The plant parasite Pratylenchus coffeae carries a minimal nematode genome

Abstract

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.

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

“…Genome size estimates based on overall coverage of known individual genes are shown in Table 2. These estimates suggest that the myxozoan genome of K. iwatai (22.5 Mb) is one of the smallest reported animal genomes, comparable to the genome of the recently reported parasitic nematode (∼20 Mb) (37). The K. iwatai genome is more than 20-fold smaller than the estimated size of the P. hydriforme genome (561 Mb) and the published genome of the cnidarian Nematostella vectensis (450 Mb) (38) and more than 40-fold smaller than the published estimated genome size of the cnidarian Hydra magnipapillata (1,005 Mb) (39).…”

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

“…The miniature by metazoan standards genome is predicted to encode about 9,000 genes-one of the lowest reported gene counts among metazoans, exceeding only the recently sequenced genomes of a myxozoan [6] and a plant-parasitic nematode [7]. The predicted genes are fairly intron rich and span an average of six exons, which in sum account for 23.1% of the genome.…”

Advances in Understanding the Molecular Mechanisms of Root Lesion Nematode Host Interactions

“…These include genomes of M. hapla, M. incognita, G. pallida, R. similis, and Bursaphelenchus xylophilus and the recent sequence for the P. coffeae genome (10). As indicated in Table 2, the published data suggest that the genome of P. coffeae is much smaller than those of other PPNs.…”

“…Comparative functional genomics suggests that a protein with xylanase activity is encoded by the migratory endoparasitic R. similis (44,56). This is also the case for Pratylenchus spp., in which putative transcripts with glycoside hydrolase 5 xylanase activity have been identified in the transcriptome of P. coffeae, and sequences putatively encoding proteins similar to those of Mi-xyl1 and Rs-xyl1 are also present in genomic sequences of P. coffeae (10) and P. thornei ( J. Fosu-Nyarko & M.G.K. Jones, unpublished data).…”