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Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.

Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.

A human genome is sequenced and assembled de novo using a pocket-sized nanopore device.

Which combination of current genome sequencing and assembly approaches results in high-quality, complete diploid genome assemblies is determined.

Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.

Methods to produce haplotype-resolved genome assemblies often rely on access to family trios. The authors present FALCON-Phase, a tool that combines ultra-long range Hi-C chromatin interaction data with a long read de novo assembly to extend haplotype phasing to the contig or scaffold level.

Trio binning assembles both haplotypes of a genome by combining long-read sequence data with short-read data from both parents.

Segmental Duplication Assembler (SDA) uses long sequence reads to resolve segmental duplications that are collapsed in current genome assemblies. These assemblies correspond in total to the length of an average human chromosome.

Factors defining wheat stem rust pathogen (Pgt) virulence remain poorly characterized. Comparative population genomics based on Pgt haplotypes suggest that structural variation and admixture through somatic hybridization and sexual recombination play an important role in broadening Pgt virulence.

Teff is an indigenous cereal critical to food security in the Horn of Africa. Here, the authors report an improved genome assembly and observe the surprisingly low levels of large-scale structural rearrangement, homoeologous exchanges, or bias gene loss after the formation of this tetraploid species.

A complete telomere-to-telomere genome assembly of the maize Mo17 inbred line uncovers structural features of the highly complex maize genome.

Selaginella lepidophylla is a clubmoss with extreme desiccation tolerance. Here, the authors assemble its highly heterozygotic haplotypes and examine gene expression changes during desiccation, which shed light on the mechanisms for maintaining a small genome size and adaptation to extreme drying.

Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.

Basidiomycete fungi typically have two mating-type loci located on different chromosomes. Here, Lucotte et al. report the convergent loss-of-function of mating-type genes across several species of phytopathogenic fungi of the genus Microbotryum.

The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights.

Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.

This Review summarizes the computational strategies for microbiome analysis using long-read sequencing data.

For sexually reproducing organisms, experimental models to study the evolution of primary sex-determining loci are scarce. This study shows male-determining loci on  proto-Y chromosomes of the housefly, containing the same gene, can genomically diverge into regions of various complexity.

Here, Tisza, Dekker, and colleagues perform large scale analysis of genome methylation in the gut commensal and pathogen, Bacteroides fragilis group, revealing immense methyl motif diversity and evidence of widespread methyltransferase exchange among phages.

Li Guo et al. assemble the genome of Nannochloropsis oceanica, finding evidence that during the secondary endosymbiosis event responsible for its speciation, its host nucleus was overthrown by a symbiont nucleus. They suggest that the symbiont nucleus became dominant over the host nucleus.

A high-quality reference genome of rose is generated by sequencing a doubled haploid line. The researchers analysed the genome structure and uncovered candidate genes associated with major ornamental traits through integrated genetic and genomic analyses.

SPI1 fusion genes in T-cell acute lymphoblastic leukemia (T-ALL) are commonly found with co-occurring NRAS mutations. Here, the authors show that the combination of these oncogenes is necessary to drive T-ALL in a murine model and that the oncogenic activity of the SPI1 fusion is dependent on β-catenin.

Mutations provide the genetic variability required for evolutionary change. Here, using pedigree-based whole genome sequencing, the authors determine that the Epaulette shark appears to have the lowest mutation rate identified in a vertebrate, providing a potential explanation for slow evolution in the shark lineage.

Analysis of monkeypox virus (MPXV) isolates circulating in Nigeria before the 2022 global outbreak of MPXV sheds light on the diversification of the virus that eventually gave rise to the 2022 MPXV lineage.

Marc Van Goethem et al. combine short- and long-read sequencing from biocrust samples to report nearly 3,000 biosynthetic gene clusters (BGCs) encoding microbial secondary metabolites. Their results demonstrate the advantage of integrated metatranscriptomic and long-read metagenomic sequencing in analyzing BGCs and provides insight into the role of secondary metabolites in maintaining phylogenetic niches in biocrusts.

Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions crucial for infection in a plant pathogenic fungus, show signatures of horizontal transfer between distant fungal species, and may facilitate the formation of new virulence genes.

Integration of long and ultra-long reads results in improved phased, diploid assemblies.

Duplications of gene segments can allow novel physiological adaptations to evolve. A detailed analysis of the TCAF gene family in primates and archaic humans suggest rapid duplication and diversification in this gene family is associated with cold or dietary adaptations.

Taurine and indicine cattle have different desirable traits making them better adapted to different climates across the world. Here, Low et al. describe a pipeline to produce haplotype-resolved, chromosome-level genomes of Angus and Brahman cattle breeds from a crossbred individual and report on comparisons of the two genomes.

Pangenomes have a number of advantages over linear reference assemblies. Here the authors use bovine haplotype-resolved assemblies to show that structural variant-based pangenomes are consistent regardless of sequence platform, assembler, or coverage, suggesting that rigid protocols may not be required.

B. salamandrivorans (Bsal) is a fungus of amphibians that has been implicated in the collapse of salamander populations. Here, the authors sequence nine Bsal isolates from six epidemic sites and describe variation in genome size and composition.

A neuromodulator produced by commensal Providencia bacteria that colonize the gut of Caenorhabditis elegans mimics the functions of the cognate host molecule to manipulate a sensory decision of the host.

The human gut microbiota can metabolize xanthan gum, a food additive that was introduced to our diets relatively recently in processed foods. A Ruminococcaceae species can degrade this complex polysaccharide and, in some individuals, Bacteroides intestinalis can grow on the released oligosaccharide products.

Assembly of haplotype-resolved human genomes is achieved by combining short and long reads.

Populus has young sex chromosomes despite ancient dioecy. This study shows that the ARR17 gene functions as a sex switch, triggering female development when on and male development when off. This single-gene system enables dynamic evolution of poplar sex chromosomes.

Genomic analyses of Citrus species including haplotype-resolved genomes of Citrus sinensis and Citrus aurantium highlight the origin of sweet orange and provide a strategy for de novo domestication of perennial crops.

Structural variants (SVs) in human genomes contribute diversity and diseases. Here, the authors use a multi-platform strategy to generate haplotype-resolved SVs for three human parent–child trios.

The recovery of two circularized genomes of the Heimdallarchaeum species from hydrothermal vent enrichment cultures reveals that these Asgard archaea carry diverse mobile genetic elements, such as an integrative viral genome and aloposons. These mobile genetic elements contain several bacteria- and phage-derived genes, modulating the shuffling of information between bacteria and archaea, and potentially influencing eukaryogenesis.

Cattle reference genomes are valuable resources but are currently heavily biased towards European breeds. Here the authors integrate assemblies for African breeds into a more representative cattle graph genome capturing global breed diversity.

The acidophilic fungus Acrodontium crateriforme is present in traps of the carnivorous plant Drosera spatulata and promotes prey digestion.

Two high-quality nanopore genome assemblies of Brassica nigra are reported, one of which has particularly high contiguity with a contig N50 of 17.1 Mb, allowing localization of active centromeres and reconstruction of the ancestral Brassica genome.

Mobile element insertions (MEIs) are a source of repetitive genetic variation and can lead to genetic disorders. Here the authors use Cas9-targeted nanopore sequencing to efficiently saturate enrichment for known and non-reference MEIs.

The rapidly evolving Y chromosome accumulates male-benefit genes but is often poorly characterized in many mammals. Here, the authors assemble the male specific region of the horse Y chromosome and investigate its evolution and function.

Barnyardgrass is a problematic agricultural weed. Here, via genomic analysis, Guo et al. identify genes potentially underlying its success, including a gene cluster activated in response to co-cultivation with rice that leads to synthesis of the allelochemical DIMBOA.