Genetic tests of ancient asexuality

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I’ve just had a manuscript published at BMC Evolutionary Biology so thought I’d share a synopsis.
I’ve been interested in root knot nematodes for a while as they are a powerful system for evolutionary genetics and amazingly successful parasites of plants- especially crop plants. Trudgill and Blok (2001) estimate that they “have host ranges that encompass the majority of flowering plants” and that Meloidogyne incognita “is possibly the single most damaging crop pathogen in the world”.
Interestingly, the 3 most damaging species are obligatory asexual mitotic parthenogens (apomicts), which is perhaps counter intuitive given the ongoing arms race between plants and nematode. Root Knot Nematodes have previously been suggested to be ancient asexuals, and I’m interested in the consequences of asexuality for the genome, and the phylogenetic pattern of genetic diversity. In this work I sequenced a number of nuclear protein-coding genes to test the predictions of ancient asexuality (in terms of allelic sequence divergence and phylogenetic clustering of alleles within morphological species). I also sequenced a sperm-specific gene to look for evidence of pseudogene formation and changes in evolutionary rate with respect to their sexual (meiotically-reproducing) close relatives. This work provides evidence that the signatures of ancient asexuality that were recovered are actually the product of a reasonably recent interspecific hybridization event.

This manuscript is free to download at the BMC site (although the correctly formatted version isn’t available yet).

Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

David H Lunt

BMC Evolutionary Biology 2008, 8:194
doi:10.1186/1471-2148-8-194
Published: 7 July 2008

Abstract

Background
The existence of “ancient asexuals”, taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of the asexual organism but also for its genome. Several genetic signatures are predicted from long-term asexual (apomictic) reproduction including (i) large “allelic” sequence divergence (ii) lack of phylogenetic clustering of “alleles” within morphological species and (iii) decay and loss of genes specific to meiosis and sexual reproduction. These genetic signatures can be difficult to assess since it is difficult to demonstrate the allelic nature of very divergent sequences, divergence levels may be complicated by processes such as inter-specific hybridization, and genes may have secondary roles unrelated to sexual reproduction. Apomictic species of Meloidogyne root knot nematodes have been suggested previously to be ancient asexuals. Their relatives reproduce by meiotic parthenogenesis or facultative sexuality, which in combination with the abundance of nematode genomic sequence data, makes them a powerful system in which to study the consequences of reproductive mode on genomic divergence.

Results
Here, sequences from nuclear protein-coding genes are used to demonstrate that the first two predictions of ancient asexuality are found within the apomictic root knot nematodes. Alleles are more divergent in the apomictic taxa than in those species exhibiting recombination and do not group phylogenetically according to recognized species. In contrast some nuclear alleles, and mtDNA, are almost identical across species. Sequencing of Major Sperm Protein, a gamete-specific gene, from both meiotic and ameiotic species reveals no increase in evolutionary rate nor change in substitution pattern in the apomictic taxa, indicating that the locus has been maintained by selection.

Conclusions
The data strongly suggests the tropical root knot nematode apomicts have a recent origin and are not anciently asexual. The results support that interspecific hybridization has been involved in the origin of this asexual group and has played a role in shaping the patterns of genetic diversity observed. This study suggests that genetic signatures of ancient asexuality must be taken with caution due to the confounding effect of interspecific hybridization, which has long been implicated in the origins of apomictic species.

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Trudgill, DL and Blok, VC (2001) Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. Annu Rev Phytopathol 39:53-77

4 Comments Add yours

  1. suicyte says:

    You seem to be an expert :-)Do you have any information when the Heterodera genome will be made available to the public? I am interested in these organisms as root cyst nematodes seem to have a ubiquitin system components meant to be active in the host plants.

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  2. suicyte says:

    small correction: Heterodera is of course a root cyst nematode, not a root knot nematode. They are closely related, though.

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  3. Dave Lunt says:

    Hi, yes they are quite closely related- although its hard to tell/calibrate how close nematodes really are! I have no information at all about the Heterodera genome. Have you seen this site about EST sequencing?http://www.nematode.net/Heterodera are very cool too, for lots of reasons. If I was choosing species rather than randomly stumbling into them by accidents of employment I might have chosen them instead!

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  4. suicyte says:

    Yes, I know about the EST site. Several months ago, there were announcements and press releases saying that the heterodera genome (glycinis, I think) has now been finished by some public/private consortium. Since that time, I have been looking for sites offering the data.Maybe this was just another case of science-by-press-release, as defined by Jonathan Eisen.

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