Volume 51 Issue 5, May 2019

The conserved ligand–receptor pair CLAVATA1–CLAVATA3, which maintains homeostasis in shoot apical meristems, responds differently to perturbation in tomato, Arabidopsis and maize. Active compensation occurs in CLE signaling peptides in tomato, but compensation is passive in Arabidopsis.

This Perspective discusses how best to interpret pLI, a measure widely used to identify genes that are intolerant to a single copy of a truncating mutation, by relating this and related measures to the underlying population-genetic theory.

The authors show that the transcription factors HNF4A and HNF4G regulate the transcriptome of the intestinal epithelium. HNF4 factors cooperate with BMP/SMAD signaling to promote enterocyte identity.

A study of a stem cell receptor–ligand signaling module across tomato, maize and Arabidopsis identifies different genetic mechanisms of compensation that contribute to homeostasis.

Genome-wide analysis identifies 30 loci associated with bipolar disorder, allowing for comparisons of shared genes and pathways with other psychiatric disorders, including schizophrenia and depression.

An expanded GWAS of birth weight and subsequent analysis using structural equation modeling and Mendelian randomization decomposes maternal and fetal genetic contributions and causal links between birth weight, blood pressure and glycemic traits.

A multi-tissue transcriptome-wide association study based on genetic predictors of expression level and alternative splicing in relevant tissues identifies 25 candidate genes associated with high-grade serous ovarian cancer.

The authors use three-dimensional live-cell imaging of colorectal carcinoma organoids to show that chromosomal instability is widespread. Single-cell sequencing identifies heterogeneity of copy number alterations and shows clonal evolution.

The authors identify the formation of dynamic topologically associating domain (TAD) cliques during differentiation and reprogramming. Their analysis indicates that TAD cliques stabilize heterochromatin at the nuclear periphery.

Maternal SETD2 deficiency leads to loss of H3K36me3, aberrant DNA methylation and ectopic H3K4me3 and H3K27me3 in mouse oocytes. Maternal depletion of SETD2 causes oocyte defects and subsequent zygotic arrest.

The authors performed whole-genome resequencing of 429 chickpea lines sampled from 45 countries. They identified 122 candidate regions (204 genes) under selection during chickpea breeding.

High-quality genome sequence of cultivated peanut comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut.

The genome sequence of segmental allotetraploid peanut suggests that diversity generated by genetic deletions and homeologous recombination helped to favor the domestication of Arachis hypogaea over its diploid relatives.

Genome assembly of durum wheat cultivar Svevo enables genome-wide genetic diversity analyses highlighting modifications imposed by thousands of years of empirical selection and breeding.

Targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat identifies regions showing the signals of wild emmer introgression, thus suggesting that historic wild-relative gene flow shaped modern bread wheat's adaptive diversity.

Exome sequencing of a worldwide panel of 487 wheat genotypes, including landraces, cultivars and modern varieties, sheds light on wheat genomic diversity and the evolution of modern bread wheat.

Signature Multivariate Analysis is a new computational tool that detects the mutational signature of homologous-recombination deficiency in clinical samples sequenced with targeted panels, enabling the identification of patients who are responsive to poly (ADP-ribose) polymerase inhibition therapy.