Fergal J. Martin

Conserved genes, discordant structure: a pangenomic view of plant mitochondrial genome evolution

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.

Decoding the naked mole-rat genome, telomere to telomere

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.

ERGA-BGE genome of Valencia hispanica (Valenciennes, 1826): a critically endangered Iberian toothcarp

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

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

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.

ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe

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

Complete de novo assembly and re-annotation of the zebrafish genome

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

The Onychomys pangenome reveals the unique molecular adaptations that confer toxin resistance

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

The genome sequence of the hemlock woolly adelgid, Adelges tsugae Annand 1924

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

ERGA-BGE genome of Stigmatoteuthis arcturi Robson, 1948: the jewelled squid

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

ERGA-BGE genome of Noah's Ark shell (Arca noae Linnaeus, 1758), a Mediterranean bivalve species

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

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.

ERGA-BGE genome of Pinctada radiata (Leach, 1814): one of the first Lessepsian migrants

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

ERGA-BGE Reference Genome of the Striped Field Mouse (Apodemus agrarius), a Widespread and Abundant Species in Central and Eastern Europe

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

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology

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

ERGA-BGE Reference Genome of the Northern chamois (Rupicapra rupicapra): Europe's most abundant mountain ungulate

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

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

Continent-wide genomic analysis of the African buffalo (Syncerus caffer).

This study presents a continent-wide genomic analysis of African buffalo, revealing three main lineages and signatures of selection related to immune response.

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

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

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

The complete sequence of a human Y chromosome

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

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

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.

A Draft Human Pangenome Reference

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

Recombination between heterologous human acrocentric chromosomes

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

Lepidoptera genomics based on 88 chromosomal reference sequences informs population genetic parameters for conservation

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 swan genome and transcriptome: its not all black and white

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

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.