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Effects of reproductive systems on crop genomic variation and breeding remain unclear. Here, the authors report that reproductive types impact genomic landscapes and grapevine breeding based on comparative genomic and population genetic analyses of wild grapevine and a complex pedigree of Pinot Noir.

Using a set of eleven maize lines that were selfed for six generations, a study examined the dynamics of heterozygosity and genome size resulting from selfing and the purging patterns of deleterious single nucleotide polymorphisms and transposable elements.

This article argues that recombination has a far more important role in the evolution of plant genomes than is currently appreciated, and that genome-wide patterns of recombination might explain some intriguing differences between plant and animal genomes.

Comprehensive integration of gene expression with epigenetic features is needed to understand the transition of kidney cells from health to injury. Here, the authors integrate dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and histone modifications to decipher the chromatin landscape of the kidney in reference and adaptive injury cell states, identifying a transcription factor network of ELF3, KLF6, and KLF10 which regulates adaptive repair and maladaptive failed repair.

By constructing a graph-based grapevine pangenome reference (Grapepan v.1.0) and incorporating structural variations and phenotypic maps, the study investigates the genetic basis of agronomic traits, empowering grapevine genomic breeding.

How plant genic DNA methylation evolves remains elusive. Using methylome data covering the phylogenetic breadth of land plants, researchers show that evolutionary patterns of methylation vary considerably across species, genes and methylation contexts.

This study identified structural variants in grapevine populations, including wild progenitors, using a de novo assembly and comparative genomics approach, and examined their evolutionary genomics and roles in domestication and phenotypic evolution.

A new study reports the genome of common bean (Phaseolus vulgaris) and genome-wide resequencing data from both wild and domesticated accessions. These data confirm that common bean was domesticated at least twice, in Mesoamerica and South America, and also provide a framework to identify genes that contributed to the phenotypic changes associated with domestication.

Grapevine is one of a few ancestrally dioecious crops that are reverted to hermaphroditism during domestication. Here, the authors identify candidate genes related to male- and female-sterility in grapes and describe the genetic process that led to hermaphroditism during domestication.

Using 1,578 resequenced genomes representing the diversity of cultivated and wild rice, this study reveals that the domestication alleles of the 993 selected genes stemmed from both O. rufipogon and O. nivara, demonstrating multiple domestications of rice.

The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.

A new study reports SNP genotypes of over 1,300 Arabidopsis thaliana accessions from throughout Eurasia, providing a resource for genome-wide association studies and studies of local adaptation. The extensive data are also used to identify targets of natural selection and to describe genome-wide patterns of recombination.

Analysis of genomic and phenotypic data in Helianthus species demonstrates that large chromosomal regions contribute to multiple traits associated with distinct ecotypes.

Stephen Wright, Detlef Weigel and colleagues report the whole-genome sequence of Capsella rubella, a highly selfing crucifer found throughout much of southern and western Europe. They compare mixed-stage flower bud transcriptomes from C. rubella and C. grandiflora, finding a shift in expression of genes associated with flowering phenotypes and providing insights into the transition to selfing.

Detlef Weigel and colleagues report the genome sequence of Arabidopsis lyrata. In comparison with the much smaller genome of A. thaliana, from which A. lyrata diverged about 10 million years ago, they find that the reduction in genome size is attributed to a large number of deletions across the genome.

The nucleotide diversity present in maize exceeds that in humans by an order of magnitude, and it has been challenging to characterize the high levels of diversity in this important crop. Doreen Ware and colleagues have identified 55 million SNPs in 103 domesticated and pre-domestication Zea mays varieties, as well as in a representative from the sister genus Tripsacum.

Potential resistance genes for Xylella fastidiosa in wild grapes are identified and resistance is shown to be climate dependent.

This Perspective explores the ways in which evolutionary processes can be considered when using species distribution models to predict responses to climate change.

A Review summarizes up-to-date understandings of the duration and demographic history of crop domestication and its effects on extant genomic variations, including structural variations about which we currently lack sufficient knowledge.

Lutnick et al. develop a cloud-based deep learning tool for whole slide image segmentation. The authors provide several examples of its application in renal pathology, for segmenting glomeruli, interstitial fibrosis and other features of interest.

Mutations can be deleterious, neutral or, in rare cases, advantageous. The relative frequencies of these types across a genome constitutes the distribution of fitness effects. The properties of this distribution have important consequences in both medical and evolutionary genetics.

Large genomic data sets are revealing that mutation rates vary across genomes at many different scales, from the effects caused by neighbouring nucleotides to patterns that affect whole chromosomes. These varying mutation rates have implications for inherited and somatic disease.