Ranking the risk of animal-to-human spillover for newly discovered viruses DOI Creative Commons
Zoë Grange, Tracey Goldstein, Christine K. Johnson

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(15)

Published: April 5, 2021

The death toll and economic loss resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are stark reminders that we vulnerable to zoonotic viral threats. Strategies needed identify characterize animal viruses pose greatest risk of spillover spread in humans inform public health interventions. Using expert opinion scientific evidence, identified host, viral, environmental factors contributing virus humans. We then developed a ranking framework interactive web tool, SpillOver, estimates score for wildlife-origin viruses, creating comparative assessment with uncharacterized potential alongside those already known be zoonotic. data testing 509,721 samples 74,635 animals as part discovery project records detections around world, ranked 887 wildlife viruses. Validating assessment, top 12 were including SARS-CoV-2. Several newly detected higher than scientifically informed process, capitalized on recent wealth systematically prioritize targets investigation. publicly accessible SpillOver platform can used by policy makers scientists research interventions prevention rapid control disease outbreaks. is living, database refined over time continue improve quality availability information threats human health.

Language: Английский

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life DOI
Donovan H. Parks, Maria Chuvochina, David W. Waite

et al.

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 36(10), P. 996 - 1004

Published: Aug. 27, 2018

Language: Английский

Citations

3030
Towards complete and error-free genome assemblies of all vertebrate species DOI Creative Commons
Arang Rhie, Shane McCarthy, Olivier Fédrigo

et al.

Nature, Journal Year: 2021, Volume and Issue: 592(7856), P. 737 - 746

Published: April 28, 2021

Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such available only a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling highly accurate nearly genomes. Here we present lessons learned from generating 16 that represent six major vertebrate lineages. We confirm long-read sequencing technologies essential maximizing quality, unresolved complex repeats haplotype heterozygosity sources assembly error when not handled correctly. Our correct substantial errors, add missing sequence in some best historical genomes, reveal biological discoveries. These include identification many false gene duplications, increases sizes, chromosome rearrangements specific lineages, repeated independent breakpoint bat canonical GC-rich pattern protein-coding genes their regulatory regions. Adopting these lessons, have embarked on Vertebrate Genomes Project (VGP), an effort generate high-quality, genomes all roughly 70,000 extant help enable new era discovery across life sciences.

Language: Английский

Citations

2020
One thousand plant transcriptomes and the phylogenomics of green plants DOI Creative Commons

Mack J.H. Leebens,

Sean W. Graham, Gane Ka‐Shu Wong

et al.

Nature, Journal Year: 2019, Volume and Issue: 574(7780), P. 679 - 685

Published: Oct. 23, 2019

Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial aquatic ecosystems. Here, as part the One Thousand Plant Transcriptomes Initiative, we sequenced vegetative transcriptomes 1,124 species that span a broad sense (Archaeplastida), including green (Viridiplantae), glaucophytes (Glaucophyta) red algae (Rhodophyta). Our analysis provides robust phylogenomic framework for examining evolution plants. Most inferred relationships are well supported across multiple tree supermatrix analyses, but discordance among plastid nuclear gene trees at few nodes highlights complexity plant genome evolution, polyploidy, periods rapid speciation, extinction. Incomplete sorting ancestral variation, polyploidization massive expansions families punctuate evolutionary history Notably, find large preceded origins plants, land vascular whereas whole-genome duplications to occurred repeatedly throughout flowering ferns. The increasing availability high-quality sequences advances functional genomics enabling research on life.

Language: Английский

Citations

1453
TimeTree 5: An Expanded Resource for Species Divergence Times DOI Creative Commons
Sudhir Kumar,

Michael Suleski,

Jack M. Craig

et al.

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(8)

Published: Aug. 1, 2022

Abstract We present the fifth edition of TimeTree Life resource (TToL5), a product timetree life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible all. Using TToL5 web portal, users can retrieve studies divergence times between species, timeline species’ evolution beginning with origin life, for given group at desired taxonomic rank. contains time information on 137,306 41% more than previous edition. The interface is now Americans Disabilities Act-compliant mobile-friendly, result comprehensive source code refactoring. also offers programmatic access species timelines through an application programming interface, which timetree.temple.edu/api. publicly available timetree.org.

Language: Английский

Citations

808
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse DOI Creative Commons
Frank Koopmans, Pim van Nierop, Maria Andres‐Alonso

et al.

Neuron, Journal Year: 2019, Volume and Issue: 103(2), P. 217 - 234.e4

Published: June 3, 2019

Language: Английский

Citations

789
Gene expression across mammalian organ development DOI
Margarida Cardoso-Moreira,

Jean Halbert,

Delphine Valloton

et al.

Nature, Journal Year: 2019, Volume and Issue: 571(7766), P. 505 - 509

Published: June 26, 2019

Language: Английский

Citations

690
D-GENIES: dot plot large genomes in an interactive, efficient and simple way DOI Creative Commons

Floréal Cabanettes,

Christophe Klopp

PeerJ, Journal Year: 2018, Volume and Issue: 6, P. e4958 - e4958

Published: June 4, 2018

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed easily generated genomic alignment dot plots, but they often limited in the input size. D-GENIES is standalone web application performing large genome alignments using minimap2 software package generating interactive plots. It enables users sort query sequences along reference, zoom plot download several image, or files. an easy-to-install, open-source (GPL) Python JavaScript. The source code available at https://github.com/genotoul-bioinfo/dgenies it can be tested http://dgenies.toulouse.inra.fr/ .

Language: Английский

Citations

584
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum DOI Creative Commons
Xing‐Xing Shen, Dana A. Opulente, Jacek Kominek

et al.

Cell, Journal Year: 2018, Volume and Issue: 175(6), P. 1533 - 1545.e20

Published: Nov. 1, 2018

Language: Английский

Citations

532
Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades DOI Creative Commons
Nicholas D. Youngblut, Georg H. Reischer,

William A. Walters

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: May 16, 2019

Abstract Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared wild counterparts. To resolve this disagreement, we analyze new, large, and highly diverse animal distal 16 S rRNA microbiome dataset, comprises 80% animals includes members of Mammalia, Aves, Reptilia, Amphibia, Actinopterygii. We decouple effects host evolutionary history diet diversity show that each factor modulates aspects diversity. Moreover, particular taxa associated with phylogeny or Mammalia stronger signal cophylogeny. Finally, find environmental filtering microbe-microbe interactions differ among clades. These findings provide robust assessment processes driving intestine.

Language: Английский

Citations

440
Progressive Cactus is a multiple-genome aligner for the thousand-genome era DOI Creative Commons
Joel Armstrong, Glenn Hickey, Mark Diekhans

et al.

Nature, Journal Year: 2020, Volume and Issue: 587(7833), P. 246 - 251

Published: Nov. 11, 2020

Abstract New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements third-generation technologies 1–3 . For example, the number of vertebrate currently NCBI (National Center for Biotechnology Information) database 4 increased by more than 50% 1,485 year from July 2018 2019. In addition this influx different species, new human de novo 5 are being produced, which enable analysis not only small polymorphisms, but also complex, large-scale structural differences between individuals haplotypes. This coming era its unprecedented amount data offer opportunity uncover many insights into evolution present challenges how adapt current methods meet scale. Cactus 6 , reference-free multiple alignment program, has shown be highly accurate, existing implementation scales poorly with numbers genomes, struggles regions duplicated sequences. Here we describe progressive extensions create Progressive Cactus, enables tens thousands large genomes while maintaining high quality. We results an 600 amniote is our knowledge largest created so far.

Language: Английский

Citations

431