NEW YORK (GenomeWeb News) - An international team of 27 laboratories has published the draft genome sequence of the root-knot nematode, Meloidogyne incognita, a parasitic organism responsible for billions of dollars in crop damage each year.
The worm infests the roots of more than 3,000 crop types, including coffee, cotton, tomatoes, melons, and cucumbers, and is currently controlled with chemical pesticides that are harmful to humans and the environment. The research team said it expects that the genome sequence of the root-knot nematode will help identify new targets that will lead to less toxic pesticides.
The researchers, led by France's National Institute for Agricultural Research, published the draft sequence of the 86-megabase genome online yesterday in Nature Biotechnology.
The researchers used ABI 3730xl sequencers to analyze the M. incognita genome and used the Arachne algorithm to assemble the reads into 2,817 supercontigs totaling 86 Mb, which was almost twice the estimated genome size, according to the authors.
The team identified 19,212 protein-coding genes. Upon further analysis, they found that M. incognita has 61 carbohydrate-active enzymes, or CAZymes, that degrade plant cell walls — an “unprecedented” set of such enzymes, according to the authors.
“The striking similarity of these enzymes to bacterial homologs suggests that these genes were acquired by multiple [horizontal gene transfer] events,” the authors wrote in the paper, adding that the candidate horizontal transfer events in the genome “involve genes with potential roles in interactions with hosts.”
The authors noted in the paper that they are currently conducting transcriptional profiling, proteomic analysis, and high-throughput RNA interference experiments in order to further understand the processes by which these nematodes cause plant disease.
They added that M. incognita can infect the model plant Arabidopsis thaliana, and that studying functional genomics for the two organisms “should provide new insights into the intimate molecular dialog governing plant-nematode interactions and allow the further development of target-specific strategies to limit crop damage.”