Ian R. Henderson

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

This study identifies centromeric repeat turnovers in Arabidopsis species, revealing evolutionary mechanisms and the role of genetic drift and centromere drive in repeat replacement.

This study uses CRISPR to reposition centromeres in Arabidopsis, showing how neo-chromosomes with altered centromere positions lead to meiotic segregation distortion and aneuploidy.

The paper identifies centromeres as a source of telomeric sequences in Arabidopsis, showing ITR domains arise from centromeres through amplification and adopt a distinct chromatin state.

The paper investigates chromosomal evolution in sedges and rushes, finding evidence of polycentromeres and their impact on genome rearrangement rates and segregation patterns.

The paper analyzes Tyba satellite DNA repeats and transposable elements in holocentric species to reveal evolutionary dynamics of repeat-based holocentromeres across a pangenome.

The paper investigates how natural genetic variation in Arabidopsis thaliana affects centromere-proximal crossover frequency and segregation distortion during meiosis.

This study uses CRISPR to target H3K4me3 methyltransferases in Arabidopsis, showing activation of gene expression and increased meiotic crossover recombination near centromeres.

The paper shows CDCA7A and CDCA7B maintain CG methylation in centromeric heterochromatin by remodeling H1-containing nucleosomes, with H1 having an inhibitory role.

COmapper uses long-read sequencing to map meiotic crossovers in Arabidopsis with high resolution, showing comparable accuracy to short-read methods and revealing crossover enrichment at gene promoters.

The paper analyzes 30 chromosome-level Drosophila genome assemblies to study the evolutionary dynamics of centromeric satellite repeats and identifies the ananassae subgroup as a model for centromere evolution.

The paper curates and presents a collection of long-read genome assemblies for Arabidopsis thaliana accessions to enhance plant genome research.

The paper shows that retrotransposons in Arabidopsis promote centromere function through epigenetically activated small RNAs, which are essential for chromosome segregation.

The paper maps meiotic crossover landscapes near centromeres in Arabidopsis, showing suppression linked to structural variation and DNA methylation.

The paper shows MSH2 promotes interfering crossovers and suppresses non-interfering ones at polymorphic loci in Arabidopsis, shaping crossover distribution based on genetic variation.

The paper compares HiFi and CLR long-read assemblies in Arabidopsis thaliana to assess centromere and rDNA cluster reconstruction, finding HiFi reduces gaps and enables gapless centromere assembly.

The paper reports the complete sequence of a 641-kb mitochondrial DNA insertion in the Arabidopsis thaliana nuclear genome using long-read sequencing technologies.

Ultra-long-read sequencing resolves Arabidopsis centromeres, revealing their genetic and epigenetic structure and dynamics.

The paper generates a high-density crossover map in Arabidopsis thaliana to study how structural variants and epigenetic features influence meiotic crossover positioning.

The paper investigates how REC8-cohesin interacts with chromatin and transcription to regulate meiotic recombination in Arabidopsis.

The paper maps meiotic crossovers in Arabidopsis thaliana disease resistance genes, finding that interhomolog divergence suppresses crossover frequency and that local context influences recombination outcomes in mutants.

The paper maps meiotic DSBs in Arabidopsis using SPO11-1-oligonucleotides and shows their association with chromatin features and transposon activity.

This study shows that disrupting H3K9me2 and non-CG DNA methylation in Arabidopsis increases meiotic DSBs in centromeres and crossovers in pericentromeric heterochromatin.

The paper increases meiotic recombination in Arabidopsis by combining HEI10 overexpression with RECQ4A/RECQ4B mutations, leading to more crossovers and specific recombination patterns.