In PLOS Biology, investigators involved with the Genomic Encyclopedia of Bacteria and Archaea, or GEBA, outline the rationale for and proposed scope of the sequencing project — a systematic approach to characterizing microbial diversity and genomics. The group argues that sequencing the complete collection of strains of bacteria and archaea that have been cultured and described so far would "allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment."
A PLOS One study by researchers from the University of Rhode Island and Brown University explores the transcriptional shifts that occur in American oysters exposed to Roseovarius crassostreae, a bacterial pathogen that can cause a high mortality condition known as Roseovarius Oyster Disease. The team used transcriptome sequencing to assess tissue samples from populations of R. crassostreae resistant or susceptible American oyster (Crassostrea virginica) that had or had not been exposed to the pathogen. For example, the analysis uncovered differences in the expression of genes contributing to everything from immune response and detoxification to cell signaling and apoptosis in the mollusks in pathogen-sensitive and -resistant oysters.
The mucormycosis infection-causing fungal pathogen Lichtheimia corymbifera appears to have undergone gene duplications and genome expansions in the absence of duplications affecting the whole genome, according to a paper in PLOS Genetics. A team from Germany, Spain, and Brazil used a combination of Roche 454 and Illumina approaches to sequence the L. corymbifera genome before comparing it to sequences from another fungal pathogen that can cause mucormycosis, called Rhizopus oryzae. The comparison indicated that the L. corymbifera genome contains a slew of duplicated genes that have taken on diverse functions, for example, but a relative lack of repeat sequences and alternative splicing.