Affiliations: Molecular Biosciences Research Group, Department of
Chemistry and Biochemistry, Texas State University, 601 University Drive, San
Marcos, TX 78666, USA
Abstract: Teleost fish genome projects involving model species are resulting
in a rapid accumulation of genomic and expressed DNA sequences in public
databases. The expressed sequence tags (ESTs) collected in the databases can be
mined for the analysis of both structural and functional genomics. In this
study, we in silico analyzed 49,430 unigenes representing a total of
692,654 ESTs from four model fish for their potential use in developing simple
sequence repeats (SSRs), or microsatellites. After bioinformatical mining, a
total of 3,018 EST derived SSRs (EST-SSRs) were identified for 2,335 SSR
containing ESTs (SSR-ESTs). The frequency of identified SSR-ESTs ranged from
1.5% for Xiphophorus to 7.3% for zebrafish. The dinucleotide repeat
motif is the most abundant SSR, accounting for 47%, 52%, 64%, and 78% for
medaka, Fundulus, zebrafish, and Xiphophorus, respectively.
Simulation analysis suggests that a majority of these EST-SSRs have sufficient
flanking sequences for polymerase chain reaction (PCR) primer design.
Comparative DNA sequence analyses of SSR-ESTs identified several cross-species
SSRs and sequences that may be used as cross-reference genes in comparative
studies. For example, the flanking sequences of one SSR (CTG)n within the
pituitary tumor-transforming gene (PTTG) 1 interacting protein (PTTGIP), showed
conservation spanning the medaka, Fundulus, human, and mouse genomes.
This study provides a large body of information on EST-SSRs that can be useful
for the development of polymorphic markers, gene mapping, and comparative
genome analysis. Functional analysis of these SSR-ESTs may reveal their role in
metabolism and gene evolution of these model species.
Keywords: Model fish, comparative genomics, in silico analysis, PTTGIP, EST, microsatellites, SSR
