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This Week in Nature: Jun 21, 2018

In this week's Nature Plants, an international research team reports data showing that an expansion of disease-resistance genes may be responsible for the long lifespans of certain trees like the oak, which can survive for centuries in the face of environmental and biological threats. The scientists sequenced, assembled, and annotated the genome of the English oak, then compared their findings with existing  whole-genome sequences for other trees and plants. They find that the English oak underwent a recent burst of tandem gene duplication that appears to have contributed to 73 percent of the its total gene family expansion. These expanded gene families are largely associated with disease-resistance genes and exhibit positive selection signatures. Notably, similar disease-resistance gene expansions were found in various other tree genomes versus those of herbaceous species.

And in Nature Methods, an MIT-led team presents GeNets, a platform for network-based genomic analyses designed to overcome the challenges of comparing the signal-to-noise ratios of different networks and identifying the optimal network with which to interpret a particular genetic dataset. With GeNets, users can train a machine-learning model — called Quack — to carry out such comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets, according to the researchers. "We believe that as more and more genetic and network datasets become available, the value of GeNets will continue to increase," they write.

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.