cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11338640
title: A Self-adjusting Platinum Surface for Acetone Hydrogenation

description: Reaction kinetics experimental data, DFT structure files, and microkinetic models for acetone hydrogenation using Pt catalyst.
DOI: 10.6084/m9.figshare.11338595
title: COPD mouse EDL muscle and serum protein regulation pre and post exercise

description: These data demonstrate the pre and post exercise regulation of proteins expression captured in muscle and serum samples from wild type and COPD mice
DOI: 10.6084/m9.figshare.11338595.v1
title: COPD mouse EDL muscle and serum protein regulation pre and post exercise

description: These data demonstrate the pre and post exercise regulation of proteins expression captured in muscle and serum samples from wild type and COPD mice
DOI: 10.6084/m9.figshare.11337716
title: Gut microbiome dynamics of Ruddy turnstones during stopover

description: We sequenced the 16S rRNA gene from fecal samples of Ruddy Turnstone which we collected between May 7-31 in Delaware Bay, DE.
DOI: 10.6084/m9.figshare.11337311
title: Clostridium perfringens TAMU antibiotic resistance annotation

description: Antibiotic resistance gene functional annotation results from CARD RGI tool (doi: 10.1093/nar/gkw1004) for <i>Clostridium perfringens</i> TAMU genome. All parameters were set to default.
DOI: 10.6084/m9.figshare.11337281
title: Source Data for GWAS in Supplementary Fig. 2c.mht

description: Source Data for GWAS in Supplementary Fig. 2c.
DOI: 10.6084/m9.figshare.11337284
title: Source Data for GWAS in Supplementary Fig. 2d.mht

description: Source Data for GWAS in Supplementary Fig. 2d
DOI: 10.6084/m9.figshare.11337290
title: Source Data for GWAS in Supplementary Fig. 2e.mht

description: Source Data for GWAS in Supplementary Fig. 2e
DOI: 10.6084/m9.figshare.11337281.v1
title: Source Data for GWAS in Supplementary Fig. 2c.mht

description: Source Data for GWAS in Supplementary Fig. 2c.
DOI: 10.6084/m9.figshare.11337290.v1
title: Source Data for GWAS in Supplementary Fig. 2e.mht

description: Source Data for GWAS in Supplementary Fig. 2e
DOI: 10.6084/m9.figshare.11337278
title: APEC virulence gene database December 2019

description: Curated APEC virulence gene database
DOI: 10.6084/m9.figshare.11337272
title: Source Data for GWAS in Supplementary Fig. 2b.mht

description: Source Data for GWAS in Supplementary Fig. 2b
DOI: 10.6084/m9.figshare.11337278.v1
title: APEC virulence gene database December 2019

description: Curated APEC virulence gene database
DOI: 10.6084/m9.figshare.11337284.v1
title: Source Data for GWAS in Supplementary Fig. 2d.mht

description: Source Data for GWAS in Supplementary Fig. 2d
DOI: 10.6084/m9.figshare.11337272.v1
title: Source Data for GWAS in Supplementary Fig. 2b.mht

description: Source Data for GWAS in Supplementary Fig. 2b
DOI: 10.6084/m9.figshare.11337245
title: Clostridium perfringens TAMU virulence factor annotations

description: Virulence factor functional annotation results from VFDB VFAnalyzer (doi: 10.1093/nar/gky1080) for <i>Clostridium perfringens</i> TAMU genome. All parameters used were set to default.
DOI: 10.6084/m9.figshare.11337245.v1
title: Clostridium perfringens TAMU VFDB annotations

description: Virulence factor functional annotation results from VFDB VFAnalyzer for <i>Clostridium perfringens</i> TAMU genome. All parameters used were set to default.
DOI: 10.6084/m9.figshare.11337245.v3
title: Clostridium perfringens TAMU virulence factor annotations

description: Virulence factor functional annotation results from VFDB VFAnalyzer (doi: 10.1093/nar/gky1080) for <i>Clostridium perfringens</i> TAMU genome. All parameters used were set to default.
DOI: 10.6084/m9.figshare.11337245.v2
title: Clostridium perfringens TAMU virulence factor annotations

description: Virulence factor functional annotation results from VFDB VFAnalyzer for <i>Clostridium perfringens</i> TAMU genome. All parameters used were set to default.
DOI: 10.6084/m9.figshare.11336846
title: analyse_results.m

description: Coding for data
DOI: 10.6084/m9.figshare.11336843
title: Supplementary Files: Twitter and Dentistry

description: Supplementary Files: Twitter and Dentistry
DOI: 10.6084/m9.figshare.11336834
title: Behavior of phengite at high temperature and high pressure: In situ IR and Raman spectroscopic studies

description: Here is the supporting information for "Behavior of phengite at high temperature and high pressure: In situ IR and Raman spectroscopic studies“
DOI: 10.6084/m9.figshare.11336843.v1
title: Supplementary Files: Twitter and Dentistry

description: Supplementary Files: Twitter and Dentistry
DOI: 10.6084/m9.figshare.11336831
title: Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

description: This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia <i>Hylia prasina</i> and Yellow-whiskered Greenbul <i>Eurillas latirostris</i>), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in <i>Eurillas</i> (∼4.1 MY). In Western Bluebill <i>Spermophaga haematina</i>, relatively divergent eastern and western lineages (∼1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin <i>Stiphrornis erythrothorax</i>, birds sampled within Ghana were from two highly divergent lineages (∼1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (∼0.36 MY). For both <i>Hylia</i> and <i>Stiphrornis</i>, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.
DOI: 10.6084/m9.figshare.11336789
title: analyse_multiple_gaze_4.m

description: Coding for processing of the below data
DOI: 10.6084/m9.figshare.11336831.v1
title: Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

description: This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia <i>Hylia prasina</i> and Yellow-whiskered Greenbul <i>Eurillas latirostris</i>), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in <i>Eurillas</i> (∼4.1 MY). In Western Bluebill <i>Spermophaga haematina</i>, relatively divergent eastern and western lineages (∼1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin <i>Stiphrornis erythrothorax</i>, birds sampled within Ghana were from two highly divergent lineages (∼1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (∼0.36 MY). For both <i>Hylia</i> and <i>Stiphrornis</i>, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.
DOI: 10.6084/m9.figshare.11336666
title: Source Data for GWAS in Supplementary Fig. 2a.mht

description: Source Data for GWAS in Supplementary Fig. 2a
DOI: 10.6084/m9.figshare.11336789.v1
title: analyse_multiple_gaze_4.m

description: Coding for processing of the below data
DOI: 10.6084/m9.figshare.11336657
title: Source Data for GWAS in Fig. 1.mht

description: Source Data for GWAS in Fig. 1
DOI: 10.6084/m9.figshare.11336495
title: My test text

description: My description<br>
DOI: 10.6084/m9.figshare.11336507
title: Metadata record for: Global karst springs hydrograph dataset for research and management of the world’s fastest-flowing groundwater

description: This dataset contains key characteristics about the data described in the Data Descriptor Global karst springs hydrograph dataset for research and management of the world’s fastest-flowing groundwater. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11336495.v2
title: My test text

description: My description<br>
DOI: 10.6084/m9.figshare.11336495.v1
title: My test text file

description: My description<br>
DOI: 10.6084/m9.figshare.11336507.v1
title: Metadata record for: Global karst springs hydrograph dataset for research and management of the world’s fastest-flowing groundwater

description: This dataset contains key characteristics about the data described in the Data Descriptor Global karst springs hydrograph dataset for research and management of the world’s fastest-flowing groundwater. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11336258
title: In and outs of Chuviridae endogenous viral elements: origin of a potentially new retrovirus and signature of ancient and ongoing arms race in mosquito genomes

description: Background: Endogenous viral elements (EVEs) are sequences of viral origin integrated into the host genome. EVEs have been characterized in various insect genomes, including mosquitoes. A large EVE content has been found in Aedes aegypti and Aedes albopictus genomes among which a recently described Chuviridae viral family is of particular interest, owing to the abundance of EVEs derived from it, the discrepancy in the endogenized gene regions and the frequent association with retrotransposons from the BEL-Pao superfamily. In order to better understand the endogenization process of chuviruses and the association between chuvirus glycoproteins and BEL-Pao retrotransposons, we performed a comparative genomics and evolutionary analysis of chuvirus-derived EVEs found in 37 mosquito genomes. Results: We identified 428 EVEs belonging to the Chuviridae family confirming the wide discrepancy between the number of genomic regions endogenized: 409 glycoproteins, 18 RNA-dependent RNA polymerases and one nucleoprotein region. Most of the glycoproteins (263 out of 409) are associated specifically with retroelements from the Pao family. Focusing only on well assembled Pao retroelement copies, we estimated that 263 out of 379 Pao elements are associated with chuvirus-derived glycoproteins. Seventy-three potentially active Pao copies were found to contain glycoproteins into their LTR boundaries. Thirteen out of these were classified as complete and likely autonomous copies, with a full LTR structure and protein domains. We also found 116 Pao copies with no trace of glycoproteins and 37 solo glycoproteins. All potential autonomous Pao copies, contained highly similar LTRs, suggesting a recent/current activity of these elements in the mosquito genomes. Conclusion: Evolutionary analysis revealed that most of the glycoproteins found are likely derived from a single or few glycoprotein endogenization events associated with a recombination event with a Pao ancestral element. A potential fully functional Pao-chuvirus hybrid (named Anakin) emerged and the glycoprotein was further replicated through retrotransposition. However, a number of solo glycoproteins, not associated with Pao elements, can still be found in some mosquito genomes 114 million years later, suggesting that these glycoproteins were likely domesticated by the host genome and may participate in an antiviral defense mechanism against both chuvirus and Anakin retrovirus.
DOI: 10.6084/m9.figshare.11336168
title: Diverse mobilome of Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae) reveals long range horizontal transfer events of DNA transposons

description: Transposable elements (TEs) are mobile DNA sequences that are able to move from one genomic location to another. These selfish elements are known as genomic parasites, since they hijack the host molecular machinery to generate new copies of themselves. The mobilization of TEs can be seem as a natural mutagen because new TE copies can insert into different loci and impact host genomic structure through different mechanisms. Although our knowledge about TEs is improving with new genomes available, there is still very limited data about the mobilome of species from the Coleoptera order, the most specious order of insects, including species from the Scarabeidae family. Therefore, the main goal of this study was to characterize the mobilome of D. (Luederwaldtinia) schiffleri, based on low coverage genome sequencing, and reconstruct their evolutionary history. We used a combination of four different approaches for TEs characterization and maximum likelihood phylogenetic analysis to study their evolution. We found a large and diverse mobilome composed of 43 TE superfamilies, 22 DNA transposon and 21 Retrotransposons, accounting for 21% of the genome. Moreover, we found a number of incongruence between the TE and host phylogenetic trees in three DNA transposon TE superfamilies, which represents 5 TE families, suggesting possible horizontal transfer events between highly divergent taxa. In summary, we found an abundant and diverse mobilome and a number of horizontal transfer events that has shaped the evolutionary history of this species.<br>
DOI: 10.6084/m9.figshare.11336126
title: freebayes.SNPs.Q40.DP6_30_max_miss_5.recode.edit.annotated.names.SOUTH.polymorphic.vcf

description: SNP with variation
DOI: 10.6084/m9.figshare.11336258.v1
title: In and outs of Chuviridae endogenous viral elements: origin of a retrovirus and signature of ancient and ongoing arms race in mosquito genomes

description: Background: Endogenous viral elements (EVEs) are sequences of viral origin integrated into the host genome. EVEs have been characterized in various insect genomes, including mosquitoes. A large EVE content has been found in Aedes aegypti and Aedes albopictus genomes among which a recently described Chuviridae viral family is of particular interest, owing to the abundance of EVEs derived from it, the discrepancy in the endogenized gene regions and the frequent association with retrotransposons from the BEL-Pao superfamily. In order to better understand the endogenization process of chuviruses and the association between chuvirus glycoproteins and BEL-Pao retrotransposons, we performed a comparative genomics and evolutionary analysis of chuvirus-derived EVEs found in 37 mosquito genomes. Results: We identified 428 EVEs belonging to the Chuviridae family confirming the wide discrepancy between the number of genomic regions endogenized: 409 glycoproteins, 18 RNA-dependent RNA polymerases and one nucleoprotein region. Most of the glycoproteins (263 out of 409) are associated specifically with retroelements from the Pao family. Focusing only on well assembled Pao retroelement copies, we estimated that 263 out of 379 Pao elements are associated with chuvirus-derived glycoproteins. Seventy-three potentially active Pao copies were found to contain glycoproteins into their LTR boundaries. Thirteen out of these were classified as complete and likely autonomous copies, with a full LTR structure and protein domains. We also found 116 Pao copies with no trace of glycoproteins and 37 solo glycoproteins. All potential autonomous Pao copies, contained highly similar LTRs, suggesting a recent/current activity of these elements in the mosquito genomes. Conclusion: Evolutionary analysis revealed that most of the glycoproteins found are likely derived from a single or few glycoprotein endogenization events associated with a recombination event with a Pao ancestral element. A potential fully functional Pao-chuvirus hybrid (named Anakin) emerged and the glycoprotein was further replicated through retrotransposition. However, a number of solo glycoproteins, not associated with Pao elements, can still be found in some mosquito genomes 114 million years later, suggesting that these glycoproteins were likely domesticated by the host genome and may participate in an antiviral defense mechanism against both chuvirus and Anakin retrovirus.
DOI: 10.6084/m9.figshare.11336126.v1
title: freebayes.SNPs.Q40.DP6_30_max_miss_5.recode.edit.annotated.names.SOUTH.polymorphic.vcf

description: SNP with variation
DOI: 10.6084/m9.figshare.11336168.v1
title: Genome-wide characterization of transposable elements of Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae): evidence of horizontal transfer events

description: @page { margin: 2cm } p { margin-bottom: 0.25cm; direction: ltr; color: #00000a; line-height: 120%; text-align: left; orphans: 2; widows: 2 } p.western { font-family: "Calibri", serif; font-size: 11pt; so-language: pt-BR } p.cjk { font-family: "Droid Sans Fallback"; font-size: 11pt; so-language: en-US } p.ctl { font-family: "Times New Roman"; font-size: 11pt; so-language: ar-SA } a:link { color: #0000ff } Transposable elements (TEs) are dispersed repetitive DNA sequences found in the vast majority of organisms studied so far. TEs activity has shaped the genome of many different species. In the genus <i>Dichotomius </i>(Coleoptera) TEs have been suggested to be associated with the dispersion and dynamics of other repetitive sequences but limited molecular data for TEs exists so far. Therefore, the objective of this study was to characterize the mobilome of <i>Dichotomius </i>(<i>Luederwaldtinia</i>) <i>schiffleri </i>using three different approaches for TEs characterization: RepeatExplorer, dnaPipeTE and RepeatMasker. Phylogenetic trees of conserved TE superfamily were constructed using the maximum likelihood method and included homologous sequences identified in NCBI and Repbase. The mobilome of <i>D.</i> (<i>L.</i>) <i>schiffleri</i> is composed of 21 retrotransposon and 22 DNA transposon superfamilies. Phylogenetic reconstruction revealed incongruences between the phylogeny of the elements and that of the host. The characterization of <i>D. </i>(<i>L.</i>)<i> schiffleri </i>elements and phylogenetic analyses allowed the identification of putative active elements and potential horizontal transfer events between highly divergent taxa.<br>
DOI: 10.17637/rh.11336084
title: Kew Museum of Economic Botany: Items Distributed, 1847-1990

description: This spreadsheet contains all recorded data on distributions or dispersals of specimens and artefacts from the Kew Museum of Economic Botany between 1847 and 1900, arranged by 'item', ie distinguishing each documented object whether distributed individually or as part of a group of objects donated in the same 'event'. (A separate spreadsheet on Figshare, arranged by distribution event, includes further details of recipient name, institution and location). The data is based on information within Kew's 'Specimens Distributed' books for the period 1881-1990, supplemented by archival data from a variety of other sources at Kew and elsewhere. The file includes information on the date of the distribution, event record, description and type of object, place and region of origin, donor name if available and archival source, together with links where appropriate to the relevant page of the Specimens Distributed books which have been digitised and are available on the Biodiversity Heritage Library website. <br> <br>https://www.royalholloway.ac.uk/mobilemuseum <br>https://www.kew.org/science/collections/economic-botany-collection <br><br><br>
DOI: 10.6084/m9.figshare.11336168.v2
title: Diverse mobilome of Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae) reveals long range horizontal transfer events of DNA transposons

description: Transposable elements (TEs) are mobile DNA sequences that are able to move from one genomic location to another. These selfish elements are known as genomic parasites, since they hijack the host molecular machinery to generate new copies of themselves. The mobilization of TEs can be seem as a natural mutagen because new TE copies can insert into different loci and impact host genomic structure through different mechanisms. Although our knowledge about TEs is improving with new genomes available, there is still very limited data about the mobilome of species from the Coleoptera order, the most specious order of insects, including species from the Scarabeidae family. Therefore, the main goal of this study was to characterize the mobilome of D. (Luederwaldtinia) schiffleri, based on low coverage genome sequencing, and reconstruct their evolutionary history. We used a combination of four different approaches for TEs characterization and maximum likelihood phylogenetic analysis to study their evolution. We found a large and diverse mobilome composed of 43 TE superfamilies, 22 DNA transposon and 21 Retrotransposons, accounting for 21% of the genome. Moreover, we found a number of incongruence between the TE and host phylogenetic trees in three DNA transposon TE superfamilies, which represents 5 TE families, suggesting possible horizontal transfer events between highly divergent taxa. In summary, we found an abundant and diverse mobilome and a number of horizontal transfer events that has shaped the evolutionary history of this species.<br>