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Genomics in the Journals: Aug 29, 2013

NEW YORK (GenomeWeb News) – In a study slated to appear online this week in BMC Genomics, a pair of researchers from the University of Illinois at Urbana-Champaign described findings from a transcriptome sequencing study of the bald notothen, Pagothenia borchgrevinki, a high altitude Antarctic fish adapted to life in icy ocean water.

The duo used Roche 454 sequencing to assess transcripts found in pooled tissue samples taken from bald notothen fish exposed to their typical water temperatures, warmer-than-usual water, or water temperatures that induced heat stress.

Within these sequences, the investigators identified and annotated nearly 18,000 contigs, which subsequently served as a reference set for organizing sequences from bald notothen gill and liver tissue sequenced with Illumina technology.

A comparison between these bald notothen transcriptomes and existing transcriptome data for the tropical zebrafish Danio rerio highlighted genes from 58 functional groups that show enhanced activity in the cold water-tolerant Antarctic fish.

"The transcriptome resource from this study will aid future investigations of cold adaptation and thermal response of polar ectothermic species," wrote the University of Illinois' Christina Cheng and corresponding author Kevin Bilyk. Bilyk was based at the University of Illinois when the research was performed and is now with Shanghai Ocean University.

Researchers from China, Australia, and Denmark re-sequenced nearly four-dozen sorghum lines as part of their effort to understand the crop plant's genetic diversity and find avenues for future crop improvement — work that they reported in Nature Communications.

The group focused on 44 sorghum lines, including wild and cultivated races of the plant that grow in different parts of the world, generating sequences that covered the sorghum reference genome to average depths of between 16-fold and 45-fold. The analysis also involved re-sequencing of the cultivated Sorghum bicolor plant's wild progenitor, S. propinquum.

With this sequence data, researchers saw signs that sorghum is far more genetically diverse than previously appreciated. The genomes contained some 1.9 million small insertions and deletions, various gains and losses, and roughly 8 million SNPs, they reported, including more than 4.9 million SNPs found in the cultivated sorghum species.

Such variant profiles have already helped the team untangle some of sorghum's relationships and domestication history. Going forward, the sequences are also expected to help those interested in teasing apart and harnessing some of the genetic factors behind key sorghum traits.

"These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum," the study's authors noted, "providing an unmatched resource for the genetic improvement of sorghum and other grass species."

An American Journal of Human Genetics study by researchers from the University College London, the University of Addis Ababa, and Roskile University suggests that the ability to digest milk has arisen as a consequence of multiple adaptations in different human populations.

The team tested samples from 356 Ethiopian individuals, including 139 individuals who could digest lactose and 188 who could not. The remaining 29 individuals appeared to be intermediate lactose digesters or could not be classified using a lactose-tolerance breath test.

By sequencing 500 bases of sequence in the enhancer region of the lactase gene LCT, the investigators discovered that Ethiopian lactose tolerance involves five regulatory alleles that can lead to production of the lactase enzyme. Four of the alleles have been found in other populations in the past, they noted, while one was new.

In contrast to European lactose tolerance — which appears to have arisen via a hard selective sweep leaving one main lactase-linked haplotype in that population — the diversity found in and around the LCT gene in Ethiopians is consistent with a so-called soft selective sweep that involved simultaneous selection for numerous variants serving similar functions.

"This study shows that several different genetic changes that allow our bodies to make lactase have emerged independently," senior author Dallas Swallow, a genetics, evolution, and environment researcher at the University College London, said in a statement. "Changes to our lifestyle over the past 10,000 years — including diet, altitude acclimatization, and infectious disease resistance — will likely have caused many genetic adaptations of this kind."