In Genome Research this week, Elzo de Wit and Sam Linsen at Hubrecht Institute-KNAW and the University Medical Center Utrecht sequenced small RNAs in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei, and Pristionchus pacificus to study the evolution of miRNAs. In addition to finding more than 100 novel expressed miRNA genes, most of which were in P. pacificus, they found that more than half of the miRNA genes are conserved "at the seed level in all four nematode species, whereas only a few miRNAs appear to be species specific," they write.
A consortium led by Andrew Jackson of the Sanger Institute performed comparative genomic analysis of the fungal pathogens Candida dubliniensis and C. albicans, looking for clues to C. albicans’ heightened ability to cause disease. They found 168 species-specific genes, 115 pseudogenes in C. dubliniensis, and importantly, "expansion of the TLO gene family of putative transcription factors and the IFA family of putative transmembrane proteins in C. albicans, which represent novel candidate virulence-associated factors," they write in the abstract.
Itai Yanai of the Technion-Israel Institute of Technology and Craig Hunter at Harvard have published a paper examining the evolution of co-expressed, neighboring genes. In comparing temporal gene expression profiles in conserved or divergent genomic positions in two genetically distant nematode species, C. elegans and C. briggsae, they found a lot of differences, but that essential developmental genes show less divergence than others. "Co-expression of gene neighbors in either species is highly divergent in the other, in particular when the neighborhood is not conserved," they say, adding that a "significant fraction of the co-expression observed among gene neighbors may be accounted for by neutral processes."
Finally, scientists at the Max Planck Institute have developed mGene, a "highly accurate gene-prediction system for eukaryotic genomes." Applying their system to the C. elegans genome, they found that mGene shows "superior performance" over other gene finders, including Fgenesh++ and Augustus, suggesting that even well-annotated genomes such as C. elegans can be improved by mGene's predictions.