Abstract
BackgroundMicrosatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms.ResultsUsing MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus) ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (AT)n, (AG)n and (CT)n were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AAT)n and (ATT)n being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms.ConclusionsContrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of two closely related Meloidogyne species. 2,245 di- to hexanucleotide loci were identified in the genome of M. incognita, providing adequate material for the future development of a wide range of microsatellite markers in this major plant parasite.
Highlights
Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes
The first one comprised the two root-knot nematode (RKN) species, M. incognita and M. hapla, which shared the lowest abundance of microsatellite loci
The variability of microsatellite number found in nematode genomes was well explained by genome size for M. incognita, M. hapla, C. elegans and P. pacificus (r2 = 0.95, F1,2 = 37.5, p = 0.03), but not when B. malayi was included (r2 = 0.10, F1,3 = 0.34, p = 0.6) (Table 1)
Summary
Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. The most conventional procedure for the isolation of microsatellite markers, i.e., enrichment of genomic DNA for microsatellite motifs cloning, screening of the resulting library and sequencing of the positive clones [4], is challenging, time-consuming and costly. There have been relatively few studies of microsatellites isolated by conventional molecular biology approaches in this phylum compared to other eukaryotes, e.g. insects or vertebrates. Such unpopularity of microsatellites as genetic markers in nematodes was attributed in part to the unusually high proportion of loci that fail to produce interpretable PCR patterns, possibly as the result of interlocus flanking sequence similarity [9]. Like in other nematodes, microsatellites, which are usually regarded as among the most appropriate tools to study variation at the individual level, have been very poorly investigated in this taxon
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