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De novo-based transcriptome profiling of male-sterile and fertile watermelon lines

The whole-genome sequence of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), a valuable horticultural crop worldwide, was released in 2013. Here, we compared a de novo-based approach (DBA) to a reference-based approach (RBA) using RNA-seq data, to aid in efforts to improve the annotatio...

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Autores principales: Rhee, Sun-Ju, Kwon, Taehyung, Seo, Minseok, Jang, Yoon Jeong, Sim, Tae Yong, Cho, Seoae, Han, Sang-Wook, Lee, Gung Pyo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5667795/
https://www.ncbi.nlm.nih.gov/pubmed/29095876
http://dx.doi.org/10.1371/journal.pone.0187147
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author Rhee, Sun-Ju
Kwon, Taehyung
Seo, Minseok
Jang, Yoon Jeong
Sim, Tae Yong
Cho, Seoae
Han, Sang-Wook
Lee, Gung Pyo
author_facet Rhee, Sun-Ju
Kwon, Taehyung
Seo, Minseok
Jang, Yoon Jeong
Sim, Tae Yong
Cho, Seoae
Han, Sang-Wook
Lee, Gung Pyo
author_sort Rhee, Sun-Ju
collection PubMed
description The whole-genome sequence of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), a valuable horticultural crop worldwide, was released in 2013. Here, we compared a de novo-based approach (DBA) to a reference-based approach (RBA) using RNA-seq data, to aid in efforts to improve the annotation of the watermelon reference genome and to obtain biological insight into male-sterility in watermelon. We applied these techniques to available data from two watermelon lines: the male-sterile line DAH3615-MS and the male-fertile line DAH3615. Using DBA, we newly annotated 855 watermelon transcripts, and found gene functional clusters predicted to be related to stimulus responses, nucleic acid binding, transmembrane transport, homeostasis, and Golgi/vesicles. Among the DBA-annotated transcripts, 138 de novo-exclusive differentially-expressed genes (DEDEGs) related to male sterility were detected. Out of 33 randomly selected newly annotated transcripts and DEDEGs, 32 were validated by RT-qPCR. This study demonstrates the usefulness and reliability of the de novo transcriptome assembly in watermelon, and provides new insights for researchers exploring transcriptional blueprints with regard to the male sterility.
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spelling pubmed-56677952017-11-17 De novo-based transcriptome profiling of male-sterile and fertile watermelon lines Rhee, Sun-Ju Kwon, Taehyung Seo, Minseok Jang, Yoon Jeong Sim, Tae Yong Cho, Seoae Han, Sang-Wook Lee, Gung Pyo PLoS One Research Article The whole-genome sequence of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), a valuable horticultural crop worldwide, was released in 2013. Here, we compared a de novo-based approach (DBA) to a reference-based approach (RBA) using RNA-seq data, to aid in efforts to improve the annotation of the watermelon reference genome and to obtain biological insight into male-sterility in watermelon. We applied these techniques to available data from two watermelon lines: the male-sterile line DAH3615-MS and the male-fertile line DAH3615. Using DBA, we newly annotated 855 watermelon transcripts, and found gene functional clusters predicted to be related to stimulus responses, nucleic acid binding, transmembrane transport, homeostasis, and Golgi/vesicles. Among the DBA-annotated transcripts, 138 de novo-exclusive differentially-expressed genes (DEDEGs) related to male sterility were detected. Out of 33 randomly selected newly annotated transcripts and DEDEGs, 32 were validated by RT-qPCR. This study demonstrates the usefulness and reliability of the de novo transcriptome assembly in watermelon, and provides new insights for researchers exploring transcriptional blueprints with regard to the male sterility. Public Library of Science 2017-11-02 /pmc/articles/PMC5667795/ /pubmed/29095876 http://dx.doi.org/10.1371/journal.pone.0187147 Text en © 2017 Rhee 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 (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Rhee, Sun-Ju
Kwon, Taehyung
Seo, Minseok
Jang, Yoon Jeong
Sim, Tae Yong
Cho, Seoae
Han, Sang-Wook
Lee, Gung Pyo
De novo-based transcriptome profiling of male-sterile and fertile watermelon lines
title De novo-based transcriptome profiling of male-sterile and fertile watermelon lines
title_full De novo-based transcriptome profiling of male-sterile and fertile watermelon lines
title_fullStr De novo-based transcriptome profiling of male-sterile and fertile watermelon lines
title_full_unstemmed De novo-based transcriptome profiling of male-sterile and fertile watermelon lines
title_short De novo-based transcriptome profiling of male-sterile and fertile watermelon lines
title_sort de novo-based transcriptome profiling of male-sterile and fertile watermelon lines
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5667795/
https://www.ncbi.nlm.nih.gov/pubmed/29095876
http://dx.doi.org/10.1371/journal.pone.0187147
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