David A. Kudrna

Oryza genome evolution through a tetraploid lens

The paper presents 11 new chromosome-level genome assemblies of Oryza species, revealing core genome conservation and subgenome plasticity, and highlights implications for crop improvement.

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa)

The paper constructs a pan-genome inversion index for Asian rice using 16 genomes and finds a high inversion rate with functional implications.

Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

The paper presents a high-quality genome assembly of the soybean cultivar JD17 and identifies genetic variations compared to other soybean genomes.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

Assembly and Validation of Two Gap-free Reference Genomes for Xian/indica Rice Reveals Insights into Plant Centromere Architecture

The paper presents two gap-free rice genomes, revealing centromere structure and gene expression insights.

Highly accurate long-read HiFi sequencing data for five complex genomes

The paper provides highly accurate long-read HiFi sequencing datasets for five complex genomes to evaluate and develop bioinformatic tools.

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

This paper presents a chromosome-scale genome assembly of Brassica juncea, revealing differences between its A and B genomes.

Gapless assembly of maize chromosomes using long read technologies

The paper presents a gapless maize genome assembly using long read technologies and optical maps, achieving telomere-to-telomere assemblies for chromosomes 3 and 9.

Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice

The paper generates 12 new high-quality rice reference genomes to expand the genetic diversity coverage of cultivated rice, forming a comprehensive pan-genome resource with 16 reference sequences.

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

The paper identifies large palindromic structures in the sex chromosome of Salix purpurea, showing convergent evolution with mammalian sex chromosomes.

The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

The paper quantifies age-related somatic mutations and epimutations in a wild Populus trichocarpa tree over 330 years, showing lower mutation rates than annuals and distinct epimutation origins.

Genome sequence of the model rice variety KitaakeX

The paper reports the de novo genome sequencing and analysis of the rice variety KitaakeX, identifying genomic variations and providing a high-quality reference for rice functional genomics.