cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7718291
title: S10 Summary_blast_anti-CRISPR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718324
title: S9 anti-CRISPR list from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718291.v2
title: S10 Summary_blast_anti-CRISPR from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718324.v2
title: S9 anti-CRISPR list from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718291.v1
title: S6 CRISPR_target_results from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718324.v1
title: S5_ARG_database from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718318
title: S8 ARG_CRISPR-Cas_Acr_pseudomonas from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718318.v2
title: S8 ARG_CRISPR-Cas_Acr_pseudomonas from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species.

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718318.v1
title: S4 PA_spacer_target_ARG from Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

description: CRISPR-Cas systems are widespread in bacterial and archaeal genomes and in their canonical role in phage defence, they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. A newly discovered feature within these evolutionary dynamics is anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In <i>Pseudomonas aeruginosa</i>, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance, is likely to be very different in particular pathogenic species and clinical environments.This article is part of the theme issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
DOI: 10.6084/m9.figshare.7718429
title: Supplementary table S3 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Shared spacers from Thermus isolates
DOI: 10.6084/m9.figshare.7718387.v2
title: Supplementary table S4 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Clustering statistics.
DOI: 10.6084/m9.figshare.7718387
title: Supplementary table S4 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Clustering statistics.
DOI: 10.6084/m9.figshare.7718396
title: Supplementary data 1. Environmental Thermus CRISPR spacers (majour) from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Sequences of CRISPR spacers from natural Thermus communities. Only majour spacers (&gt;10 occurrences in each sample) are included.
DOI: 10.6084/m9.figshare.7718429.v2
title: Supplementary table S3 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Shared spacers from Thermus isolates
DOI: 10.6084/m9.figshare.7718387.v1
title: Table S4 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange

description: Clustering statistics.
DOI: 10.6084/m9.figshare.7718396.v2
title: Supplementary data 1. Environmental Thermus CRISPR spacers (majour) from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Sequences of CRISPR spacers from natural Thermus communities. Only majour spacers (&gt;10 occurrences in each sample) are included.
DOI: 10.6084/m9.figshare.7718429.v1
title: Table S3 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange

description: Shared spacers from Thermus isolates
DOI: 10.6084/m9.figshare.7718390
title: Supplementary data 2. Environmental Thermus CRISPR spacers (all) from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Sequences of CRISPR spacers from natural Thermus communities. All spacers are included.
DOI: 10.6084/m9.figshare.7718423
title: Supplementary table S5 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Reconstructed CRISPR arrays.
DOI: 10.6084/m9.figshare.7718423.v2
title: Supplementary table S5 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Reconstructed CRISPR arrays.
DOI: 10.6084/m9.figshare.7718396.v1
title: Data S1. Environmental Thermus CRISPR spacers (majour) from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange

description: Sequences of CRISPR spacers from natural Thermus communities. Only majour spacers (&gt;10 occurrences in each sample) are included.
DOI: 10.6084/m9.figshare.7718399
title: Supplementary table S1 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Primers used in this study
DOI: 10.6084/m9.figshare.7718390.v2
title: Supplementary data 2. Environmental Thermus CRISPR spacers (all) from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Sequences of CRISPR spacers from natural Thermus communities. All spacers are included.
DOI: 10.6084/m9.figshare.7718423.v1
title: Table S5 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange

description: Reconstructed CRISPR arrays.
DOI: 10.6084/m9.figshare.7718411
title: Supplementary table S2 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: A full list of 26 Thermus isolates analyzed in this work.
DOI: 10.6084/m9.figshare.7718390.v1
title: Data S2. Environmental Thermus CRISPR spacers (all) from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange

description: Sequences of CRISPR spacers from natural Thermus communities. All spacers are included.
DOI: 10.6084/m9.figshare.7718399.v2
title: Supplementary table S1 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: Primers used in this study
DOI: 10.6084/m9.figshare.7718399.v1
title: Table S1 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange

description: Primers used in this study
DOI: 10.6084/m9.figshare.7718411.v2
title: Supplementary table S2 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange.

description: A full list of 26 Thermus isolates analyzed in this work.
DOI: 10.6084/m9.figshare.7718411.v1
title: Table S2 from Natural diversity of CRISPR spacers of <i>Thermus</i>: evidence of local spacer acquisition and global spacer exchange

description: A full list of 26 Thermus isolates analyzed in this work.
DOI: 10.6084/m9.figshare.7734950
title: Drag forces and coefficients from the CFD simulations from Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs.

description: Ichthyosaurs are an extinct group of fully marine tetrapods that were well adapted to aquatic locomotion. During their approximately 160 Myr existence, they evolved from elongate and serpentine forms into stockier, fish-like animals, convergent with sharks and dolphins. Here, we use computational fluid dynamics (CFD) to quantify the impact of this transition on the energy demands of ichthyosaur swimming, to our knowledge for the first time. We run computational simulations of water flow using three-dimensional digital models of nine ichthyosaurs and an extant functional analogue, a bottlenose dolphin, providing, to our knowledge, the first quantitative evaluation of ichthyosaur hydrodynamics across phylogeny. Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time. We show that even the early ichthyosaurs produced low levels of drag for a given volume, comparable to those of a modern dolphin, and that deep ‘torpedo-shaped’ bodies did not reduce the cost of locomotion. Our analysis also provides important insight into the choice of scaling parameters for CFD applied to swimming mechanics, and underlines the great influence of body size evolution on ichthyosaur locomotion. A combination of large bodies and efficient swimming modes lowered the cost of steady swimming as ichthyosaurs became increasingly adapted to a pelagic existence.