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This Week in PNAS: Jun 11, 2013

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from France, the US, and the Netherlands report on findings from a sequencing study of the algae-infecting virus PgV-16T — the most massive DNA virus found in eukaryotes so far. Using sequence reads from PgV-16T grown in the phytoplankton species Phaeocystis globosa, the group pieced together a nearly 460,000 base genome assembly de novo. In addition to characterizing the protein-coding content of the genome itself, the researchers went on to look at PgV-16T's place in a viral phylogenetic tree, determining that it's more closely related to a clade of hefty viruses known as Megaviridae than it is to other microalgae-infecting viruses.

Another PNAS study uses transcriptome sequence data from horses, donkeys, and crosses between the two to look at gene expression patterns and imprinting in the placenta. The study, done by a Cornell University team, revealed preferential expression of paternal alleles for numerous genes in trophoblast tissue from the placenta. That was particularly true for a set of 15 ancient imprinted genes, 10 of which showed signs of paternal expression in the study. Imprinting status was somewhat more tenuous across a group of 78 candidate imprinted genes that the study's authors identified — variability that appears to set the stage for inter-individual differences in the uterine environment — though paternal expression still tended to predominate.

Investigators with the J. Craig Venter Institute and other centers in the US and Russia describe the "mini-metagenome" approach they used sequence the genome sequence of a representative from the uncultivated bacterial phylum dubbed TM6. From swab samples collected from a biofilm in the sink of a hospital's public restroom, the team narrowed in on individual bacterial cells using fluorescence activated cell sorting and other techniques. After amplifying and sequencing DNA in individual bacteria cells, investigators put together an assembly comprised of reads from cells with shared 16S ribosomal RNA sequences, covering around 90 percent of the genome for a TM6 bug called TM6SC1.