Skip to main content
Premium Trial:

Request an Annual Quote

This Week in Genome Research: Aug 8, 2013

The University of Colorado's Rob Knight and colleagues brought together 16S ribosomal RNA profiles from various human microbiomes sampled for past studies as part of their meta-analysis of these microbial communities. Using information from the QIIME database, the team saw that some subtle microbiome patterns could not be picked up across the studies owing to technical differences, among other challenges. But other microbiome differences — such as gut microbiome shifts between individuals from Western cultures and agrarian societies, for instance, or between individuals with or without ileal Crohn's disease — were pronounced enough to show up even in the face of such biases.

A team from Japan, Tanzania, and Indonesia describe findings from a genome sequencing study of two coelacanth species, Latimeria chalumnae and L. menadoensis. By sequencing five coelacanths — three L. chalumnae from Tanzania, one L. chalumnae from Comoros, and one L. menadoensis from Indonesia — the researchers determined that the ancient-looking fish have markedly low genetic diversity, perhaps due to small population sizes or plodding evolutionary rates. Within a 2.74 billion coelacanth reference genome cobbled together using sequences from the Tanzanian fish, they tracked down a slew of repetitive element sequences, along with olfactory genes and limb enhancer elements reminiscent of those found in existing tetrapod creatures. The latter finding supports the notion that the new genomes "will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals," the researchers say.

The variation between human populations involves not only genetic, but also epigenetic differences, according to another Genome Research study. Researchers from Spain, the US, and Japan did array-based cytosine DNA methylation profiling in cell lines generated for almost 300 American individuals of Caucasian, African, or Han Chinese descent. Among the sites with variable methylation from one population to the next were promoter sequences from genes contributing to processes such as drug metabolism, sensory perception, immune genes, and more. Moreover, around one third of the differentially methylated sites that the team unearthed in the three populations occurred independently of genetic variants.