NEW YORK (GenomeWeb News) – Researchers have sequenced the complete genome of the northern root-knot nematode, Meloidogyne hapla — a soil worm that parasitizes the roots of plants, including many crop plants.
The work, which appears online this week in the Proceedings of the National Academies of Science, suggests that the M. hapla genome, the smallest multicellular animal genome sequenced to date, has been pruned down in many areas compared to other nematode genomes, but has expanded in other regions — particularly those containing parasitism-related genes. And, researchers say, the new genome sequence may open the door to a more complete understanding of the nature and evolution of plant parasitism.
“Having 99 percent of the genome sequenced allows you to not only know what’s there, but to compare it to other nematodes to see what’s missing from this genome,” co-lead author David Bird, a plant pathologist and co-director of North Carolina State University’s Center for the Biology of Nematode Parasitism, said in a statement. “Finding potential Achilles’ heels, what the nematode is getting from the plant and how it is really interacting with the plant are all more possible now.”
Over the past decade, research groups have sequenced the genomes of several free-living nematodes, including Caenorhabditis elegans, C. briggsae, and Pristionchus pacificus. But although plant-parasitizing nematodes cause billions of dollars of damage to agricultural crops around the world each year, the genomes of these and other parasitic nematodes are just starting to be revealed.
In July, an international team of researchers reported in Nature Biotechnology that they had sequenced the draft genome of a root-knot nematode or RKN called Meloidogyne incognita.
For the latest paper, researchers from North Carolina State University, the University of California at Davis, the Department of Energy’s Joint Genome Institute, and the University of California at Berkeley focused on another RKN: M. hapla, a root-knot nematode belonging to the “largest uncontrolled group of plant pathogens worldwide.”
They sequenced the roughly 54 million base pairs of the M. hapla genome to about ten times coverage using whole-genome shotgun sequencing with ABI 3730 and MegaBase sequencers and assembled it using Arachne software from the Broad Institute.
Their subsequent analysis predicted that the small, but dense, M. hapla genome contains 14,420 protein-coding genes — thousands fewer genes than the C. elegans genome. Several gene families, including those for the G protein-coupled receptor, nuclear steroid hormone receptor, and collagen genes, were also sharply abbreviated compared to those in C. elegans.
While nearly half of the M. hapla genes with known functions shared high similarities with genes from C. elegans, others — which appear to have been acquired, in part, through horizontal gene transfer — resembled genes in parasitic bacteria and fungi.
And despite the pared-down nature of the M. hapla genome, the researchers found that it was expanded in areas involved in parasitism. They also identified proteins that they suspect play a role in interactions between the nematode and its plant hosts.
With the M. hapla genome in hand, the researchers can directly compare its genome with that of free-living organisms, including C. elegans, as well as other parasites such as M. incognita and the human pathogen Brugia malayi.
In the future, the authors noted, by combining sequence information with whole-genome transcriptome profiling and other types of analysis, it should be possible to delve even deeper into M. hapla’s pathogenicity, development, and evolution. Such information may help researchers understand how the worm infects plants — and, eventually, could provide new targets for anti-nematode therapeutics.
“Plant-parasitic nematodes are among the most damaging and difficult-to-control pests of world agriculture,” the authors wrote. “Meeting current and future worldwide demands for food, fiber, and bioenergy will necessitate minimizing these losses and will require development of new control paradigms.”
The M. hapla sequence is available through NCBI, North Carolina State University’s Center for the Biology of Nematode Parasitism site, through www.hapla.org or www.rootknot.org, and WormBase.