Jonathan M. D. Wood

High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

Elevated recessive lethal frequencies drive hatching failure following near extinction in 'Alala, the Hawaiian crow

The paper investigates hatching failure in Alala, the Hawaiian crow, after a near-extinction event, identifying recessive lethal haplotypes as the main cause.

A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.

The paper presents a new phased assembly of the Antarctic spiny plunderfish and identifies genomic features linked to cold adaptation in notothenioids.

Genomic comparisons shed light on the adaptive basis of brain size plasticity and chromosomal instability in the Eurasian common shrew

The paper identifies genomic and transcriptomic changes associated with chromosomal instability and seasonal brain size plasticity in the Eurasian common shrew.

MicroFinder: Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes

MicroFinder improves bird genome curation by identifying conserved microchromosome genes to anchor manual assembly of fragmented microchromosomes.

The mouse pangenome reveals the structural complexity of the murine protein coding landscape

The paper presents a mouse pangenome with 17 strains, resolving structural complexity and improving RNA-Seq analysis by identifying non-reference genes and VNTR polymorphisms.

Genomic resources for comparative analyses of obligate avian brood parasitism

The paper generates genome assemblies for ten brood parasitic bird species and their outgroups, enabling comparative genomic analyses of obligate brood parasitism evolution.

Forty New Genomes Shed Light on Sexual Reproduction and the Origin of Tetraploidy in Microsporidia

The paper presents 40 new microsporidian genomes, revealing evidence of sexual reproduction and autopolyploidy, with tetraploid genomes organized into diploid compartments.

Genomic and genetic insights into speciation and pigment pattern diversification in Danio fishes

This study investigates the genomic and genetic factors underlying speciation and pigment pattern diversification in Danio fishes, revealing introgression, functional divergence of specific genes, and evolutionary changes in protein and regulatory sequences.

Whole genome sequencing reveals how plasticity and genetic differentiation underlie sympatric morphs of Arctic charr

The paper uses whole genome sequencing to analyze genetic differentiation and plasticity in sympatric morphs of Arctic charr across multiple lakes, revealing a polygenic basis and varying levels of reproductive isolation.

Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation

This study examines two Neotropical butterfly radiations, revealing high rates of hybridization and chromosomal rearrangements as drivers of diversification.

A chromosome-level genome of the king penguin (Aptenodytes patagonicus): a resource for linking genotype to fitness in a long-lived vertebrate

The paper presents a high-quality chromosome-level genome of the king penguin, improving assembly contiguity and annotation for studying genotype-fitness relationships.

Insights into the Evolution of Ancient Shark and Ray Sex Chromosomes

The paper examines sex chromosomes in 14 elasmobranch species, identifying conserved X chromosomes and a shared candidate gene for sex determination.

ERGA-BGE genome of Cheirolophus tagananensis: an IUCN endangered shrub endemic to the Canary Islands

The paper presents the reference genome of Cheirolophus tagananensis, providing tools for studying genetic adaptation and supporting conservation strategies.

Chromosome-level reference genome assembly for the mountain hare (Lepus timidus)

This paper presents a high-quality chromosome-level genome assembly for the mountain hare, contributing to the European Reference Genome Atlas initiative.

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

This study presents a chromosome-scale genome assembly and annotation of Alopecurus aequalis, revealing its genetic similarity to barley and expansion of herbicide resistance genes.

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis

This paper presents a new chromosome-scale genome assembly of Littorina saxatilis with improved contiguity and completeness, enabling better study of chromosomal inversions and their role in speciation.

High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding

The paper presents a high-quality chromosome-level genome assembly of the brown hare, providing insights into chromosomal evolution and hybridization with the mountain hare.

Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

The paper generates and analyzes genome assemblies for 24 Antarctic notothenioid fish species to study cold adaptations, identifying genomic changes related to antifreeze proteins and haemoglobin loss.

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

The paper analyzes genomes of leatherback and green turtles to identify gene family expansions and demographic differences that may influence their ecological adaptations and conservation status.

Automated assembly of high-quality diploid human reference genomes

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

Widespread false gene gains caused by duplication errors in genome assemblies

The paper quantifies false duplications in genome assemblies of platypus, zebra finch, and Anna's hummingbird, showing they lead to overestimated gene family expansions.

False gene and chromosome losses affected by assembly and sequence errors

The paper evaluates new vertebrate genome assemblies from the VGP against previous references, finding significant improvements in completeness and accuracy.

Genome sequence assembly evaluation using long-range sequencing data

This paper introduces Asset, a tool to evaluate genome assemblies using long-range data, demonstrating its ability to detect structural misassemblies in human, goat, and fish genomes.

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck)

The paper presents a high-quality genome and transcriptome of the tufted duck, comparing short and long-read sequencing technologies for transcriptome assembly.

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

Towards complete and error-free genome assemblies of all vertebrate species

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.