This week in Genome Biology, researchers describe their extensive annotation of the immune and stress gene repertoire of Acyrthosiphon pisum, the pea aphid, whose genome was sequenced and reported in PLoS Biology this week. Nicole Gerardo of Emory University and her colleagues write that they were surprised to find that pea aphids appear to be missing genes present in other insect genomes which appear to be critical for recognizing, signaling, and killing microbes. “The absence of genes suspected to be essential for the insect immune response suggests that the traditional view of insect immunity may not be as broadly applicable as once thought,” the team writes.
National Human Genome Research Institute investigators describe their assessment of single-nucleotide variants that cause exon skipping, and their development of a Web tool, Skippy, to score coding variants for splice-modulating features. The NHGRI team deciphered a number of features which appear to discriminate splice-affecting variants including splicing silencers of the exon and intronic movement, changes in the number of exonic splicing enhancers and silencers, and evolutionary constraints, among others.
Also in Genome Biology this week, Duke University researchers report their development of cERMIT, a computational analytical tool for studying genome-wide quantitative regulatory evidence. cERMIT utilizes information across all sequence regions in search of high-scoring motifs. The Duke team writes that their program “substantially outperforms state-of-the-art approaches on curated ChIP-chip datasets, and easily scales to current mammalian ChIP-seq experiments with data on thousands of non-coding regions.”
A European team has analyzed and quantified the limitations of researchers sequencing many genomes with low coverage, rather than fewer genomes with high coverage. The authors write that, when inferring genome content evolution, low-coverage genomes generate false gene losses and aberrant artifacts in gene duplication. “We show that the artifactual gains are caused by the low coverage of genome sequence per se rather than by the increased taxon sampling in a biased portion of the species tree,” they write, adding they think it will remain difficult to separate artifacts from true changes in genome evolution “until there is better homogeneity in both taxon sampling and high-coverage sequencing.”