Genome informatics articles from across Nature Portfolio

Genome sequencing data can be used to infer transmission dynamics for pathogens of public health concern such as N. gonorrhoeae. Here, the authors sequence and analyse 5881 genomes from Victoria, Australia from 2017–2021, and assess impacts of COVID-19 restrictions on transmission.

Integration of genome-wide association analysis of 406,504 individuals in the UK Biobank and scATAC–seq data reveals that variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.

Formalin fixation is commonly used in tissue storage; however, this process has traditionally limited downstream whole genome sequencing usage. Here, the authors identify artefactual signatures in FFPE-derived sequencing data and demonstrate the preservation of clinical utility, thus enabling FFPE whole genome sequencing when required.

As we age, our cells acquire DNA mutations, resulting in cell-to-cell genomic heterogeneity. We characterized the landscape of mitochondrial DNA (mtDNA) heterogeneity in healthy human cells. Our observations provide deeper insight into the frequency of new mitochondrial mutations and the mechanisms that propagate low-level mutations in mtDNA over a lifetime.

Genetic constraint identifies genes under selection against loss-of-function, but existing methods are inaccurate for shorter genes. A new study overcomes this key limitation to ascribe more confident predictions to all human protein-coding genes.

Identifying substrates of metabolic gene products is important to understand their function in physiology and disease. We developed GeneMAP, a multiomics platform for predicting metabolic gene functions using models of gene expression. We experimentally validated a top-scoring gene–metabolite association, thereby revealing a role for SLC25A48 in mitochondrial choline import.

Many plant products eaten daily in human diets — such as potato or banana — are polyploid and are notoriously difficult to breed. In this study, the fusion of clonal gametes from distinct diploid tomato parents is used as a blueprint for the design of polyploid genomes in crops.

Diploid assembly is a difficult task that requires several types of genomic sequencing data, including — but not limited to — HiFi reads and parental sequences. Hypo-assembler, an assembly algorithm, uses high quality solid k-mers extracted from Illumina data alongside Nanopore reads to produce a high-quality diploid assembly using only Nanopore and Illumina data.