An overview of duplicated gene detection methods: Why the duplication mechanism has to be accounted for in their choice

T Lallemand, M Leduc, C Landès, C Rizzon, E Lerat - Genes, 2020 - mdpi.com
Gene duplication is an important evolutionary mechanism allowing to provide new genetic
material and thus opportunities to acquire new gene functions for an organism, with major …

The inference of gene trees with species trees

GJ Szöllősi, E Tannier, V Daubin… - Systematic …, 2015 - academic.oup.com
This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

I Braasch, AR Gehrke, JJ Smith, K Kawasaki… - Nature …, 2016 - nature.com
To connect human biology to fish biomedical models, we sequenced the genome of spotted
gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome …

Two types of TNF-α exist in teleost fish: phylogeny, expression, and bioactivity analysis of type-II TNF-α3 in rainbow trout Oncorhynchus mykiss

S Hong, R Li, Q Xu, CJ Secombes… - The Journal of …, 2013 - journals.aai.org
TNF-α is a cytokine involved in systemic inflammation and regulation of immune cells. It is
produced chiefly by activated macrophages as a membrane or secreted form. In rainbow …

Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors

NTT Nguyen, P Vincens, JF Dufayard… - Nucleic Acids …, 2022 - academic.oup.com
Genomicus is a database and web-server dedicated to comparative genomics in
eukaryotes. Its main functionality is to graphically represent the conservation of genomic …

A duplicated amh is the master sex-determining gene for Sebastes rockfish in the Northwest Pacific

W Song, Y Xie, M Sun, X Li, CK Fitzpatrick… - Open …, 2021 - royalsocietypublishing.org
Teleost fish are the most diverse group of vertebrates and provide opportunities to study the
evolution of sex determination (SD) systems. Using genomic and functional analyses, we …

Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

M Muffato, A Louis, NTT Nguyen, J Lucas… - Nature Ecology & …, 2023 - nature.com
Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies
and can trace small-scale sequence modifications through the evolution of genomes and …

OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates

PP Singh, H Isambert - Nucleic acids research, 2020 - academic.oup.com
All vertebrates including human have evolved from an ancestor that underwent two rounds
of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional …

Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins

VB Indjeian, GA Kingman, FC Jones, CA Guenther… - Cell, 2016 - cell.com
Changes in bone size and shape are defining features of many vertebrates. Here we use
genetic crosses and comparative genomics to identify specific regulatory DNA alterations …

The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants

N Mansilla, S Racca, DE Gras, DH Gonzalez… - International journal of …, 2018 - mdpi.com
Mitochondrial respiration is an energy producing process that involves the coordinated
action of several protein complexes embedded in the inner membrane to finally produce …