Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.

The open sharing of genomic data provides an incredibly rich resource for the study of bacterial evolution and function and even anthropogenic activities such as the widespread use of antimicrobials. However, these data consist of genomes assembled with different tools and levels of quality checking...

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Autores principales: Grace A Blackwell, Martin Hunt, Kerri M Malone, Leandro Lima, Gal Horesh, Blaise T F Alako, Nicholas R Thomson, Zamin Iqbal
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Publicado: Public Library of Science (PLoS) 2021
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spelling oai:doaj.org-article:abce2d8928ac4d6098a60f51ffb57a542021-12-02T19:54:26ZExploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.1544-91731545-788510.1371/journal.pbio.3001421https://doaj.org/article/abce2d8928ac4d6098a60f51ffb57a542021-11-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.3001421https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885The open sharing of genomic data provides an incredibly rich resource for the study of bacterial evolution and function and even anthropogenic activities such as the widespread use of antimicrobials. However, these data consist of genomes assembled with different tools and levels of quality checking, and of large volumes of completely unprocessed raw sequence data. In both cases, considerable computational effort is required before biological questions can be addressed. Here, we assembled and characterised 661,405 bacterial genomes retrieved from the European Nucleotide Archive (ENA) in November of 2018 using a uniform standardised approach. Of these, 311,006 did not previously have an assembly. We produced a searchable COmpact Bit-sliced Signature (COBS) index, facilitating the easy interrogation of the entire dataset for a specific sequence (e.g., gene, mutation, or plasmid). Additional MinHash and pp-sketch indices support genome-wide comparisons and estimations of genomic distance. Combined, this resource will allow data to be easily subset and searched, phylogenetic relationships between genomes to be quickly elucidated, and hypotheses rapidly generated and tested. We believe that this combination of uniform processing and variety of search/filter functionalities will make this a resource of very wide utility. In terms of diversity within the data, a breakdown of the 639,981 high-quality genomes emphasised the uneven species composition of the ENA/public databases, with just 20 of the total 2,336 species making up 90% of the genomes. The overrepresented species tend to be acute/common human pathogens, aligning with research priorities at different levels from individual interests to funding bodies and national and global public health agencies.Grace A BlackwellMartin HuntKerri M MaloneLeandro LimaGal HoreshBlaise T F AlakoNicholas R ThomsonZamin IqbalPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 19, Iss 11, p e3001421 (2021)
institution DOAJ
collection DOAJ
language EN
topic Biology (General)
QH301-705.5
spellingShingle Biology (General)
QH301-705.5
Grace A Blackwell
Martin Hunt
Kerri M Malone
Leandro Lima
Gal Horesh
Blaise T F Alako
Nicholas R Thomson
Zamin Iqbal
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.
description The open sharing of genomic data provides an incredibly rich resource for the study of bacterial evolution and function and even anthropogenic activities such as the widespread use of antimicrobials. However, these data consist of genomes assembled with different tools and levels of quality checking, and of large volumes of completely unprocessed raw sequence data. In both cases, considerable computational effort is required before biological questions can be addressed. Here, we assembled and characterised 661,405 bacterial genomes retrieved from the European Nucleotide Archive (ENA) in November of 2018 using a uniform standardised approach. Of these, 311,006 did not previously have an assembly. We produced a searchable COmpact Bit-sliced Signature (COBS) index, facilitating the easy interrogation of the entire dataset for a specific sequence (e.g., gene, mutation, or plasmid). Additional MinHash and pp-sketch indices support genome-wide comparisons and estimations of genomic distance. Combined, this resource will allow data to be easily subset and searched, phylogenetic relationships between genomes to be quickly elucidated, and hypotheses rapidly generated and tested. We believe that this combination of uniform processing and variety of search/filter functionalities will make this a resource of very wide utility. In terms of diversity within the data, a breakdown of the 639,981 high-quality genomes emphasised the uneven species composition of the ENA/public databases, with just 20 of the total 2,336 species making up 90% of the genomes. The overrepresented species tend to be acute/common human pathogens, aligning with research priorities at different levels from individual interests to funding bodies and national and global public health agencies.
format article
author Grace A Blackwell
Martin Hunt
Kerri M Malone
Leandro Lima
Gal Horesh
Blaise T F Alako
Nicholas R Thomson
Zamin Iqbal
author_facet Grace A Blackwell
Martin Hunt
Kerri M Malone
Leandro Lima
Gal Horesh
Blaise T F Alako
Nicholas R Thomson
Zamin Iqbal
author_sort Grace A Blackwell
title Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.
title_short Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.
title_full Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.
title_fullStr Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.
title_full_unstemmed Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.
title_sort exploring bacterial diversity via a curated and searchable snapshot of archived dna sequences.
publisher Public Library of Science (PLoS)
publishDate 2021
url https://doaj.org/article/abce2d8928ac4d6098a60f51ffb57a54
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