Chromosomal and Genetic Variations

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

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.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

From 338 beetle genomes, eight ancestral linkage groups were inferred; rearrangement rates vary widely, peaking in major radiations, and the X chromosome dates to Holometabola's ancestor.

A deep-time landscape of plant cis-regulatory sequence evolution

Conservatory, an orthogroup-centric conserved noncoding sequence finder, catalogs 2.3 million unique CNSs across 314 plant genomes and reveals regulatory elements older than angiosperms and seed plants.

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes

In spatial transcriptomes from five plant species, segmental (including whole-genome) duplicates show higher, broader, spatially variable expression and redundancy, while small-scale duplicates diverge asymmetrically.

The variation and evolution of complete human centromeres

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

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).

RepeatModeler2: automated genomic discovery of transposable element families

With a new structural LTR module, RepeatModeler2 recovers 2.9 to 4.7 times more curated TE families near-perfectly than RepeatModeler 1.0.11 in fruit fly, zebrafish, and rice.