Microsatellite markers derived from bay scallop Argopecten irradians expressed sequence tags

Abstract

When data mining was performed on the National Center for Biotechnology Information database, a total of 2038 sequences from five different expressed sequence tag libraries were registered. Eighty sequences (3.9%) were found to contain 91 microsatellites. Clustering analysis indicated that 23 sequences of these expressed sequence tags fell into five clusters and that the remaining 57 sequences were independent. The di-and tri-nucleotide repeat motifs accounted for approximately 62.1% of the total microsatellites. The most abundant dinucleotide microsatellite was TA, followed by GA and CA, and the trinucleotide microsatellites GAT and GGT showed a high abundance. Nineteen sequences representing di-, tri-, tetra-and penta-nucleotides motifs were chosen for the design of polymerase chain reaction (PCR) primers. Of primer pairs, 16 successfully amplified scorable PCR products and 11 revealed polymorphism, with the average polymorphic information content value of 0.5082 and 3.1 alleles per locus. A transferability analysis on three other related scallop species, Chlamys farreri, Chlamys nobilis and Patinopecten yessoenssis, showed that only 1 of 16 primer pairs could amplify PCR products with the expected size in Chlamys nobilis.

Isolation and characterization of 12 microsatellite loci in the Peruvian scallop Argopecten purpuratus and cross-species amplification in other scallop species (family Pectinidae)

“…No successful amplification was detected in P. albicans samples. Poor microsatellite transferability among related species has also been observed in previous studies in marine bivalves (Zhan et al 2005;Hedgecock et al 2004). …”

Development of novel EST-SSR markers in common carp by data mining from public EST sequences

“…black tiger shrimp (Penaeus monodon) (13.7%, Maneeruttanarungroj et al, 2006), Japanese pufferfish (Fugu rubripes) (11.5%, Edwards et al, 1998) and channel catfish (11.2%, Serapion et al, 2004), but higher than those in some other species e.g. Chinese shrimp (Fenneropenaeus chinensis) (2.2%, Wang et al, 2005), bay scallop (Argopecten irradians) (3.9%, Zhan et al, 2005), and red sea bream (Chrysophrys major) (4%, Chen et al, 2005). The abundance of EST-derived microsatellites seems to be highly species-specific in aquacultured animals studied.…”

“…Since Serapion et al (2004) first demonstrated the development of Type I marker (EST-SSRs) in an aquaculture species by using bioinformatic analysis, mining EST-SSRs from EST databases have been reported in several other aquaculture animals including fish (Yue et al, 2004;Rexroad et al, 2005;Chen et al, 2005), shrimp Pérez et al, 2005;Maneeruttanarungroj et al, 2006) and scallop (Zhan et al, 2005). Online resources of EST sequences have been increasingly accumulated in fish.…”

Isolation and characterization of 48 polymorphic microsatellite markers for the blood clam Scapharca broughtonii (Arcidae)

“…Molecular markers, especially microsatellites, are effective markers that have been widely applied to the development of marker-assisted breeding technology and conservation of this species, because of the high degree of polymorphism, abundance, neutrality, and codominant inheritance (Zhan et al, 2005;Schwartz et al, 2007). Therefore, the development of new polymorphic microsatellite markers opens new perspectives for population genetics (Chen et al, 2005).…”