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This Week in PNAS: Mar 4, 2014

In the early, online edition of the Proceedings of the National Academy of Sciences, members of an international team led by investigators in China and Mexico report on findings from a genome sequencing study of pepper plants. The group did whole-genome sequencing and de novo genome assembly for a cultivated Capsicum annuum accession from China and for the pepper's wild progenitor plant, known as Chiltepin. Along with RNA sequencing data from various pepper tissues and re-sequencing data on 20 more pepper plants, the new reference sequences made it possible to characterize the pepper genome and compare it to sequences from related plants in the same Solanaceae family. In particular, the researchers focused on genes under artificial selection during pepper domestication, along with players in key pepper processes such as fruit development and the production of flavor-related compounds. GenomeWeb Daily News has more on the study, here.

A German team turned to RNA sequencing to fine-map the gene expression events involved in bovine oocyte activation and different stages of early embryonic development. By sequencing transcripts in both bovine oocytes and bovine embryos from the four-cell, eight-cell, 16-cell, or blastocyst stages developed in vitro, the researchers tallied up the genes expressed during each phase of development as well as their function and parental allele source. Those involved in the study say the effort "provides the largest transcriptome data set of bovine oocyte maturation and early embryonic development and detailed insight into the timing of embryonic activation of specific genes."

Researchers from France and Russia describe a giant DNA virus that they discovered in a 30,000-year-old permafrost sample from Siberia. The virus, dubbed Pithovirus sibericum, shares morphological features with pandoraviruses, the team notes. But when researchers scrutinized the new virus' 600,000 base genome, they found that its gene content more closely resembles that of icosahedral viruses such as Iridoviruses and Marseillevirus. As such, the virus appears to represent a third type of giant, amoeba-infecting virus, distinct from the very large Megaviridae and Pandoroviruses described recently. "The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health," the study's authors write.