Abstract
Microsatellites have been widely utilized for molecular marker development. Codominant and multiallelic nature of these simple repeats have several advantages over other types of molecular markers. Their broad applicability in the area of molecular biology like gene mapping, genome characterization, genome evolution, and gene regulation has been reported in various crop plants, animals and fungi. Considering these benefits of the SSR markers, a MMDB (Magnaporthe oryzae Microsatellite Database) was developed to help in understanding about the pathogen and its diversity at strains level of a particular geographic region, which can help us to make a proper utilization of blast resistance genes in the region. This microsatellite database is based on whole genome sequence of two M. oryzae isolates, RML-29 (2665 SSRs from 43037792 bp) and RP-2421 (3169 SSRs from 45510614 bp). Although, first M. oryzae genome (70-15) was sequenced in 2005, but this sequenced isolate is not a true field isolate of M. oryzae. Therefore, MMDB has great potential in the study of diversification and characterization of M. oryzae and other related fungi.Availability: http://14.139.229.199/home.aspx
Highlights
Methodology of database development: A database of simple sequence repeats (SSRs) markers identified in the M. oryzae genomes was developed and named as MMDB (Magnaporthe oryzae Microsatellite Database).The database was constructed with the help of Microsoft Visual Studio 2013 for designing web pages, which were programmed through ASP.NET framework 4.0 using C# programming language
Genomes of two M. oryzae isolates were sequenced by using Illumina HiSeq-100 and Roche 454 platforms
We found about 3-4 Mb sized contigs in both the genomes after assembly which did not match with the reference genome
Summary
Rice blast disease caused by a fungal pathogen Magnaporthe oryzae, which results up to 90% crop yield loss during severe epidemics [1]. Microsatellite or simple sequence repeat markers are stretches of DNA in which the same short nucleotide sequence is tandemly repeated within the genome [2]. SSR is generally a 1-6 nucleotide sequence variations present across the eukaryotic genome [3,4,5].
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