The results of the genome sequencing project of M. incognita are published in the review Nature Biotechnology. Abad et al. (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita, 26 (8) 909-915.
The key points of this sequencing project analysis that are of interest are as follows:
This is the first whole genome of a plant parasitic metazoan to be sequenced and analyzed. Several genomes of plant parasitic prokaryotes or fungi of agronomical interest have been sequenced, but to date there is no information about the full content of any plant parasitic metazoan genome. Our analysis represents the first opportunity to complete our vision of the adaptations by which plant-bioagressors are able to invade their hosts.
The observation that most of the assembly is present as pairs of homologous but divergent segments. This suggests that despite being a parthenogenetic diploid, M. incognita is evolving, in the absence of sex, towards effective haploidy as proposed for other invertebrates such as bdelloid rotifers (Figure 1 and Figure 2). These so far poorly known mechanisms of genetic plasticity could account for the rapid adaptation to environmental changes, the extremely wide host range and geographic distribution of this worm. As the first obligate pathogenetic animal to be sequenced, M. incognita could constitute a model for evaluating the impact of these mechanisms at the genomic scale.
Figure 1: Representation of allelic relationships for the five largest supercontigs of the M. incognita assembly. The five largest supercontigs are shown with plots of gene density (orange curve), conservation with C. elegans at amino acid level (green curve) and EST density (pink curve). These are linked to 70 other supercontigs through the highest matching protein sequence matches for each predicted gene (blue lines). EST-rich scaffolds (for example 2 and 4) show a high number of links.
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Figure 2. Example of two allelic regions in the M. incognita assembly. Exons are represented by red boxes and are linked together to form genes (arrows indicate the direction of transcription). Grey boxes show assembly gaps. Highly diverged allelic genes are linked together using blue boxes. Gene order is well conserved between the two allelic regions, with only minor differences in predicted gene structure. Percentages of sequence identity at the protein level between the two allelic regions are indicated.
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The spectacular presence of an extensive set of plant cell wall-degrading enzymes in M. incognita, which has no equivalent in any animal studied to date (Table 1). This "suite" of enzymes likely modifies and subverts the host to support nematode growth. As M. incognita can infect the model plant Arabidopsis thaliana, our data make it a key model system for the understanding of adaptations to plant parasitism by a metazoan.
Table 1. Enzymes with candidate activity on the plant cell wall in M. incognita in comparison with C. elegans and D. melanogaster. Number of genes encoding enzymes with candidate activity on different substrate is listed in the three selected species. GH stands for Glycoside Hydrolases, PL for Polysaccharide Lyases and EXPN for expansin-like proteins, following the CAZy nomenclature (http://www.cazy.org). A total of nine and two cellulose-binding modules of family CBM2 (bacterial type) were found appended to candidate expansins and cellulases, respectively.
The striking similarity of candidate pathogenicity genes to bacterial homologues, suggesting that these genes were acquired by multiple horizontal gene transfer (HGT) events. While HGT has been a major component of evolution in prokaryotes and some protozoa, HGT into metazoan genomes is relatively rare. Our data suggest that acquisition of new capabilities via HGT is probably a key component for adaptation of a metazoan animal to plant parasitism.
The identification of new potential antiparasitic drug targets. For instance, we identified M. incognita-restricted genes and protein domains, M. incognita-specific gene family expansions and reductions as well as a set of M. incognita proteins whose orthologs are nematode-restricted and return lethal phenotype in C. elegans RNA inactivation experiments.
This is an unprecedented image of "what singularities may contribute to a parasitic lifestyle in nematodes thanks to a three-way comparison with the human parasite Brugia malayi and the free-living nematode Caenorhabditis elegans. Our study also revealed profound genomic diversity within this phylum, helping to account for the unmatched, evolutionary success of these metazoans.
Plant-Nematode interaction team, Inra Paca Creation date: 13 May 2009 Update: 15 January 2010