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De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)

BACKGROUND: Wax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases. METHODOLOGY/PRINCIPAL FINDINGS: In this study,...

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Detalles Bibliográficos
Autores principales: Jiang, Biao, Xie, Dasen, Liu, Wenrui, Peng, Qingwu, He, Xiaoming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738631/
https://www.ncbi.nlm.nih.gov/pubmed/23951078
http://dx.doi.org/10.1371/journal.pone.0071054
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author Jiang, Biao
Xie, Dasen
Liu, Wenrui
Peng, Qingwu
He, Xiaoming
author_facet Jiang, Biao
Xie, Dasen
Liu, Wenrui
Peng, Qingwu
He, Xiaoming
author_sort Jiang, Biao
collection PubMed
description BACKGROUND: Wax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we examined transcriptome in wax gourd. More than 44 million of high quality reads were generated from five different tissues of wax gourd using Illumina paired-end sequencing technology. Approximately 4 Gbp data were generated, and de novo assembled into 65,059 unigenes, with an N50 of 1,132 bp. Based on sequence similarity search with known protein database, 36,070 (55.4%) showed significant similarity to known proteins in Nr database, and 24,969 (38.4%) had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 14,994 of wax gourd unigenes were assigned to GO term annotation, and 23,977 were found to have COG classifications. In addition, a total of 18,713 unigenes were assigned to 281 KEGG pathways. Furthermore, 6,242 microsatellites (simple sequence repeats) were detected as potential molecular markers in wax gourd. Two hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism. The result showed that 170 of the 200 primer pairs were successfully amplified and 49 (28.8%) of them exhibited polymorphisms. CONCLUSION/SIGNIFICANCE: Our study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop.
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spelling pubmed-37386312013-08-15 De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida) Jiang, Biao Xie, Dasen Liu, Wenrui Peng, Qingwu He, Xiaoming PLoS One Research Article BACKGROUND: Wax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we examined transcriptome in wax gourd. More than 44 million of high quality reads were generated from five different tissues of wax gourd using Illumina paired-end sequencing technology. Approximately 4 Gbp data were generated, and de novo assembled into 65,059 unigenes, with an N50 of 1,132 bp. Based on sequence similarity search with known protein database, 36,070 (55.4%) showed significant similarity to known proteins in Nr database, and 24,969 (38.4%) had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 14,994 of wax gourd unigenes were assigned to GO term annotation, and 23,977 were found to have COG classifications. In addition, a total of 18,713 unigenes were assigned to 281 KEGG pathways. Furthermore, 6,242 microsatellites (simple sequence repeats) were detected as potential molecular markers in wax gourd. Two hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism. The result showed that 170 of the 200 primer pairs were successfully amplified and 49 (28.8%) of them exhibited polymorphisms. CONCLUSION/SIGNIFICANCE: Our study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop. Public Library of Science 2013-08-08 /pmc/articles/PMC3738631/ /pubmed/23951078 http://dx.doi.org/10.1371/journal.pone.0071054 Text en © 2013 Jiang 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
Jiang, Biao
Xie, Dasen
Liu, Wenrui
Peng, Qingwu
He, Xiaoming
De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)
title De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)
title_full De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)
title_fullStr De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)
title_full_unstemmed De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)
title_short De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)
title_sort de novo assembly and characterization of the transcriptome, and development of ssr markers in wax gourd (benicasa hispida)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738631/
https://www.ncbi.nlm.nih.gov/pubmed/23951078
http://dx.doi.org/10.1371/journal.pone.0071054
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