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This Week in PNAS: Nov 26, 2013

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In a study slated to appear online this week in the Proceedings of the National Academy of Sciences, a Stanford University-led team describes a hybrid sequencing strategy it used to profile transcriptome patterns in human embryonic stem cells. By bringing together Illumina short-read sequence data and longer Pacific Biosciences RS reads and analyzing these human embryonic stem cell sequences with a program designed to pick up splice junctions, the researchers identified nearly 8,100 full-length transcript isoforms and 5,459 more predicted isoforms. Included in the set were many newly identified isoforms, they note, in some cases arising from sites in the genome not previously known to contain coding loci.

For another PNAS study, the French National Institute for Agricultural Research's Francis Martin and colleagues from centers around the world sequenced the genome of an asexual fungus called Rhizophagus irregularis from a lineage known for establishing symbiotic interactions with plant roots. When they sequenced and assessed the 153 million base R. irregularis genome, the investigators saw that it contained tens of thousand of genes. But while some genes found in other fungal species were missing, including those coding for fungal enzymes that damage plant cell walls, the team saw expansions to other gene families — particularly those coding for components contributing to cellular communication, phosphorus capture, and mating-related processes.

Researchers from Uppsala University report on findings from a computational analysis focused on phylogenetic relationships between retroviruses that have worked their way into host genomes. Based on patterns found in almost 90,000 such endogenous retroviruses, identified in the genomes of 60 vertebrate host genomes, the group determined the host distribution of various viruses and estimated the diversity of those yet to be detected. From their findings so far, for instance, the study's authors argue that "current infectious exogenous retrovirus diversity may be underestimated, adding credence to the possibility that many additional exogenous retroviruses may remain to be discovered in vertebrate taxa."