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This Week in Genome Research: May 28, 2014

A Ghent University-led group turned to genome or transcriptome sequence data representing 41 different plants to look back at ancient whole genome duplication events in the angiosperm plant lineage. The researchers' analysis of genome sequences for 38 plants — and transcriptome sequences for three more — supported the notion that genome duplication took place at roughly the same time as the so-called Cretaceous-Paleogene extinction, which occurred some 66 million years ago. Based on their findings, the study's authors speculated that polyploidization might have been apt to occur in the presence of environmental stressors that wipe out some other organisms.

Using a computational tool called TranspoSeq, researchers at Harvard, the Broad Institute, the Dana-Farber Cancer Institute, and Brigham and Women's Hospital searched for somatic retrotransposon insertions in whole-genome sequence data from 200 matched tumor and normal samples as part of The Cancer Genome Atlas' Pan Cancer Project. The group detected 810 somatic retrotransposon insertions across the 11 cancer types tested, though the insertions were especially common in colorectal, head and neck, endometrial carcinoma, and lung squamous tumors. The investigators narrowed in on almost three dozen more somatic retrotransposon insertions when they used a newly developed method called TranspoSeq-Exome to look at protein-coding sequences from 767 more tumor samples.

A hybrid zone region of Ecuador that's home to the co-mimetic butterfly species Heliconius erato and H. melpomene also contains a cryptic population of butterflies from H. timareta, according to an international team led by investigators in the UK and Puerto Rico. With the help of genetic markers identified through restriction-associated DNA sequencing, the researchers tested butterfly populations in hybrid zones from Peru and Ecuador. In the process, they not only narrowed in on divergent loci in the mimetic butterfly genomes — including those involved in color patterning — but also detected the cryptic H. timareta population at low altitudes in Ecuador species that shares physical features with H. melpomene malleti.