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Riccardo Velasco and colleagues report the genome sequence of the 'Golden Delicious' domesticated apple. These data shed new insight into the genomic events that preceded the origin of this crop.

Multi-ancestry genome-wide association analyses and systematic variant-to-gene mapping strategies implicate new genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.

The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.

Gastrointestinal motility disorders affect over 20% of the population, yet current therapies provide limited relief. Here, the authors show that in a swine model a closed-loop GI neuroprosthesis restores peristalsis and enhances metabolic responses via targeted electrical and chemical stimulation

Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties and one wild pineapple relative. Their analysis supports the use of the pineapple as a reference genome for monocot comparative genomics and provides insight into the evolution of crassulacean acid metabolism photosynthesis.

Li et al. propose a conceptual framework to study the phenomenon of falling asleep based on electroencephalogram data. They show that a tipping point marks the brain’s nonlinear wake-to-sleep transition and that the unfolding process can be tracked in real time.

Forecasts of COVID-19 mortality have been critical inputs into a range of policies, and decision-makers need information about their predictive performance. Here, the authors gather a panel of global epidemiological models and assess their predictive performance across time and space.

Patients with cancer undergoing anti-PD-1 immune checkpoint blockade can experience immune-related adverse effects. Wherry and colleagues examined the immunity elicited upon immunization of patients with cancer and report that anti-PD-1 immunotherapy dynamically affects influenza vaccine-induced immune responses.

Negative data composition critically shapes machine learning robustness in sequence-based biological tasks. Training data composition and its implications are investigated on biological rule discoveries.

MARBLE uses geometric deep learning to map dynamics such as neural activity into a latent representation, which can then be used to decode the neural activity or compare it across systems.

Apple is one of the most important fruit crops. Here, the authors perform deep genome resequencing of 117 diverse accessions and reveal comprehensive models of apple origin, speciation, domestication, and fruit size evolution as well as candidate genes associated with important agronomic traits.

Here, the authors integrate genomic, proteomic, and phenotypic data from UK Biobank, identifying over 1,100 gene-environment interactions. They catalogue interactions between 101 blood proteins and 153 exposures, which may refine biomarker discovery.

The haplotype-resolved genome of tetraploid modern rose, along with a variation map of 233 wild and cultivated Rosa accessions, reveals the complex genome composition of modern roses and elucidates the genomic bases of their origin and breeding.

Genome-wide association analyses of blood glucose measurements under nonstandardized conditions provide insights into the biology of glucose regulation, diabetes complications and pathways for treatment stratification.

Proteins involved in epigenetic regulation are frequently mutated in several paediatric cancers. Here, Huether et al.characterize the somatic mutation frequency across 21 paediatric cancer subtypes by sequencing 633 epigenetic genes in over 1,000 tumours; generating a rich data set for investigating epigenetic dysregulation.

Integrative genomic and transcriptomic analyses reveal molecular events defining Richter transformation from CLL, and highlight the potential of cell-free DNA for early detection.

Genomic and clinical analysis of 916 bacterial isolates from neonates with sepsis in seven low- and middle-income countries (the BARNARDS study) reveals that the main species present were antimicrobial-resistant Klebsiella, Escherichia coli and Enterobacter.

Fort et al. identify CYRI as a conserved negative modulator of Scar–WAVE-induced lamellipodia by interacting directly with active Rac1, thereby conferring pseudopod plasticity and dynamics during motility.

Characterization of the myotis bat morbillivirus shows that infection in human cells is restricted by innate immune responses in vitro and cross-neutralization by sera from measles, mumps and rubella vaccinees.

An improved reference genome of sweet orange and newly sequenced genomes of its somatic mutants uncover the global pattern of somatic variations, the diversification and dispersal history of sweet orange and candidate genes controlling fruit taste and flavour.

Studies of fruit quality traits in pears are lagging behind the other major fruit trees. Here, the authors conduct GWAS of fruit quality and phenological traits in a panel of 312 sand pear accessions using SNPs called from resequencing data, and reveal the involvement of a lignin formation-related protein in regulating stone cell development.

Date palm is a perennial fruit tree crop that thrives in arid environments of North Africa and the Middle East. Here Hazzouriet al. analyze the date palm germplasm by re-sequencing 62 different varieties and uncover selection signatures and candidate genes associated with important agronomic traits.

Defining the dimension in bounded, inhomogeneous or discrete physical systems may be challenging. The authors introduce here a dynamics-based notion of dimension by analysing diffusive processes in space, relevant for non-ideal physical systems and networks.

Boron nitride nanotubes (BNNTS) have only been shown to dissolve in chlorosulfonic acid (CSA) at low concentrations. Here the authors successfully demonstrate the formation of liquid crystals of BNNTs in CSA that can be used to produce macroscopically aligned neat fibers of BNNTs.

Directional selectivity in the detection of moving visual stimuli critically depends on starburst amacrine cells, which have been studied primarily in rabbit retina; a large-scale reconstruction of the mouse retina at a single-synapse level, along with experimental and theoretical analysis, shows that mouse retinal circuitry is adapted to the smaller eye size of mice.

Phased diploid genomes of the cultivated apple Malus domestica cv. Gala and its two major wild progenitors M. sieversii and M. sylvestris, as well as pan-genome analyses, provide insights into the genetic history of apple domestication.

Aberrant synchronous oscillations have been associated with numerous brain disorders, including essential tremor. The authors show that synchronous cerebellar activity can casually affect essential tremor and that its underlying mechanism may be related to the temporal coherence of the tremulous movement.

There is lack of therapies targeting the PAX3-FOXO1 fusion oncogene in fusion-positive rhabdomyosarcoma (FP-RMS). Here, the authors identify and characterise an inhibitor with highest inhibition of histone lysine demethylase 3B that suppresses PAX3-FOXO1 activity in FP-RMS.

This Consensus Statement presents the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines.

Primitive, wild and cultivated citrus have different abilities in synthesizing anthocyanins. The subfunctionalization of the Ruby2–Ruby1 cluster contributes to the variation and evolution of the anthocyanin biosynthesis regulation in citrus.

The severity of SARS-CoV-2 infection varied over the course of the pandemic due to factors such as changes in variant characteristics and population immunity from previous infection or vaccination. Here, the authors estimate infection hospitalisation and infection fatality rates in England over time from the start of the pandemic until March 2023.

Harmful algal blooms threaten water resources across the globe. This study quantifies how temperature affects the occurrence and concentration of microcystin in lakes across the United States and finds that regions with temperatures that promote high microcystin concentrations will shift to higher latitudes in the coming decades.

Nitrogen isotope data from sediments deposited during the earliest stage of the Great Oxidation Event show evidence for the emergence of a pervasive aerobic marine nitrogen cycle.