Are positively-selected effectors of the root-knot nematode Meloidogyne incognita involved in plant resistance

The tropical root-knot nematode Meloidogyne incognita is a global problem in tomato and many other vegetable crops. The obligate endoparasitic M. incognita can cause about 5% crop loss annually. Chemical pesticides can no longer be used to control M. incognita because of environmental and public health concerns. Meanwhile, the most frequently used Mi-1 resistance in tomato is increasingly being broken by virulent populations of M. incognita. Virulent root knot nematodes are thought to have acquired effectors that enable them to avoid recognition by resistance proteins in plants. Therefore, insight into the repertoire of effectors of M. incognita can help to identify new sources of resistance to which the field populations of nematodes in tomato-producing areas have not yet adapted.

To  identify positively-selected effector families in the genome sequence of M. incognita, a bioinformatics pipeline centred on the algorithms PRANK, Codeml, and Phobius was constructed. In total, 77 positively-selected clusters of paralogous genes were identified in the genome of M. incognita, which encode a total of 254 secretory proteins. The effectiveness of the pipeline was demonstrated by the fact that several positively-selected clusters of paralogous genes have been identified as effectors of M. incognita in earlier studies. Highly ranking candidate effectors from the pipeline are currently being functionally characterized in plants using transient and stable overexpression and using host-delivered RNA-interference in nematodes.