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

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.

Genome-wide distribution and organization of microsatellites in six species of birds

“…Some studies also revealed that trinucleotide repeats were predominant in most insect genomes (Castagnone-Sereno et al, 2010;Wang et al, 2008). However, tetranucleotides in contrast to dinucleotides, appeared significantly overrepresented in G. gallus, M. gallopavo, G. Fortis, and C. livia.…”

“…Such a propensity may be to suppress the other categories of SSRs, thus reducing the incidence of frameshift mutations in coding regions caused by nontriplet repeats (Metzgar et al, 2000;Labbe et al, 2011). What's more, microsatellites which are located in coding regions may affect evolution of protein structure and function in this species (Castagnone-Sereno et al, 2010). Our study of SSRs in G. gallus and five other bird species genomes is a significant step towards a better understanding of the nature of these important sequences.…”

“…Study on the distribution of microsatellites will both describe the basic patterns of microsatellite distribution and diversity across whole genomes and began to address fundamental aspects of their evolution in a comparative setting (Pannebakker et al, 2010). Recent studies have focussed on the genome-wide distribution of SSRs in different species (Subramanian et al, 2003;Castagnone-Sereno et al, 2010;Hickner et al, 2010). A better insight into the occurrence of microsatellites in a range of taxa may help to understand the evolution of simple repeats.…”

“…What's more, the most conventional procedure for SSR isolation (i.e., constructing SSR-enriched libraries, screening of the resulting library, and sequencing of the positive clones (Zane et al, 2002)) are labor-intensive, time-consuming, and costly. Such methods generally use one or a few specific repeated motifs that are most often selected without prior knowledge of their abundance in the genome (Castagnone-Sereno et al, 2010).…”

Development and characterization of multiplex panels of microsatellite markers for Syphacia obvelata, a parasite of the house mouse (Mus musculus), using a high throughput DNA sequencing approach

“…Microsatellites markers are widely used to infer information about dispersal, relatedness, effective population size, parentage, etc. [7], but until recently their development was complex, time-consuming and expensive [8]. Here, we aimed to develop microsatellite markers for S. obvelata to allow insights into the population biology of this important parasite.…”