Mammalian transposable elements and their impacts on genome evolution

RN Platt, MW Vandewege, DA Ray - Chromosome Research, 2018 - Springer
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate
themselves in a genome. Mammalian genomes are dominated by TEs, which can reach …

Evolution and diversity of transposable elements in vertebrate genomes

CG Sotero-Caio, RN Platt, A Suh… - Genome biology and …, 2017 - academic.oup.com
Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via
transposition or retrotransposition and often make up large fractions of vertebrate genomes …

Six reference-quality genomes reveal evolution of bat adaptations

D Jebb, Z Huang, M Pippel, GM Hughes… - Nature, 2020 - nature.com
Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity
and unique immunity. High-quality genomes are crucial for understanding the molecular …

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 …

Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline

T Baril, J Galbraith, A Hayward - Molecular Biology and …, 2024 - academic.oup.com
Transposable elements (TEs) are major components of eukaryotic genomes and are
implicated in a range of evolutionary processes. Yet, TE annotation and characterization …

Insights into mammalian TE diversity through the curation of 248 genome assemblies

AB Osmanski, NS Paulat, J Korstian, JR Grimshaw… - Science, 2023 - science.org
We examined transposable element (TE) content of 248 placental mammal genome
assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that …

Genomics of cold adaptations in the Antarctic notothenioid fish radiation

I Bista, JMD Wood, T Desvignes, SA McCarthy… - Nature …, 2023 - nature.com
Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish
group in the freezing seas of the Southern Ocean. To improve understanding of the …

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

V Peona, MPK Blom, L Xu, R Burri… - Molecular ecology …, 2021 - Wiley Online Library
Genome assemblies are currently being produced at an impressive rate by consortia and
individual laboratories. The low costs and increasing efficiency of sequencing technologies …

Evolution of bird genomes—a transposon's‐eye view

A Kapusta, A Suh - Annals of the New York Academy of …, 2017 - Wiley Online Library
Birds, the most species‐rich monophyletic group of land vertebrates, have been subject to
some of the most intense sequencing efforts to date, making them an ideal case study for …

DeepTE: a computational method for de novo classification of transposons with convolutional neural network

H Yan, A Bombarely, S Li - Bioinformatics, 2020 - academic.oup.com
Abstract Motivation Transposable elements (TEs) classification is an essential step to
decode their roles in genome evolution. With a large number of genomes from non-model …