Phylogenetic tree building in the genomic age

P Kapli, Z Yang, MJ Telford - Nature Reviews Genetics, 2020 - nature.com
Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …

Extreme genome reduction in symbiotic bacteria

JP McCutcheon, NA Moran - Nature Reviews Microbiology, 2012 - nature.com
Since 2006, numerous cases of bacterial symbionts with extraordinarily small genomes
have been reported. These organisms represent independent lineages from diverse …

The nature of the last universal common ancestor and its impact on the early Earth system

ERR Moody, S Álvarez-Carretero… - Nature Ecology & …, 2024 - nature.com
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth
system have been the subject of vigorous debate across diverse disciplines, often based on …

Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics

CS McFadden, LP Van Ofwegen… - Bulletin of the Society of …, 2022 - ssbbulletin.org
The anthozoan sub-class Octocorallia includes over 3500 nominal species of soft corals and
gorgonian sea fans, many of which serve as critical foundation species in benthic marine …

Global diversity and systematics of Hymenochaetaceae with poroid hymenophore

F Wu, LW Zhou, J Vlasák, YC Dai - Fungal Diversity, 2022 - Springer
Taxonomy and phylogeny of poroid Hymenochaetaceae based on the most comprehensive
phylogenetic analyses are presented. A phylogeny based on a combined dataset of ITS and …

Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus

JM Song, Z Guan, J Hu, C Guo, Z Yang, S Wang, D Liu… - Nature plants, 2020 - nature.com
Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the
genetic diversity underlying its massive phenotypic variations remains largely unexplored …

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold

T Aramaki, R Blanc-Mathieu, H Endo, K Ohkubo… - …, 2020 - academic.oup.com
KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by
homology search against a database of profile hidden Markov models (KOfam) with pre …

Phytophthora: taxonomic and phylogenetic revision of the genus

ZG Abad, TI Burgess, T Bourret, K Bensch… - Studies in …, 2023 - ingentaconnect.com
Many members of the Oomycota genus Phytophthora cause economic and environmental
impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of …

MAFFT-DASH: integrated protein sequence and structural alignment

J Rozewicki, S Li, KM Amada, DM Standley… - Nucleic acids …, 2019 - academic.oup.com
Here, we describe a web server that integrates structural alignments with the MAFFT
multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based …

Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality

EP Santoro, RM Borges, JL Espinoza, M Freire… - Science …, 2021 - science.org
Beneficial microorganisms for corals (BMCs) ameliorate environmental stress, but whether
they can prevent mortality and the underlying host response mechanisms remains elusive …