title: Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs).
abstract: BACKGROUND
  Phlebotomus 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.
  
  
  RESULTS
  Simple 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 (AX)n repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Biological Sciences, Faculty of Science and Technology, Al-Quds University, PO Box 51000, Jerusalem, Palestine. ohamarsheh@science.alquds.edu
authors.forename: Omar
authors.initials: O
authors.lastname: Hamarsheh
authors.forename: Ahmad
authors.initials: A
authors.lastname: Amro
mesh_terms: D000818:Animals; D017931:DNA Primers / Q000235:genetics; D020224:Expressed Sequence Tags; D049750:Genome, Insect; D007303:Insect Vectors / Q000235:genetics*; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010691:Phlebotomus / Q000235:genetics*
chemical_list: D017931:DNA Primers