROUND: The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce’s disease of grapevines. The functional complexity of the transcriptome of H. vitripennis h...

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Autores principales: Nandety, Raja Sekhar, Kamita, Shizuo G., Hammock, Bruce D., Falk, Bryce W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858241/
https://www.ncbi.nlm.nih.gov/pubmed/24339955
http://dx.doi.org/10.1371/journal.pone.0081681
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author Nandety, Raja Sekhar
Kamita, Shizuo G.
Hammock, Bruce D.
Falk, Bryce W.
author_facet Nandety, Raja Sekhar
Kamita, Shizuo G.
Hammock, Bruce D.
Falk, Bryce W.
author_sort Nandety, Raja Sekhar
collection PubMed
description BACKGROUND: The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce’s disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference. RESULTS: Here we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1(−5)) with known proteins. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences) from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements. CONCLUSIONS: Our data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that govern H. vitripennis, but may also lead to the identification of novel targets for biorationally designed control strategies.
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spelling pubmed-38582412013-12-11 Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis) Nandety, Raja Sekhar Kamita, Shizuo G. Hammock, Bruce D. Falk, Bryce W. PLoS One Research Article BACKGROUND: The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce’s disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference. RESULTS: Here we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1(−5)) with known proteins. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences) from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements. CONCLUSIONS: Our data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that govern H. vitripennis, but may also lead to the identification of novel targets for biorationally designed control strategies. Public Library of Science 2013-12-10 /pmc/articles/PMC3858241/ /pubmed/24339955 http://dx.doi.org/10.1371/journal.pone.0081681 Text en © 2013 Nandety et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Nandety, Raja Sekhar
Kamita, Shizuo G.
Hammock, Bruce D.
Falk, Bryce W.
Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)
title Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)
title_full Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)
title_fullStr Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)
title_full_unstemmed Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)
title_short Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)
title_sort sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (homalodisca vitripennis)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858241/
https://www.ncbi.nlm.nih.gov/pubmed/24339955
http://dx.doi.org/10.1371/journal.pone.0081681
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