Mitochondrial genomes revisited: why do different lineages retain different genes?

A Butenko, J Lukeš, D Speijer, JG Wideman - BMC biology, 2024 - Springer
The mitochondria contain their own genome derived from an alphaproteobacterial
endosymbiont. From thousands of protein-coding genes originally encoded by their …

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

M Uliano-Silva, JGRN Ferreira, K Krasheninnikova… - BMC …, 2023 - Springer
Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb)
and highly accurate (> Q20). Because of these properties, they have revolutionised genome …

Significantly improving the quality of genome assemblies through curation

K Howe, W Chow, J Collins, S Pelan, DL Pointon… - …, 2021 - academic.oup.com
Genome sequence assemblies provide the basis for our understanding of biology.
Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of …

Towards complete and error-free genome assemblies of all vertebrate species

A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti… - Nature, 2021 - nature.com
High-quality and complete reference genome assemblies are fundamental for the
application of genomics to biology, disease, and biodiversity conservation. However, such …

Semi-automated assembly of high-quality diploid human reference genomes

ED Jarvis, G Formenti, A Rhie, A Guarracino, C Yang… - Nature, 2022 - nature.com
The current human reference genome, GRCh38, represents over 20 years of effort to
generate a high-quality assembly, which has benefitted society,. However, it still has many …

Fourth report on chicken genes and chromosomes 2022

J Smith, JM Alfieri, N Anthony, P Arensburger… - … and genome research, 2023 - karger.com
The chicken continues to hold its position as a leading model organism within many areas of
research, as well as being a major source of protein for human consumption. The First …

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

D Larivière, L Abueg, N Brajuka, C Gallardo-Alba… - Nature …, 2024 - nature.com
The Earth BioGenome Project aims to produce reference genomes for all~ 1.8 million known
eukaryotic species over the next decade 1–4. Achieving this goal will require the current …

Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

M Alvarenga, AKP D'Elia, G Rocha, CA Arantes… - BMC genomics, 2024 - Springer
Background Phylogenetic gaps of public databases of reference sequences are a major
obstacle for comparative genomics and management of marine resources, particularly in the …

Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

P Montaña-Lozano, M Moreno-Carmona… - Scientific reports, 2022 - nature.com
Vertebrate mitochondrial genomes have been extensively studied for genetic and
evolutionary purposes, these are normally believed to be extremely conserved, however …

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks

AT Sendell-Price, FJ Tulenko, M Pettersson… - Nature …, 2023 - nature.com
Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often
acting as apex predators. They are considered a slow-evolving lineage and have been …