Structure, Function and Evolution of The Nematode Genome

Abstract

In the past few years, an increasing number of draft genome sequences of multiple free‐living and parasitic nematodes have been published. Although nematode genomes vary in size within an order of magnitude, compared with mammalian genomes, they are all very small. Nevertheless, nematodes possess only marginally fewer genes than mammals do. Nematode genomes are very compact and therefore form a highly attractive system for comparative studies of genome structure and evolution. Strikingly, approximately one‐third of the genes in every sequenced nematode genome has no recognisable homologues outside their genus. One observes high rates of gene losses and gains, among them numerous examples of gene acquisition by horizontal gene transfer. Not only does the ‘gene for parasitism’ not exist, but also there appear to be no common genomic characteristics of parasitic nematode genomes which would distinguish them from genomes of free‐living nematodes.

Key Concepts:

  • Nematode genomes tend to be compact.

  • Nematode genomes vary in their gene composition due to extensive gene gain and loss.

  • Genes are lost through gene deletion or rapid evolutionary change beyond the point where they can be recognised as homologous to a gene in another species.

  • Genes are acquired through gene duplication, de novo formation and horizontal gene transfer.

  • Horizontal gene transfer allows nematode species to acquire new physiological properties.

  • All nematode genomes sequenced so far contain operons, multigene transcription units giving rise to a single pre‐mRNA, which is broken up into single protein coding mRNAs by trans‐splicing and polyadenylation.

  • Within the nematodes parasitism has arisen multiple times independently and a ‘gene for parasitism’ or unifying parasite genomic features were not identified.

Keywords: nematodes; parasites; evolution of genomes; horizontal gene transfer; gene loss; gene gain

Figure 1.

Phylogenetic relationship of the nematodes with published genome sequences. The phylogeny follows Blaxter et al. (). Roman numerals denote the clade.

Figure 2.

Evolution of orphan genes. (a) Number of genes per nematode for seven nematode genomes. Genes that lack homologues in any other nematode species are denoted ‘orphan’ genes, otherwise as genus specific or as conserved across other nematode genera. Approximately one‐third of genes in each genome are classified as orphan or genus specific. (b) Saturation analysis of translated EST data from 25 nematode species (from nematode.net). For any number of species, the mean total number of ESTs and the mean number of ‘orphan’ ESTs without homologues in any other species is shown. The number of orphan ESTs increases linearly with the number of species suggesting that the nematode protein space is still undersampled. Error bars indicate standard deviations for different species permutations.

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How to Cite close
Rödelsperger, Christian, Streit, Adrian, and Sommer, Ralf J(Feb 2013) Structure, Function and Evolution of The Nematode Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024603]