Genome Analysis of Plant Parasitic Nematodes

Abstract

Plant nematology has entered an era of genomics with the completion of the genome sequences of two root knot nematode (RKN) species: Meloidogyne incognita and M. hapla. Comparative analysis of these two RKN genomes reveals striking differences in their organizations and sheds light on the mechanisms and evolution of parasitism. The M. hapla genome with 54 Mbp and 14,454 genes represents the smallest metazoan genome characterized so far. By contrast, the organization of the M. incognita genome with 86 Mbp and 19,212 genes is much more unusual and provides insight into the genetic consequences of reproduction by asexual parthenogenesis. Most of its genome is represented as pairs of homologous but divergent segments suggesting that despite being a parthenogenetic aneuploid species, M. incognita is evolving towards effective haploidy. As the first obligate plant pathogenetic animal to be sequenced, M. incognita could constitute a model for evaluating the impact of these mechanisms at the genomic scale. One of the most remarkable findings that has emerged from these two RKN genome studies is the identification of an extensive set of plant cell wall-degrading, carbohydrate-active enzymes (CAZymes), which has no counterpart in any other animal genome. All family members were possibly acquired by horizontal gene transfer (HGT) because the most similar genes are from those of unicellular organisms and bacteria. Finally, based on comparative analysis with nematodes from other ecological niches such as the free-living species and human parasites, we profile several approaches that are being explored using genome information toward the development of environmentally sustainable parasite control strategies and toward better understanding of the evolution and biology in plant-parasitic nematodes.