Figure 1.
Major taxonomic groups of the phylum Nematoda and species whose genomes sequenced.
The major clades of Blaxter et al [89] are labeled I, II, III, IV, V and minor clades of van Megen [3] have Arabic numeral identifiers (1 to 12). The trophic mode indicated by the following abbreviations [90]: AP, animal parasite; BV, bacteriovore; FV, fungivore; OM, omnivore; PP, plant parasite.
Figure 2.
The life cycle of the pine wood nematode Bursaphelenchus xylophilus.
The nematode developmental cycles are shown with brown arrows. The nematodes develop through four moults (ie. four larval stages L1, L2, L3, L4 and adult) and reproduce within wood tissue while food is available. When conditions are adverse (ie. food becomes limiting) B. xylophilus enters specialized third-stage dauer larva (DL3). When stimulated by the presence of the vector beetle, the DL3 molts to become the fourth-stage dispersal larva (DL4) in preparation to board the vector. As the adult beetle emerges the nematodes move and settle beneath the elytra or within the trachea of the beetles and are transported to another food source. After invading healthy trees the nematodes feed on parenchymal cells and migrate through the tissues to spread over the tree, leading to wilting symptoms that result in the death of the tree within a year of infection. When the tree is dying B. xylophilus feeds on fungi which invade the tree and reproduces quickly.
Table 1.
B. xylophilus genome general features.
Table 2.
Summary of repeat families in B. xylophilus genome.
Figure 3.
Scaffolds of B. xylophilus display a macrosyntenic relationship with chromosomes of C. elegans.
Orthologues of C. elegans genes are highlighted on the five largest B. xylophilus scaffolds, coloured according to the C. elegans chromosome on which they are found. Scaffolds tend to have a predominance of orthologues from a particular C. elegans chromosome, e.g. chromosome V for scaffold00713 and chromosome III for scaffold00116.
Figure 4.
The most frequent Pfam domains found in B. xylophilus compared with those in C. elegans.
Hits with E-value score better than 1e-5 were retrieved and counted. Numbers in parentheses indicate the frequency rankings of each domain in C. elegans.
Figure 5.
Evolutionary dynamics of gene families in nematodes.
Phylogeny is a Bayesian nucleotide phylogeny based on 23 well-aligned single-copy genes present in all 10 species. Values on nodes are Bayesian posterior probabilities. Values on edges represent the inferred numbers of births (+) and deaths (−) of gene families along that edge. Note that our approach cannot distinguish gene family losses from gains on the basal branches of this tree, so for example the value of 1276 gene family gains on the Brugia lineage will include gene families lost on the branch leading to the other 9 spp., and similarly the 2282 gains on this branch will include Brugia-specific gene family losses. Pie charts in the centre represent the gene family composition of each genome – the area of the circle is proportional to the predicted proteome size, and the four wedges represent the relative numbers of proteins predicted to be either singleton genes (i.e. not members of any gene family), members of gene families common to all 10 sequenced Rhabditida genomes, and members of gene families present only in a single genome, and members of other gene families, present in between 2 and 9 genomes.
Figure 6.
Distribution of orthologous gene families across five selected nematode genomes.
Sizes of each region are approximately proportional to the number of genes shared by the overlapping species, which are distinguished by different fill colour and different border styles. The selected genomes represent both taxonomically and ecologically diverse nematodes – C. elegans is a free-living bacteriovore, Brugia malayi is an animal parasite, Bursaphelenchus xylophilus and Meloidogyne incognita are plant parasites, while Pristionchus pacificus has a close ecological association with a beetle host, but is not parasitic. A phylogeny for these 5 species is shown in Figure 5. A number of overlapping regions are labelled with the number of gene families, as are a number of regions representing comparisons of particular ecological or taxonomic relevance.
Table 3.
B. xylophilus enzymes with predicted plant/fungal cell wall–degrading activities, compared with those in other nematodes.
Table 4.
CAZyme families with substantial expansions in B. xylophilus other than those having putative cell wall degrading process.
Table 5.
Summary of peptidases in B. xylophilus and other nematodes.
Table 6.
Putatively laterally transferred genes, supported by phylogenetic evidence.
Table 7.
B. xylophilus effector candidates.
Table 8.
Main phase I, II, and III detoxification enzymes in B. xylophilus and other nematodes.