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 …

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 …

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

T Zhu, L Wang, H Rimbert, JC Rodriguez… - The Plant …, 2021 - Wiley Online Library
Until recently, achieving a reference‐quality genome sequence for bread wheat was long
thought beyond the limits of genome sequencing and assembly technology, primarily due to …

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

SJ Hoyt, JM Storer, GA Hartley, PGS Grady… - Science, 2022 - science.org
Mobile elements and repetitive genomic regions are sources of lineage-specific genomic
innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such …

[HTML][HTML] Pan-genome of wild and cultivated soybeans

Y Liu, H Du, P Li, Y Shen, H Peng, S Liu, GA Zhou… - Cell, 2020 - cell.com
Soybean is one of the most important vegetable oil and protein feed crops. To capture the
entire genomic diversity, it is needed to construct a complete high-quality pan-genome from …

Long-read sequence assembly: a technical evaluation in barley

M Mascher, T Wicker, J Jenkins, C Plott, T Lux… - The Plant …, 2021 - academic.oup.com
Sequence assembly of large and repeat-rich plant genomes has been challenging,
requiring substantial computational resources and often several complementary sequence …

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

S Ou, W Su, Y Liao, K Chougule, JRA Agda… - Genome biology, 2019 - Springer
Background Sequencing technology and assembly algorithms have matured to the point
that high-quality de novo assembly is possible for large, repetitive genomes. Current …

RepeatModeler2 for automated genomic discovery of transposable element families

JM Flynn, R Hubley, C Goubert, J Rosen… - Proceedings of the …, 2020 - pnas.org
The accelerating pace of genome sequencing throughout the tree of life is driving the need
for improved unsupervised annotation of genome components such as transposable …

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 …

Transposable elements as essential elements in the control of gene expression

A Gebrie - Mobile DNA, 2023 - Springer
Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile
elements, make up a significant portion of the genomes of higher animals. TEs contribute in …