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This Week in Genome Biology: Mar 23, 2016

An international team presents findings from a genome and transcriptome sequencing study of the Mesoamerican common bean, Phaseolus vulgaris. The researchers used a combination of sequencing technologies to put together an almost 550-million-base genome assembly for P. vulgaris, roughly one-third of which was made up of repeats. Together with transcriptome sequences for more than two dozen common bean tissues or developmental stages, the genome helped to uncover 30,491 predicted protein-coding genes, the investigators report. Meanwhile, comparisons with sequences from the Andean common bean and other plants highlighted gene duplications, long non-coding RNAs, and other features contributing to the common bean's tissue- or development-specific expression patterns. GenomeWeb has more on the study, here

Researchers from the US, UK, and Brazil explore sequence introgression in butterflies from the Heliconius genus. After looking in general at Heliconius butterfly relationships with one another using genome-wide SNP data for 79 individuals from 29 species, the team used genotyping patterns in windows across the genome to look for introgression between two distantly related species with wing patterns that resemble one another, H. besckei and H. melpomene nanna. The search led to dozens of sequences stemming from potential introgression events, including sequence upstream of a wing pattern-related gene that appears to have originated in the H. melpomene butterfly and introgressed into the H. besckei genome. "Gene flow has been ongoing, with evidence of gene exchange at multiple time points, and bidirectional," the study's authors write.

Finally, a European Molecular Biology Laboratory-led group considers protein complex co-expression in 11 mammalian cell types and several points in time as mouse embryonic stem cells were reprogrammed to produce induced pluripotent stem cells. Using literature searches and other available resources, the team narrowed in on 279 protein complexes of interest. Of those, 182 protein complexes turned up in the publicly available proteomic datasets they profiled for the analysis. From these data, authors of the study saw a combination of protein complex co-regulation coupled with stoichiometric changes and compositional signatures that seemed to reflect the type of protein complex, tissue, and temporal state involved.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.