Leanne S. Haggerty

This study analyzes over 300 plant mitochondrial genomes to show that gene content is conserved but structural complexity varies, driven by repeat proliferation and recombination rather than intergenomic DNA transfer.

The paper presents a telomere-to-telomere genome assembly of the naked mole-rat and compares it with a related species to identify gene losses and duplications associated with unique traits.

The paper presents the chromosome-level genome assembly of Valencia hispanica, a critically endangered fish, to support conservation and ecological studies.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

MirMachine 2 annotates microRNAs across thousands of animal genomes, revealing methodological biases in apparent microRNA absence.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

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.

The paper presents the chromosome-level genome assembly of Androsace saussurei, a plant adapted to extreme alpine environments.

The paper presents a new zebrafish genome assembly with increased sequence coverage and improved annotation, along with a pangenome resource for variant analysis.

This study identifies molecular adaptations in Onychomys species that confer toxin resistance through genome analysis and positive selection detection.

The paper presents the genome sequence of the hemlock woolly adelgid, including chromosome assembly, gene annotation, and mitogenome data.

The paper presents the chromosome-level genome assembly of Stigmatoteuthis arcturi, providing insights into the evolutionary biology of deep-sea squids.

The paper presents the chromosome-level genome assembly of Arca noae, a Mediterranean bivalve, providing evolutionary insights and genomic resources for studying environmental adaptation.

The paper presents the genome of Pinctada radiata, a Lessepsian migrant, providing insights into its genetic adaptations to environmental changes and supporting conservation efforts.

The paper presents a chromosome-level reference genome for the striped field mouse, providing resources for phylogenetic studies and understanding its geographical distribution.

The paper presents an updated reference genome for the naked mole-rat, identifying gene losses and gains linked to its unique physiological traits.

The paper presents a chromosome-level reference genome for the Northern chamois, providing insights into its genetic adaptation to extreme environments.

This paper presents chromosome-scale assemblies of Astyanax mexicanus surface and cave populations to study genetic basis of adaptation to cave environments.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

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.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

This study uses long-read sequencing to analyze 88 Lepidoptera genomes, identifying genomic signatures linked to conservation concerns like low heterozygosity and high inbreeding.

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.

The paper presents a chromosome-level genome assembly of Atlantic herring, enabling the detection of a supergene and improved analysis of selection signals.