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This Week in Nature: Feb 28, 2019

In this week's Nature Genetics, a multi-institute team publishes a nearly complete reference genome of the cultivated octoploid strawberry, which resulted from the hybridization of two wild octoploid species that descended from the merger of four diploid progenitor species into a single nucleus more than one million years ago. The researchers uncovered evidence of the plant's North American origin, as well as the existence of a dominant subgenome that largely controls metabolomic and disease-resistance traits. "We anticipate that this new reference genome, combined with insights into subgenome dominance, will greatly accelerate molecular breeding efforts in the cultivated garden strawberry," the authors write. GenomeWeb has more on this, here

And in Nature Ecology & Evolution, researchers from the US and Korea present a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus — a so-called white blooded vertebrate that lacks functional red blood cells and functional hemoglobin genes. The researchers identified genes involved in protection from ice damage — including genes encoding antifreeze glycoprotein and zona pellucida proteins — that are highly expanded in the icefish genome. They also found an expansion of genes that encode enzymes that help to control cellular redox state, likely as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. Meanwhile, some crucial regulators of circadian homeostasis are found to be absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment, they write.

Meanwhile, in Nature Cell Biology, a group from Peking University reports a microRNA-inducible CRISPR-Cas9 platform that can both measure miRNA activity at the cellular level and control the expression of endogenous genes or mutate specific DNA bases on a cell type-specific basis. They use the system to study the heterogeneity of miRNA activity and uncover a previously undefined layer of heterogeneity associated with miR-21a activity in mouse embryonic stem cells. "These results highlight the utility of an miRNA-induced CRISPR–Cas9 system as miRNA sensors and cell-type-specific genome regulation tools," the investigators 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.