Joanna Collins

The paper reports extreme programmed DNA elimination in Auanema rhodense during embryogenesis, revealing extensive loss of germline-specific DNA from somatic cells.

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

The paper reconstructs ancestral linkage groups in 340 dipteran genomes to study chromosome evolution, finding conserved groups in Nematoceran lineages and chromosomal fissions in Brachycera.

This study examines genome evolution in parthenogenetic nematodes, revealing chromosome fusions, rearrangements, and evidence of rare sexual reproduction events.

The paper presents the genome of Echinomermella matsi, a sea urchin parasite, and places it within the nematode order Plectida, highlighting its evolutionary significance for studying aquatic parasitism.

The paper identifies programmed DNA elimination in three Caenorhabditis species, showing it was present in their last common ancestor and later lost in some lineages.

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.

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.

The paper analyzes genomic diversity loss in whooping cranes despite population recovery, finding 70% genetic diversity loss and increased inbreeding.

This study presents a chromosome-scale genome assembly of Triticum timopheevii using PacBio HiFi and Hi-C data, revealing genomic features and relationships between wheat genomes.

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.

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.

The paper presents a pangenome for the barn swallow and identifies genes under selection linked to synanthropy and domestication traits.

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.

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 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.

This paper presents a chromosome-level genome assembly of Acanthopagrus latus using PacBio and Hi-C technologies, enabling research on sex reversal mechanisms.

gEVAL-assisted manual curation of 111 VGP and DToL assemblies averaged 221 interventions per Gb, raising mean scaffold N50 by 40% and cutting scaffold counts by 29%.

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.

This paper evaluates GRCh38 and de novo haploid assemblies, finding that GRCh38 remains superior for complex genomic regions and coding sequences despite improvements in newer assemblies.