Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

摘要: Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Tags (ESTs) have been as SSR source plants of economic relevance application to non-model species still modest. Here, we explored the use publicly ESTs (GenBank at National Center Biotechnology Information-NCBI) plants, focusing on genera listed International Union Conservation Nature (IUCN). We also search two model with fully annotated genomes EST-SSRs, Arabidopsis Oryza, them controls genome distribution analyses. Overall, downloaded 16 031 555 sequences 258 plant which were mined SSRsand primers help QDD1. Genome analyses Oryza done blasting against sativa thaliana reference implemented Basal Local Alignment Tool (BLAST) NCBI website. Finally, performed empirical test determine performance our EST-SSRs a few individuals from four eudicot genera, Trifolium Centaurea. total 14 498 726 EST dbEST database (NCBI) 257 IUCN Red List. identify very large number (17 102) ready-to-test most (193) no cost. dinucleotide trinucleotide repeats prevalent types abundance various repeat differed between taxonomic groups. Control revealed that mostly located coding regions while largely associated untranslated regions. Our results considerable amplification success transferability congenerics. present work represents first large-scale study developing utilizing accessible databases threatened plants. Here provide EST-SSR 193 genera. cross-species suggests possible target would be large. Since abundant mainly linked exons they might useful evolutionary conservation studies. Altogether, highly supports extremely affordable fast