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Characterization of New Schistosoma mansoni  Microsatellite Loci in Sequences Obtained from Public DNA Databases and Microsatellite Enriched Genomic Libraries
NB Rodrigues; PT LoVerde; AJ Romanha & G Oliveira
Abstract
In the last decade microsatellites have become one of the
most useful genetic markers used in a large number of organisms due to their
abundance and high level of polymorphism. Microsatellites have been used
for individual identification, paternity tests, forensic studies and population
genetics. Data on microsatellite abundance comes preferentially from microsatellite
enriched libraries and DNA sequence databases. We have conducted a search
in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences.
In addition, we obtained 300 sequences from CA and AT microsatellite enriched
genomic libraries. The sequences were searched for simple repeats using
the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences
that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds).
Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs
per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining
ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%)
contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds).
The 1,598 BAC end sequences 80 were grouped into 17 clusters containing
3 to 17 BAC end sequences per cluster. Microsatellites were present in 67
out of 300 sequences from microsatellite enriched libraries (55 perfect,
38 imperfect and 15 compounds). From all of the observed loci 55 were selected
for having the longest perfect repeats and flanking regions that allowed
the design of primers for PCR amplification. Additionally we describe two
new polymorphic microsatellite loci.
Keywords
Schistosoma mansoni - microsatellite repeats - polymorphism - DNA sequence analysis - nucleic acid database - computational biology
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