Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

RM Bowers, NC Kyrpides, R Stepanauskas… - Nature …, 2017 - nature.com
We present two standards developed by the Genomic Standards Consortium (GSC) for
reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum …

Functional horizontal gene transfer from bacteria to eukaryotes

F Husnik, JP McCutcheon - Nature Reviews Microbiology, 2018 - nature.com
Bacteria influence eukaryotic biology as parasitic, commensal or beneficial symbionts. Aside
from these organismal interactions, bacteria have also been important sources of new …

BlobToolKit–interactive quality assessment of genome assemblies

R Challis, E Richards, J Rajan… - G3: Genes …, 2020 - academic.oup.com
Reconstruction of target genomes from sequence data produced by instruments that are
agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether …

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

NM Davis, DM Proctor, SP Holmes, DA Relman… - Microbiome, 2018 - Springer
Background The accuracy of microbial community surveys based on marker-gene and
metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA …

Mirusviruses link herpesviruses to giant viruses

M Gaïa, L Meng, E Pelletier, P Forterre, C Vanni… - Nature, 2023 - nature.com
DNA viruses have a major influence on the ecology and evolution of cellular organisms,,–,
but their overall diversity and evolutionary trajectories remain elusive. Here we carried out a …

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

TO Delmont, C Quince, A Shaiber, ÖC Esen… - Nature …, 2018 - nature.com
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and
thus microbial primary productivity. Until now, cyanobacterial populations have been viewed …

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

TO Delmont, M Gaia, DD Hinsinger, P Fremont… - Cell Genomics, 2022 - cell.com
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate.
However, their poor representation in culture collections limits our understanding of the …

Contamination detection in genomic data: more is not enough

L Cornet, D Baurain - Genome Biology, 2022 - Springer
The decreasing cost of sequencing and concomitant augmentation of publicly available
genomes have created an acute need for automated software to assess genomic …

Accurate and complete genomes from metagenomes

LX Chen, K Anantharaman, A Shaiber… - Genome …, 2020 - genome.cshlp.org
Genomes are an integral component of the biological information about an organism; thus,
the more complete the genome, the more informative it is. Historically, bacterial and …

No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

G Koutsovoulos, S Kumar… - Proceedings of the …, 2016 - National Acad Sciences
Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of
Arthropoda. Many species of Tardigrada can survive extreme conditions through …