Yoav Gilad and colleagues report an RNA-seq analysis combined with de novo gene assembly for 16 mammalian species, including humans and 11 nonhuman primates (Genome Res., published online 29 December 2011; doi:10.1101/gr.130468.111). They sequenced the RNA from liver from each of these species. Because many of these species have no sequenced genome, they developed a new algorithm using a de Bruijn graph–based approach for de novo assembly and alignment of gene sequences across species. They characterized levels of genetic diversity and estimated phylogenies based either on gene sequences or gene expression, which reassuringly recapitulated the known primate phylogeny. They found evidence of positive selection on 499 candidate genes, with an enrichment for peroxisomal genes among the top-ranked genes. As many of the included species are on the International Union for Conservation of Nature (IUCN) endangered list, they examined genetic diversity by conservation status but found no clear relationship. Interestingly, the highest genetic diversity was found in the two most endangered species in the study, the black-and-white ruffed lemur and Coquerel's sifaka. This report presents the first genome-scale datasets and genetic diversity estimates for many of these species, providing a resource for comparative genomic studies and ongoing conservation efforts.
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