Pan-genome and pan-3D-genome analyses reveal evolutionary relationships between transposon-driven variations in genome size and chromatin topology innovation in the Gossypium genus, and delineate the genomic basis of the evolution of cotton fiber from coarse sparse to slender spinnable. Today, the allotetraploid cotton Gossypium hirsutum is widely cultivated around the world.

See Wang et al.

In normal somatic cells, human genes reside on 23 pairs of chromosomes, but in cancer cells oncogenes can unleash themselves in circular extrachromosomal DNA (ecDNA). Hung et al. describe a CRISPR-based strategy to selectively ‘handpick’ and analyze ecDNA (magenta) and chromosomal DNA (white) from cancer cells.

See Hung et al.

The image represents normal hematopoietic cells, each with a unique ‘fingerprint’ or identity defined by its genetic, epigenetic and transcriptional state. Single-cell multi-omic technologies define how somatic mutations (bright dots) in clonal mosaicism alter phenotype as a function of the underlying cell identity.

See Nam et al.

Unraveling the tissue-specific genetic regulation of gene expression is essential for both biological discovery and genetic improvement in farm animals. In this analysis, the FarmGTEx consortium builds a multi-tissue atlas of regulatory variants in cattle and shows the importance of this resource to understanding regulatory mechanisms underlying complex traits of economic value. The FarmGTEx consortium is working on other farm animal species now.

See Liu et al.

The lethality and treatment-refractory nature of pancreatic cancer are largely mediated by collaborative interactions between cancer cells and other cell types in the tumor microenvironment, including cancer-associated fibroblasts and immune cells. By constructing a high-resolution molecular landscape of the multicellular subtypes and spatial communities that compose pancreatic cancer and the dynamic remodeling associated with cytotoxic selection pressure, additional therapeutic vulnerabilities are identified to augment precision oncology efforts in pancreatic cancer.

See Hwang et al.

In celebration of the 200th anniversary of Gregor Mendel’s birth and the 30th anniversary of the launch of Nature Genetics, we look both forwards and backwards at how far the genetics field has come. This cover image is inspired by the cover of the first issue of Nature Genetics in 1992.

This figure is a graphical representation of transcriptional changes that occur in human CD4 T cells as they go through activation. The different colored dots depict individual T cells at different stages of activation that are circulating in the blood during an active immune response. Single-cell transcriptional profiling was used to capture how gene expression is regulated by common genetic variants during this crucial process of immune response.

See Soskic et al.

Papaya (Carica papaya L.) originated and was domesticated in Central America. Transgenic papaya resistant to papaya ringspot virus (PRSV) saved the Hawaiian papaya industry from collapse and is a widely publicized success story of genetically modified crops. Comparative genomic analysis of transgenic SunUp and non-transgenic progenitor Sunset revealed a single complex 1.64-Mb insertion that contains all three transgenic fragments, including the functional PRSV coat protein gene (cp) that confers resistance to the virus.

See Yue et al.

HLA alleles influence the amino acid compositions of T cell receptors (TCRs). The DNA ‘yarn’ has different HLA alleles, represented by different colors, which create the TCR ‘knit’. The red HLA allele is the risk allele that increases pathogenic TCRs, damaging the surrounding knit. Ishigaki et al. developed a statistical approach to map and quantify the HLA genetic control over TCRs.

See Ishigaki et al.

The diagnostic odyssey can last indefinitely when the gene that underlies a patient’s disorder remains unknown. The ability to identify undiagnosed patients who ‘match’ based on facial features can be a crucial precursor to identifying the underlying disease-causing genes. GestaltMatcher can establish these matches, igniting the necessary process of delineating new disease entities and diagnoses.

See Hsieh et al.

Analysis of how human genetic variation associates with gut microbiome traits, including microbial composition and species abundance, can provide insights into the relationship between host and microbial genetics.

See Lopera-Maya et al.

Sequencing of the genome of the lychee cultivar ‘Feizixiao’, along with analysis of 72 re-sequenced lychee accessions, identifies two different domestication events: one in Yunnan, and one in Hainan.

See Hu et al.