Journal Articles

The plant parasite Pratylenchus coffeae carries a minimal nematode genome

April 11, 2015

The plant parasite Pratylenchus coffeae carries a minimal nematode genome,  11 Apr 2015, Nematology, Mark BURKE 1,2,3, Elizabeth H. SCHOLL 4, DavidMcK. BIRD 1,4, Jennifer E. SCHAFF 5, Steve COLEMAN 2, Randy CROWELL 6, Stephen DIENER 3, Oksana GORDON 6, Steven GRAHAM 3, Xinguo WANG 6, EricWINDHAM 3, Garron M. WRIGHT 3 and Charles H. OPPERMAN 4,
1 Bioinformatics Research Center, NC State University, Box 7614, Raleigh, NC 27695-7614, USA
2 David H. Murdock Research Institute, General Administration, 150 Research Campus Drive, Kannapolis, NC 28081, USA
3 David H. Murdock Research Institute, Information Resources & Bioinformatics, 150 Research Campus Drive, Kannapolis, NC 28081, USA
4 Plant Nematode Genetics Group, Department of Plant Pathology, NC State University, Box 7253, Raleigh, NC 27695-7253, USA
5 Genomic Sciences Laboratory, NC State University, Box 7614, Raleigh, NC 27695-7614, USA
6 David H. Murdock Research Institute, Genomics Sequencing Laboratory, 150 Research Campus Drive, Kannapolis, NC 28081, USA

Summary – Here we report the genome sequence of the lesion nematode, Pratylenchus coffeae, a significant pest of banana and
other staple crops in tropical and sub-tropical regions worldwide. Initial analysis of the 19.67 Mb genome reveals 6712 protein
encoding genes, the smallest number found in a metazoan, although sufficient to make a nematode. Significantly, no developmental
or physiological pathways are obviously missing when compared to the model free-living nematode Caenorhabditis elegans, which
possesses approximately 21 000 genes. The highly streamlined P. coffeae genome may reveal a remarkable functional plasticity in
nematode genomes and may also indicate evolutionary routes to increased specialisation in other nematode genera. In addition, the P.
coffeae genome may begin to reveal the core set of genes necessary to make a multicellular animal. Nematodes exhibit striking diversity
in the niches they occupy, and the sequence of P. coffeae is a tool to begin to unravel the mechanisms that enable the extraordinary
success of this phylum as both free-living and parasitic forms. Unlike the sedentary endoparasitic root-knot nematodes (Meloidogyne
spp.), P. coffeae is a root-lesion nematode that does not establish a feeding site within the root. Because the P. coffeae nematode genome
encodes fewer than half the number of genes found in the genomes of root-knot nematodes, comparative analysis to determine genes
P. coffeae does not carry may help to define development of more sophisticated forms of nematode-plant interactions. The P. coffeae
genome sequence may help to define timelines related to evolution of parasitism amongst nematodes. The genome of P. coffeae is a
significant new tool to understand not only nematode evolution but animal biology in general.

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