SSR data mined from expressed sequence tags of phytoparasitic nematodes

Abstract

SummarySSR markers have become the most popular resource for studying population genetic variation in eukaryotes. However, few studies with SSR markers have been carried out with phytoparasitic nematodes. In this study a primary survey on EST-SSRs was made utilizing bioinformatics methods to derive SSRs from expressed sequence tags (ESTs) of 16 species of PPN, which belong to 7 genera and 5 families. The results showed that trinucleotide repeats were the most abundant SSRs in coding ESTs, while tetranucleotide SSRs were predominant in non-coding ESTs and genome sequences. AG/CT, AAC/GTT and (AAAN) n motifs were predominant, and CG/GC, ACT/AGT motifs were scanty in the ESTs of most genera and species. SSRs were more abundant in non-coding ESTs than in coding ESTs. The distribution frequencies of SSR motifs in coding ESTs, non-coding ESTs and genomes are different. Our results will provide useful information for screening SSRs from each genus and species for further genetic study of phytoparastic nematodes.Keywords: microsatellites; expressed sequence tags; plantparasitic nematodes IntroductionPhytoparasitic nematodes (PPN) are an important group in Nematoda. Among the 20,000 species of nematodes described so far, about 3000 are parasites of plants (Castagnone-Sereno, 2002). Many of them are important plant pathogens such as root-knot, cyst, and lesion nematodes. Infestations of these nematodes pose a significant agronomic problem, causing yield losses in many important agronomical plants. PPN may cause US $77 billion of damage or more worldwide each year (Lambert & Bekal, 2002). Genetic studies can help to understand differences in pathogenicity and the changes that may occur in nematode populations within fields to overcome plant resis-…….tance. Simple sequence repeats (SSRs, also called microsatellites) are effective molecular markers for population genetic study, and are distributed extensively in both coding and non-coding sequences of eukaryotic genomes (Tautz & Renz, 1984). Because SSRs are highly polymorphic, easy to detect (by PCR), specific, and exhibit codominant transmission (Powell et al., 1996), they are widely used in studies of population genetics (Perera et al., 2000;Viard et al., 2001), molecular environmental genetics (Schwartz et al., 2003;Williams et al., 2003), and molecular adaptation (Saint-Laurent et al., 2003;Storz, 2002). But there have been relatively few studies on SSRs in nematodes. The most detailed information comes from studies in the freeliving nematode Caenorhabditis elegans (Haber et al., 2005) and a few animal parasitic nematodes (Criscione et al., 2007;Fisher &Viney, 1996;Grillo et al., 2006;Johnson et al., 2006;Otsen et al., 2000). Only a few PPN SSRs have been developed (De Luca et al., 2002;He et al., 2003;Plantard & Porte, 2003;Thiery & Mugniery, 2000;Zhou et al., 2007). The rapidly expanding databases of ESTs (expressed sequence tags) provide available data for developing SSRs. Mining SSRs from ESTs through bioinformatic methods is an effective and rapid approach, and cou...

Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

“…The vast majority (>99%) of them are trinucleotide repeats. This result confirms a recent report indicating that trinucleotide repeats were the most abundant microsatellites in coding ESTs from 16 species of plant-parasitic nematodes belonging to seven genera, including Meloidogyne [27]. Moreover, in agreement with these authors, we found that (AAC) n repeats were the most abundant in M. incognita CDS, while (ATG) n or (TTA) n , that could act as start or stop codon, respectively, were not detected.…”

“…Such a distribution bias in favour of trinucleotides has been reported for some other eukaryotes, e.g., the fungus Neurospora crassa [ 25 ] or the insect Tribolium castaneum [ 26 ]. Also, a recent data-mining analysis of ESTs from phytoparasitic nematodes, including some RKN species, showed that trinucleotide repeats were the most abundant microsatellites in coding ESTs [ 27 ].…”

Isolation of microsatellites from an enriched genomic library of the plant-parasitic nematode Meloidogyne incognita and their detection in other root-knot nematode species

“…in M. artiellia, a species assumed to reproduce by both amphimix and facultative meiotic parthenogenesis (De Luca et al 2002). Recently, simple sequence repeats were identified by a bioinformatic data-mining analysis in ESTs from phytoparasitic nematodes, including some root-knot nematode species, but no information was provided about regions flanking these loci (Huang et al 2010). Here, we evaluate the feasability of microsatellite isolation by screening an enriched genomic library from M. incognita, and report the subsequent characterization of 15 microsatellite loci in this nematode.…”