Alex Harkess

Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools

CBS-tools identifies, phases, and annotates sex chromosomes using k-mer analysis from whole-genome sequencing data across multiple species.

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

The paper develops crop-specific Nanopore basecalling models for Rosaceae species to improve sequencing quality and enables community use of these models.

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

The paper presents chromosome-level genome assemblies for four Amaranthus species, revealing conserved sex chromosome inversions and providing resources for evolutionary and agronomic research.

The Polyploid History of Cultivated Dahlia

The paper assembles and annotates the genome of a tetraploid Dahlia variabilis cultivar, identifying it as a segmental tetraploid with evidence of auto- and allopolyploidy.

A newly arisen indel governs a leaf shape polymorphism in the Ivy Leaf Morning Glory (Ipomoea hederacea)

The paper identifies a 117 kb indel associated with leaf shape polymorphism in Ipomoea hederacea and shows it is a novel genetic mechanism distinct from related species.

An X-linked sex determination mechanism in cannabis and hop

The paper identifies an X-linked sex determination mechanism in cannabis and hop, showing that an X-linked gene involved in ethylene biosynthesis controls female inflorescence development, while the Y chromosome lacks clear sex-determining genes.

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

This paper presents the first chromosome-scale, haplotype-resolved genome assembly and annotation for Carya glabra, revealing it as an autotetraploid and providing resources for ecological and agricultural studies.

Dissecting the regulatory and genomic drivers of the dichogamy determining G-locus in pecan

The paper identifies the genetic drivers of the G-locus in pecan trees using pangenome-integrated quantitative genomics, revealing a Mendelian super-gene responsible for dichogamy.

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

The paper presents a chromosome-scale, haplotype-resolved genome assembly for Quercus virginiana, contributing to genomic resources for studying hybridization and structural genomic changes in oaks.

Leveraging whole-genome re-sequencing for diversity, population structure, and a public mid-density genotyping enrichment panel in crimson clover (Trifolium incarnatum L.) for breeding purposes

This paper uses whole-genome resequencing to analyze diversity and structure in crimson clover and develops a mid-density SNP capture panel for breeding applications.

Two independent origins of XY sex chromosomes in Asparagus

This study compares the evolution of XY sex chromosomes in two closely related Asparagus clades, revealing distinct genetic mechanisms and timing for the origin of dioecy.

Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts

Elevated CO2 Reshapes the 3D Chromatin Landscape of Arabidopsis thaliana

This study shows elevated CO2 causes broad 3D chromatin reorganization in Arabidopsis thaliana, with intergenerational persistence and involvement of RdDM and PcG pathways.

A High-throughput Sequencing Screen to Identify Apomixis in Plants

The paper develops a short-read skim-seq method to identify apomictic genotypes in plants, finding 17 new apomictic genotypes in Malus species.

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

This study presents a chromosome-level genome of Myrothamnus flabellifolia and transcriptomic data, revealing its desiccation tolerance mechanisms and sex determination system.

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

This study investigates the genomic basis of species richness disparity in Asteraceae by analyzing genome duplications and regulatory evolution.

Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome

This study constructs a chromosome-scale cannabis pangenome to explore genomic diversity and evolution, revealing low diversity in cannabinoid synthase genes and high diversity in other regions.

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

The paper estimates de novo mutation rates in Panthera and Neofelis species using pedigrees, finding rates between 0.5 and 1.4e-08 per generation per base pair.

Long-Read Low-Pass Sequencing for High-Resolution Trait Mapping

This study develops and applies long-read low-pass sequencing for high-resolution trait mapping in peanut, showing improved variant detection and cost-effectiveness compared to short-read methods.

Chromosome Numbers and Reproductive Life Cycles in Green Plants: A phylo-transcriptomic perspective

This study investigates the relationship between heterosporous reproduction and chromosome number reduction in green plants using phylo-transcriptomic analyses and gene family evolution models.

ZW sex chromosome structure in Amborella trichopoda

The paper presents a haplotype-resolved genome assembly of Amborella trichopoda, identifying a young ZW sex chromosome system with a 3-Megabase sex-determination region that shows limited degeneration.

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae

The paper presents a chromosome-level genome assembly for the gray fox, confirming the loss of PRDM9 functionality in the basal canid lineage.

A Haplotype-resolved, Chromosome-scale Genome for Malus domestica 'WA 38'

The paper presents a haplotype-resolved, chromosome-scale genome for the apple cultivar WA 38, using short and long read sequencing data to assemble and segregate parental haplotomes.

A chromosome-scale assembly for dAnjou pear

This paper presents a chromosome-scale, phased genome assembly for the dAnjou pear, revealing gene content and duplication patterns.

Genome of the North American wild apple species Malus angustifolia

The paper reports the genome assembly and annotation of Malus angustifolia, identifies SNPs and structural variants, and explores phylogenetic relationships with Eurasian Malus species.

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus.

This paper presents a high-quality, haplotype-resolved genome assembly of Malus fusca and identifies structural variants and a fire blight resistance locus.

A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica)

The paper presents a fully phased, chromosome-scale genome of Honeycrisp apple, providing insights into genetic mechanisms of horticulturally important traits.

GENESPACE: syntenic pan-genome annotations for eukaryotes

GENESPACE provides pan-genome annotations to analyze syntenic relationships across diverse eukaryotic genomes, revealing structural variation at multiple biological scales.

Sex chromosome evolution via two genes

The paper shows sex chromosomes can evolve from autosomes through two genes: one suppressing female function and one promoting male function.

Retrotransposon proliferation coincident with the evolution of dioecy in Asparagus

The paper investigates genome size expansion in dioecious Asparagus species and finds retrotransposon proliferation, not polyploidization, is the main driver.