Mining and characterizing microsatellites from citrus ESTs

Abstract

Freely available computer programs were arranged in a pipeline to extract microsatellites from public citrus EST sequences, retrieved from the NCBI. In total, 3,278 bi- to hexa-type SSR-containing sequences were identified from 56,199 citrus ESTs. On an average, one SSR was found per 5.2 kb of EST sequence, with the tri-nucleotide motifs as the most abundant. Primer sequences flanking SSR motifs were successfully identified from 2,295 citrus ESTs. Among those, a subset (100 pairs) were synthesized and tested to determine polymorphism and heterozygosity between/within two genera, sweet orange (C. sinensis) and Poncirus (P. trifoliata), which are the parents of the citrus core mapping population selected for an international citrus genomics effort. Eighty-seven pairs of primers gave PCR amplification to the anticipated SSRs, of which 52 and 35 appear to be homozygous and heterozygous, respectively, in sweet orange, and 67 and 20, respectively, in Poncirus. By pairing the loci between the two intergeneric species, it was found that 40 are heterozygous in at least one species with two alleles (9), three alleles (28), or four alleles (3), and the remaining 47 are homozygous in both species with either one allele (31) or two alleles (16). These EST-derived SSRs can be a resource used for understanding of the citrus SSR distribution and frequency, and development of citrus EST-SSR genetic and physical maps. These SSR primer sequences are available upon request.

Identification and validation of novel EST-SSR markers in olives

“…In olive transcriptome data, the most abundant dinucleotide SSR motif was GA/TC, while the motif GAA/TTC was the most common among trinucleotide SSRs, which support findings of Adawy et al (2015). Furthermore, similar results have also been obtained in studies on citrus fruits (Chen et al, 2006), grapes (Huang et al, 2011), and mangos (Dillon et al, 2014).…”

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

“…Dinucleotides are the dominant type of microsatellite repeats in most aquaculture species characterized so far, although trinucleotide repeats are most abundant in plants (Chen et al, 2006;Kantety et al, 2002). Of the dinucleotides, CA repeat is the most abundant in common carp (Fig.…”

“…As a byproduct of EST projects in many organisms in which a vast amount of sequence data were Aquaculture 271 (2007) 558 -574 www.elsevier.com/locate/aqua-online generated, microsatellite-mining from SSR-containing ESTs is inexpensive and time-saving, and has proved to be an effective approach to develop microsatellies for genetic mapping and population genetics in animals (Serapion et al, 2004;Yue et al, 2004;Wang et al, 2005;Chen et al, 2005;Pérez et al, 2005;Maneeruttanarungroj et al, 2006) and plants (Cordeiro et al, 2001;Kantety et al, 2002;Chen et al, 2006). In aquaculture animals, Serapion et al (2004) reported a pioneer study on the development of EST-SSRs by bioinformatic mining from the channel catfish (Ictalurus punctatus) databases.…”

Development of Microsatellite Markers by Data Mining from DNA Sequences

“…These processes are necessary for many organisms but normally time-consuming and laborintensive. Mining SSR from public databases has been streamlined with technological advance and protocol optimization to make the process cheaper, more efficient and more successful, and has proved to be an effective approach to develop microsatellies for genetic map and population genetics studies in animals (Serapion et al, 2004;Yue et al, 2004;Wang et al, 2005;Chen et al, 2005;Pérez et al, 2005;Maneeruttanarungroj et al, 2006) and plants (Cordeiro et al, 2001;Kantety et al, 2002;Chen et al, 2006). Here, we demonstrate how to mine SSRs from common carp EST data step by step.…”