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This Week in Genome Biology: Jun 14, 2017

Researchers from the Sorbonne examined the dynamics of the sex-determining regions of seven brown algal species. Using the Saccharina japonica genome sequence along with genome and transcriptome data on six other brown algal species, the researchers found that a core set of sex-linked genes is conserved across the algae and also uncovered lineage-specific gene loss, gene gain, or gene movement affecting the UV sex chromosomes. Genes gained by sex chromosomes — through duplication or transposition — tend to have a sex-linked role, they note. The researchers add that genes have also moved off the sex chromosome, and could compensate for gene loss in the non-recombining region.

Harvard Medical School researchers led by George Church have developed a software tool that enables a number of genomes to be simultaneously compared for genome-engineering studies. The tool, called Millstone, is a web-based software platform that supports iterative multiplex mutation analysis and genome engineering. In particular, it automates read alignment and variant calling for hundreds of genomes and allows users to compare mutations among samples to create successive reference genomes and design new edits for subsequent editing rounds. The researchers note that Millstone is open source and available through Amazon Web Services.

A team of researchers from Texas and China generated methylomes for domesticated allotetraploid cottons as well as for their wild tetraploid and diploid relatives. By combining methylome and transcriptome data, they uncovered 500 putative epialleles that may have influenced the morphological and physiological changes that took place during domestication. For instance, they traced one epiallele — COL2D is repressed in wild cotton, but expressed in domesticated cotton due to methylation loss — to photoperiodic flowering.