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This Week in Genome Biology: Dec 28, 2016

An international team led by investigators in the Netherlands used circular chromosome conformation capture sequencing, or 4C-seq, to assess chromatin patterns at non-coding DNA regulatory element sites previously found to interact with inflammatory bowel disease risk loci. Focusing on 92 non-coding DNA regulatory elements found to co-localize with IBD risk loci in the past, the researchers relied on 4C-seq to map chromatin interactions in monocyte, lymphocyte, and intestinal epithelial cell types — a search that led to more than 900 new candidate genes suspected of contributing to IBD. "Our study provides the first systematic analysis of chromatin interactions between disease-associated [non-coding DNA regulatory elements] and candidate genes in IBD," they note.

Researchers from Spain and the US describe demographic patterns in the Iberian lynx, Lynx pardinus with the help of new genome sequences. Using a combination of short- and long-read sequencing strategies, the team produced a draft genome assembly for an inbred male Iberian lynx from southern Spain before re-sequencing 10 more Iberian lynx and one Eurasian lynx. With these sequences, the investigators saw signs of apparent erosion in the Iberian lynx genome, which seem to have stemmed from past demographic bottlenecks. "Our analyses provided novel insights into the evolutionary and demographic history of the Iberian lynx," they write, "revealing a recent divergence and continued admixture with the Eurasian lynx and several drastic population bottlenecks in the last millennia." 

A University of Oregon-led team takes a look at the genome of the Gulf pipefish, Syngnathus scovelli to understand its unusual, derived body plan and specialized traits such as male pregnancy and brood pouch development. The researchers used a combination of sequencing, genetic mapping, and de novo assembly to put together a 307 million base genome for the Gulf pipefish, a member of the family that contains seahorses and seadragons. Along with expression data generated from pregnant and non-pregnant brood pouch samples and other Gulf pipefish tissues, the genome provided insights into its relationships with other fish, as well as alterations in the genome that may explain some of the derived physical features found in the Gulf pipefish.