[HTML][HTML] Protein domain identification methods and online resources

Y Wang, H Zhang, H Zhong, Z Xue - Computational and structural …, 2021 - Elsevier
Protein domains are the basic units of proteins that can fold, function, and evolve
independently. Knowledge of protein domains is critical for protein classification …

Shifting the limits in wheat research and breeding using a fully annotated reference genome

International Wheat Genome Sequencing Consortium … - Science, 2018 - science.org
INTRODUCTION Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth,
contributing about a fifth of the total calories consumed by humans. Consequently, wheat …

Clades of huge phages from across Earth's ecosystems

B Al-Shayeb, R Sachdeva, LX Chen, F Ward, P Munk… - Nature, 2020 - nature.com
Bacteriophages typically have small genomes and depend on their bacterial hosts for
replication. Here we sequenced DNA from diverse ecosystems and found hundreds of …

The distinction of CPR bacteria from other bacteria based on protein family content

R Méheust, D Burstein, CJ Castelle… - Nature communications, 2019 - nature.com
Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but
the organismal distribution of their protein families remains unclear. Here, we leveraged …

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

A Rastogi, U Maheswari, RG Dorrell, FRJ Vieira… - Scientific reports, 2018 - nature.com
Diatoms are one of the most successful and ecologically important groups of eukaryotic
phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better …

Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog

R Méheust, CJ Castelle, PB Matheus Carnevali… - The ISME …, 2020 - academic.oup.com
Currently described members of Elusimicrobia, a relatively recently defined phylum, are
animal-associated and rely on fermentation. However, free-living Elusimicrobia have been …

Community‐level responses to iron availability in open ocean plankton ecosystems

L Caputi, Q Carradec, D Eveillard… - Global …, 2019 - Wiley Online Library
Predicting responses of plankton to variations in essential nutrients is hampered by limited
in situ measurements, a poor understanding of community composition, and the lack of …

Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea

CJ Castelle, R Méheust, AL Jaffe, K Seitz… - Frontiers in …, 2021 - frontiersin.org
DPANN are small-celled archaea that are generally predicted to be symbionts, and in some
cases are known episymbionts of other archaea. As the monophyly of the DPANN remains …

Hidden variation in polyploid wheat drives local adaptation

LJ Gardiner, R Joynson, J Omony… - Genome …, 2018 - genome.cshlp.org
Wheat has been domesticated into a large number of agricultural environments and has the
ability to adapt to diverse environments. To understand this process, we survey genotype …

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

A Ugarte, R Vicedomini, J Bernardes, A Carbone - Microbiome, 2018 - Springer
Background Biochemical and regulatory pathways have until recently been thought and
modelled within one cell type, one organism and one species. This vision is being …