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De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on...

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Autores principales: Kim, Hyun A, Shin, Ah-Young, Lee, Min-Seon, Lee, Hee-Jeong, Lee, Heung-Ryul, Ahn, Jongmoon, Nahm, Seokhyeon, Jo, Sung-Hwan, Park, Jeong Mee, Kwon, Suk-Yoon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Korean Society for Molecular and Cellular Biology 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757802/
https://www.ncbi.nlm.nih.gov/pubmed/26743902
http://dx.doi.org/10.14348/molcells.2016.2264
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author Kim, Hyun A
Shin, Ah-Young
Lee, Min-Seon
Lee, Hee-Jeong
Lee, Heung-Ryul
Ahn, Jongmoon
Nahm, Seokhyeon
Jo, Sung-Hwan
Park, Jeong Mee
Kwon, Suk-Yoon
author_facet Kim, Hyun A
Shin, Ah-Young
Lee, Min-Seon
Lee, Hee-Jeong
Lee, Heung-Ryul
Ahn, Jongmoon
Nahm, Seokhyeon
Jo, Sung-Hwan
Park, Jeong Mee
Kwon, Suk-Yoon
author_sort Kim, Hyun A
collection PubMed
description Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.
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spelling pubmed-47578022016-03-03 De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa Kim, Hyun A Shin, Ah-Young Lee, Min-Seon Lee, Hee-Jeong Lee, Heung-Ryul Ahn, Jongmoon Nahm, Seokhyeon Jo, Sung-Hwan Park, Jeong Mee Kwon, Suk-Yoon Mol Cells Article Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family. Korean Society for Molecular and Cellular Biology 2016-02-29 2016-01-07 /pmc/articles/PMC4757802/ /pubmed/26743902 http://dx.doi.org/10.14348/molcells.2016.2264 Text en © The Korean Society for Molecular and Cellular Biology. All rights reserved. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/
spellingShingle Article
Kim, Hyun A
Shin, Ah-Young
Lee, Min-Seon
Lee, Hee-Jeong
Lee, Heung-Ryul
Ahn, Jongmoon
Nahm, Seokhyeon
Jo, Sung-Hwan
Park, Jeong Mee
Kwon, Suk-Yoon
De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa
title De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa
title_full De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa
title_fullStr De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa
title_full_unstemmed De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa
title_short De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa
title_sort de novo transcriptome analysis of cucumis melo l. var. makuwa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757802/
https://www.ncbi.nlm.nih.gov/pubmed/26743902
http://dx.doi.org/10.14348/molcells.2016.2264
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