Frequency and distribution of microsatellites from ESTs of citrus

Abstract

Nearly 65,000 citrus EST (Expressed Sequence Tags) have been investigated using the CitEST project database. Microsatellites were investigated in the unigene sequences from Citrus spp. and Poncirus trifoliata. From these sequences, approximately 35% of the non-redundant ESTs contained SSRs. The frequencies of different SSR motifs were similar between Citrus spp and trifoliate orange. In general, mononucleotide repeats appeared to be the most abundant SSRs in the CitEST database, but we also identify di-, tri-, tetra-, penta-and hexanucleotide repeats. The AG/CT and AAG/CTT were the most common dinucleotide and trinucleotide motifs, with frequencies of 54.4% and 25.2%, respectively. Primer sequences flanking SSR motifs were successfully designed and synthesized. After in silico polymorphism analysis, a subset of sixty-eight primers was validated in different Citrus spp. and Poncirus trifoliata. PCR-amplification revealed polymorphism in citrus with all tested primer pairs and showed the potential of these markers for linkage mapping. Our study showed that the CitEST database can be exploited for the development of SSR markers that can amplify Citrus spp. and related genus for comparative mapping and other genetic analyses.

Transcriptome analysis of potential simple sequence repeat markers in Ammopiptanthus mongolicus

“…Based on the results of the GO functional analysis, the majority of transcripts were assigned "cell" in the cellular component category, involved in "binding" in the molecular function category, and involved in "metabolic activity" in the biological process in A. mongolicus. Similar results were reported in date palm (Zhao et al, 2012) and citrus (Palmieri et al, 2007).…”

In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

“…SSRs were analyzed for type, abundance, and distribution (genic and intergenic regions). A total of 1,567 SSRs were identified, with an average frequency of 1.26 SSR per kb, which is a low EV Tambarussi et al frequency compared to the rice chloroplasts (6.5 SSR per kb) (Rajendrakumar et al 2007) and is higher when compared with Eucalyptus ESTs (0.37 SSR per kb) (Ceresini et al 2005) and Citrus ESTs (0.5 SSR per kb) (Palmieri et al 2007). This was expected since the occurrence of particular microsatellite motifs and repeats (especially the non-trimeric ones) could have implications on how the gene coding region is transcribed, due to risks of frameshift mutations (Metzgar et al 2000).…”

Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

“…From a total of 1,785,569 bp that represents these plastomes, we identified 2427 cpSSRs, with an average frequency of 1.36 cpSSR per kb, which is higher than that of Eucalyptus ESTs (expressed sequence tags) (0.37 SSR per kb) (Ceresini et al, 2005) and Citrus ESTs (0.5 SSR per kb) (Palmieri et al, 2007). This was expected since the occurrence of particular microsatellite motifs and repeats (especially the non-trimeric ones) could have implications on how the gene coding region is transcribed due to risks of frameshift mutations (Metzgar et al, 2000).…”