C. elegans

C. briggsae is ~20 Myr divergent, yet almost identical morphologically, but their genomes have changed a lot. While most genes are still present as simple single gene orthologs, almost a third of genes have been duplicated in one or the other genome, or both, while 10% are so divergent they cannot be clearly related between the two species!

IB404 - Caenorhabditis elegans 2 - Feb 13

More rapidly evolving gene families, like the large families of 7TM candidate chemoreceptors I studied, commonly show expansions. Most chemoreceptors are orthologs in this comparison, but paralogous expansions are evident (C. briggsae genes are highlighted in blue), and usually in tandem array (bottom). Gene losses are also clear.

Comparison of one chromosomeA. Synteny blocks - only broken near the ends.B. Genes/100kb - fairly uniform, except ends.C. Orthologs/genes/100kb - divergent genes at endsD. “Orphans” without cross-species matches, again mostly at ends.E. Genes mutatable or RNAi knockdownable to lethals - most in middle.F. Repetitive elements and transposons/100kb - most at ends.G. Ka/Ks of ortholog pairs /100kb - rapidly evolving genes at ends.H. Ks of ortholog pairs /100kb, suggesting that mutation rates are actually faster at the ends!

Rapid genome change but physical conservation in nematodes over 20 Myr. How does this comparison rate against insects and mammals? Humans and mice have undergone much more morphological evolution since they parted 85 million years ago, but have more stable genomes. Flies and mosquitoes, separated by 250 million years, have an intermediate rate of change. The units on the y-axis are rates relative to the human–mouse divergence rates (which are set at 1). Stars represent the rate of loss and gain of introns; squares, the rate of genome re-organization like inversions and translocations; hexagons, the number of blocks of genes whose order is conserved; circles, the rate of silent base-pair changes (except the fly–mosquito pair which are too divergent).

So these nematodes are far more rapidly evolving at the molecular level, and this is a general story. The rate of molecular evolution rises with shorter generation times, consistent with most mutations occurring during DNA replication, and hence accumulating neutrally. Indeed, most intergenic regions and introns cannot be confidently aligned between these two nematodes in the same genus!

Today at least 10 nematode genomes are available, including four from the genus Caenorhabditis, plus others like Brugia malaya (cause of river blindness transmitted by mosquitoes). The overall picture is an extension of the above comparison, but some novel findings:

1. There are few, if any, reciprocal translocations between chromosomes, unlike yeasts (and mammals), but like Drosophila flies. No idea why!

2. What regions of introns can be aligned, and are hence somewhat conserved, are implicated in regulation of alternative splicing, that is, determining which alternative splice sites will be utilized. Specifically a UCUAUC sequence was identified that was later shown to be bound by the ortholog of a human RNA-splicing factor, and regulates alternative splicing of multiple genes, although how it is all coordinated is unclear.

Unfortunately, no closer relatives of C. elegans have been discovered, nevertheless, even 4-way comparisons have proven useful for study of regulatory regions (like the yeast example, and later flies and mammals), but not yet other conserved features of genomes (mammals later).

As an example, this is “phylogenetic footprinting” of the upstream promoter region for the lin-11 gene, which encodes a homeobox-containing transcription factor (TF) that regulates formation of the vulva, several neurons, and some uterine cells. Dots indicate identity between elegans (top), and briggsae, remanei, and brenneri. The boxes indicate

the locations of enhancers bound by four TFs.

In November 2011 a remarkable new study was published, showing that Caenorhabditis nematodes are not “soil” nematodes, as previously thought, but rather “fruit worms”, a joke on “fruit flies” for Drosophila.

They found that most naturally occur in rotting flowers and fruits, much like Drosophila flies. By sampling hundreds of such habitats they discovered 16 new species (38 total). Here are some of their habitats.

But sadly, none of these are closer to C. elegans than are briggsae, remanei, and brenneri, the sequenced species. With the current ease of genome sequencing they will surely all soon be sequenced.

Species were differentiated by mating tests, and a few minor morphological differences. This molecular phylogeny is based on six genes. Most are not named yet, but one of the earlier discovered species has been named for Sydney Brenner. The level of molecular divergence between these species and groups is roughly comparable to that between the various Drosophila species we will see later.

The morphological differences are primarily in the features of the male tail, which contains both extensive chemical sensory organs, plus the genitalia, and varies the most, much as male insect genitalia are commonly used for species identification.

There are good synapomorphies for the two super-groupings, but also some convergences. Spiral mating (bottom right) has evolved uniquely in the angaria group within the Drosophilae super-group.

Species status? They collected many strains of most of these species. Sequencing of the ITS2 (internal transcribed spacer 2 between the 5.8S and 28S rRNA genes) shows that there is relatively little genetic divergence within these species, except remanei and sp8, so this provides an easy ID.

This is a form of “DNA bar coding”, which usually employs a region of the mitochondrial cytochrome oxidase 1 (CO1) gene.

Distribution. C. elegans and briggsae were known to be cosmopolitan, reminiscent of D. melanogaster and simulans, while others amongst these new ones are temperate or tropical, and a few are regional, eg. sp5 in China.Others are specialists on particular flowers, much like D. sechellia, and there is even one species living on carrion and another in inflamed cow’s ears.

Finally, they note that this is still probably the tip of the iceberg, with just 38 species described to date, so this genus might rival Drosophila for numbers of species (~2000, but ~800 in Hawaii alone).