A field guide to eukaryotic transposable elements

JN Wells, C Feschotte - Annual review of genetics, 2020 - annualreviews.org
Transposable elements (TEs) are mobile DNA sequences that propagate within genomes.
Through diverse invasion strategies, TEs have come to occupy a substantial fraction of …

Repetitive DNA sequence detection and its role in the human genome

X Liao, W Zhu, J Zhou, H Li, X Xu, B Zhang… - Communications …, 2023 - nature.com
Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and
regulating gene expression. In this review, we summarized the definition, arrangement, and …

Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2

P Novák, P Neumann, J Macas - Nature Protocols, 2020 - nature.com
RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based
clustering of next-generation sequencing reads for characterization of repetitive DNA in …

The giant diploid faba genome unlocks variation in a global protein crop

M Jayakodi, AA Golicz, J Kreplak, LI Fechete, D Angra… - Nature, 2023 - nature.com
Increasing the proportion of locally produced plant protein in currently meat-rich diets could
substantially reduce greenhouse gas emissions and loss of biodiversity. However, plant …

Repeat-based holocentromeres influence genome architecture and karyotype evolution

PG Hofstatter, G Thangavel, T Lux, P Neumann… - Cell, 2022 - cell.com
The centromere represents a single region in most eukaryotic chromosomes. However,
several plant and animal lineages assemble holocentromeres along the entire chromosome …

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

RG Zhang, GY Li, XL Wang, J Dainat… - Horticulture …, 2022 - academic.oup.com
Dear Editor, Transposable elements (TEs) constitute the largest portion of repetitive
sequences in many eukaryotic genomes, with long terminal repeat retrotransposons (LTR …

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

K Du, M Stöck, S Kneitz, C Klopp… - Nature ecology & …, 2020 - nature.com
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage
place it in a key phylogenetic position at the base of the~ 30,000 modern teleost fish …

A beginner's guide to manual curation of transposable elements

C Goubert, RJ Craig, AF Bilat, V Peona, AA Vogan… - Mobile DNA, 2022 - Springer
Background In the study of transposable elements (TEs), the generation of a high
confidence set of consensus sequences that represent the diversity of TEs found in a given …

Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat

JA Fawcett, R Takeshima, S Kikuchi, E Yazaki… - Nature Plants, 2023 - nature.com
Common buckwheat, Fagopyrum esculentum, is an orphan crop domesticated in southwest
China that exhibits heterostylous self-incompatibility. Here we present chromosome-scale …

A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome

S Perumal, CS Koh, L **, M Buchwaldt, EE Higgins… - Nature plants, 2020 - nature.com
It is only recently, with the advent of long-read sequencing technologies, that we are
beginning to uncover previously uncharted regions of complex and inherently recursive …