Characterization of simple sequence repeats SSRs from Phlebotomus papatasi Diptera: Psychodidae expressed sequence tags ESTsReportar como inadecuado




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Parasites and Vectors

, 4:189

First Online: 29 September 2011Received: 01 September 2011Accepted: 29 September 2011

Abstract

BackgroundPhlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats SSRs, or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers.

ResultsSimple sequence repeats SSRs were characterized in P. papatasi expressed sequence tags ESTs derived from a public database, National Center for Biotechnology Information NCBI. A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of AXn repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation.

ConclusionThe first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-3305-4-189 contains supplementary material, which is available to authorized users.

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Autor: Omar Hamarsheh - Ahmad Amro

Fuente: https://link.springer.com/







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