Insect mitochondrial genomics: implications for evolution and phylogeny

SL Cameron - Annual review of entomology, 2014 - annualreviews.org
The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in
insects, outnumbering nuclear genomes tenfold and representing all orders versus very few …

Is serotonin an upper or a downer? The evolution of the serotonergic system and its role in depression and the antidepressant response

PW Andrews, A Bharwani, KR Lee, M Fox… - Neuroscience & …, 2015 - Elsevier
The role of serotonin in depression and antidepressant treatment remains unresolved
despite decades of research. In this paper, we make three major claims. First, serotonin …

Strand-preferred base editing of organellar and nuclear genomes using CyDENT

J Hu, Y Sun, B Li, Z Liu, Z Wang, Q Gao, M Guo… - Nature …, 2024 - nature.com
Transcription-activator-like effector (TALE)-based tools for base editing of nuclear and
organellar DNA rely on double-stranded DNA deaminases, which edit substrate bases on …

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

JJ **, WB Yu, JB Yang, Y Song, CW DePamphilis… - Genome biology, 2020 - Springer
GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from
whole genome sequencing data. It recruits organelle-associated reads using a modified …

[LIBRO][B] Environmental DNA: For biodiversity research and monitoring

P Taberlet, A Bonin, L Zinger, E Coissac - 2018 - books.google.com
Environmental DNA (eDNA) refers to DNA that can be extracted from environmental
samples (such as soil, water, feces, or air) without the prior isolation of any target organism …

Chloroplot: an online program for the versatile plotting of organelle genomes

S Zheng, P Poczai, J Hyvönen, J Tang… - Frontiers in …, 2020 - frontiersin.org
Understanding the complexity of genomic structures and their unique architecture is linked
with the power of visualization tools used to represent these features. Such tools should be …

MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline

W Iwasaki, T Fukunaga, R Isagozawa… - Molecular biology …, 2013 - academic.oup.com
Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful
and precise de novo annotations for mitogenome sequences. Fish occupy an important …

Automatic annotation of organellar genomes with DOGMA

SK Wyman, RK Jansen, JL Boore - Bioinformatics, 2004 - academic.oup.com
The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar
(plant chloroplast and animal mitochondrial) genomes. It is a Web-based package that …

Structure and variation of the mitochondrial genome of fishes

TP Satoh, M Miya, K Mabuchi, M Nishida - BMC genomics, 2016 - Springer
Background The mitochondrial (mt) genome has been used as an effective tool for
phylogenetic and population genetic analyses in vertebrates. However, the structure and …

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

Q Li, Y Luo, A Sha, W **ao, Z **ong, X Chen… - Frontiers in …, 2023 - frontiersin.org
Introduction Codon basis is a common and complex natural phenomenon observed in many
kinds of organisms. Methods In the present study, we analyzed the base bias of 12 …