Analysis and functional classification of transcripts from the nematode Meloidogyne incognita

Abstract

Background: Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita.

Results: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases.

Conclusions: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.

Figure 1

Histogram showing the distribution of ESTs by cluster size. For example, there were seven clusters of size 14 containing a sum of 98 ESTs. Distribution of contig sizes is not shown.

Figure 2

Percentage representation of gene ontology (GO) mappings for M. incognita clusters. (a) Biological process; (b) cellular component; (c) molecular function. More detailed information is provided in Table 2 (see also Additional data files). Note that individual GO categories can have multiple mappings. For instance, GO:0015662: P-type ATPase (cluster-MI00952, Interpro domain IPR004014) is a nucleic-acid-binding protein, a hydrolase enzyme and a transporter.

Figure 3

Venn diagram showing distribution of M. incognita BLAST matches by database. Databases used were: for C. elegans, Wormpep v.54 and mitochondrial protein sequences; for other nematodes, all GenBank nucleotide data for nematodes except C. elegans and M. incognita; and for non-nematodes, SWIR v.21 with all nematode sequences removed.

Figure 4

Distribution of contigs by size of longest ORF. Solid line, contigs with any database homology by BLASTX (1,445). Dotted line, contigs without database homology (353).

Figure 5

A comparison of phenotype distribution between all RNAi-surveyed C. elegans genes with phenotypes (4,786) versus only those C. elegans genes with homology to M. incognita (221).