In PLOS Genetics, researchers from the UK, Singapore, and Saudi Arabia present findings from a comparative genomic study of Plasmodium knowlesi, a parasite found in macaques that has been linked to human malaria cases in Malaysia and other parts of Southeast Asia. Using a high-quality P. knowlesi reference genome assembled with long read sequence data, the team assessed dozens more isolates from Malaysian Borneo, Peninsular Malaysian, and the Philippines. Although organellar genomes partitioned the strains into three distinct lineages, the analysis revealed recombination between segments of certain nuclear. "Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats," the authors note. "The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition."
For a paper appearing in PLOS Neglected Tropical Diseases, a team from Korea characterizes the genome of a severe fever with thrombocytopenia syndrome (SFTS)-causing virus strain from Korea, focusing on isolates from the Haemaphysalis longicornis tick. The researchers came up with a whole-genome assembly for the so-called KAGWT strain using Sanger sequencing and isolates from ticks in South Korea, comparing the KAGWT sequences with those from SFTS strains obtained from infected patients at the Chungbuk National University Hospital. They went on to explore relationships between the SFTS-causing viruses, uncovering genetic ties between the KAGWT strain and an isolate known as KAGWH3 from a patient in the same region the ticks were collected. All told, the results pointed to four main SFTS virus genotypes in South Korea.
Finally, investigators from China and the US report on an RNA sequence-based search for reference genes to normalize quantitative gene expression data in apple root tissues for a study in PLOS One. Starting with 15 genes that appeared relatively stable in available RNA sequence datasets, the team did high-throughput messenger RNA, spectrophotometer-based RNA quantification, RNA integrity analyses, and RNA stability assessments to narrow in on a handful of genes with the most stable expression in the apple root. "Our data indicated that, for these carefully validated reference genes, [a] single reference gene is sufficient for reliable normalization of the quantitative gene expression data in apple roots," they write, though "the most suitable reference genes can be variable depending on root tissue types or treatments."