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CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.

- PLoS ONE (2015)

Bottom Line: Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family.We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family.CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

View Article: PubMed Central - PubMed

Affiliation: National Bureau of Plant Genetic Resources, Genomics resources div., New Delhi-12, India.

ABSTRACT
Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

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Database processing pipeline.
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pone.0118630.g001: Database processing pipeline.

Mentions: The draft of whole genome sequences of Cucumis melo L. [34] was downloaded in FASTA format from the melonomics website [35] and fed to Micro Satellite (MISA) identification tool [36] to identify the microsatellite markers with the following search criteria: 6 repeat units used for dinucleotide repeats (DNRs), 5 repeat units used for rest all nucleotides including trinucleotide repeats (TNRs), tetranucleotide repeats (TeNRs), pentanucleotide repeats (PNRs) and hexanucleotide repeats (HNRs). The primer pairs were designed from either side of flanking regions of the identified microsatellite markers using integrated Perl 5 interface module of MISA-Primer3 software [36]. The identified microsatellite markers were mapped by using BLAST software [37] with default E-value onto the melon's chromosomes. The flanking sequences of microsatellite markers of melon were then submitted to BLAST [37] against genome sequences of cucumber and watermelon to study the marker-assisted syntenic relationships among the chromosomes of C. melo, cucumber and watermelon. A cutoff E-value of 1e-05 was considered significant for the BLAST analysis. Finally, the identified microsatellites with their corresponding primer pairs and the syntenic information were stored in MySQL database [38]. Fig 1 represents the entire processing pipeline of CmMDb.


CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.

- PLoS ONE (2015)

Database processing pipeline.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401682&req=5

pone.0118630.g001: Database processing pipeline.
Mentions: The draft of whole genome sequences of Cucumis melo L. [34] was downloaded in FASTA format from the melonomics website [35] and fed to Micro Satellite (MISA) identification tool [36] to identify the microsatellite markers with the following search criteria: 6 repeat units used for dinucleotide repeats (DNRs), 5 repeat units used for rest all nucleotides including trinucleotide repeats (TNRs), tetranucleotide repeats (TeNRs), pentanucleotide repeats (PNRs) and hexanucleotide repeats (HNRs). The primer pairs were designed from either side of flanking regions of the identified microsatellite markers using integrated Perl 5 interface module of MISA-Primer3 software [36]. The identified microsatellite markers were mapped by using BLAST software [37] with default E-value onto the melon's chromosomes. The flanking sequences of microsatellite markers of melon were then submitted to BLAST [37] against genome sequences of cucumber and watermelon to study the marker-assisted syntenic relationships among the chromosomes of C. melo, cucumber and watermelon. A cutoff E-value of 1e-05 was considered significant for the BLAST analysis. Finally, the identified microsatellites with their corresponding primer pairs and the syntenic information were stored in MySQL database [38]. Fig 1 represents the entire processing pipeline of CmMDb.

Bottom Line: Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family.We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family.CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

View Article: PubMed Central - PubMed

Affiliation: National Bureau of Plant Genetic Resources, Genomics resources div., New Delhi-12, India.

ABSTRACT
Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

Show MeSH