cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11104278
title: Audio clips of real-world experiments (DeFTAN-II)

description: Noisy, enhanced, clean speech of real-world experiments using DeFTAN-II (100 audio clips)
DOI: 10.5281/zenodo.11104279
title: Audio clips of real-world experiments (DeFTAN-II)

description: Noisy, enhanced, clean speech of real-world experiments using DeFTAN-II (100 audio clips)
DOI: 10.15468/dl.65jmrm
title: Occurrence Download

description: A dataset containing 515 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Crotalus enyo Cope, 1861"
 ]
}

 The dataset includes 515 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004787-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txwwgs
title: Occurrence Download

description: A dataset containing 238143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is CAS Invertebrate Zoology (IZ)"
 ]
}

 The dataset includes 238143 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043383-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.jap.25607490
title: Supplemental Material: Nature of point defects in monolayer MoS2 and the Mo2/(111)-Au heterojunction

description: Supplemental Material
DOI: 10.5281/zenodo.11103499
title: Genome annotations for: Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes

description: Peter Thorpe1, Simone Altmann1, Rosa Lopez-Cobollo2, Nadine Douglas3, Javaid Iqbal2, Sadia Kanvil2, Jean-Christophe Simon4, James C. Carolan3, Jorunn Bos1*, Colin Turnbull2* 




1School of Life Sciences, University of Dundee, UK; 2Department of Life Sciences, Imperial College London, UK; 3Department of Biology, Maynooth University, Republic of Ireland; 4 INRAE , France. *Authors for correspondence: j.bos@dundee.ac.uk, c.turnbull@imperial.ac.uk.  

 

This is a repository for the version3 gene predictions and annotation for the pea aphid used for the publication:

 

Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes 

 



ABSTRACT




Background. Compatibility between aphids and plant hosts is genetically determined by both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues. Subsets of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating particular effectors with virulence or avirulence outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host genetics to test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes. 




Results. We compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F1 progeny on Medicago truncatula genotypes carrying or lacking the RAP1 resistance quantitative trait locus. Differential expression analysis based on RNA sequencing of whole body and head samples, in combination with proteomics of saliva and salivary glands, enabled us to pinpoint proteins associated with virulence/avirulence phenotypes. There was relatively little impact of host genotype, whereas large numbers of transcripts and proteins were differentially expressed between parental aphids, likely a reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer transcripts intersected with the equivalent differential expression patterns in the bulked F1 progeny, providing an effective filter for removing genomic background effects. Overall, there were more upregulated genes detected in the F1 avirulent dataset compared with the virulent one. Some of the differentially expressed transcripts were also found in the differentially expressed proteomes, with aminopeptidase N proteins being the most frequent differentially expressed family. In addition, a substantial proportion (26%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered.  




Conclusions. Especially when combined with tightly controlled genetics of both insect and host, multi-omic approaches are powerful tools for revealing and filtering candidate lists down to plausible genes for further functional analysis as putative aphid effectors.
DOI: 10.5281/zenodo.11103500
title: Genome annotations for: Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes

description: Peter Thorpe1, Simone Altmann1, Rosa Lopez-Cobollo2, Nadine Douglas3, Javaid Iqbal2, Sadia Kanvil2, Jean-Christophe Simon4, James C. Carolan3, Jorunn Bos1*, Colin Turnbull2* 




1School of Life Sciences, University of Dundee, UK; 2Department of Life Sciences, Imperial College London, UK; 3Department of Biology, Maynooth University, Republic of Ireland; 4 INRAE , France. *Authors for correspondence: j.bos@dundee.ac.uk, c.turnbull@imperial.ac.uk.  

 

This is a repository for the version3 gene predictions and annotation for the pea aphid used for the publication:

 

Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes 

 



ABSTRACT




Background. Compatibility between aphids and plant hosts is genetically determined by both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues. Subsets of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating particular effectors with virulence or avirulence outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host genetics to test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes. 




Results. We compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F1 progeny on Medicago truncatula genotypes carrying or lacking the RAP1 resistance quantitative trait locus. Differential expression analysis based on RNA sequencing of whole body and head samples, in combination with proteomics of saliva and salivary glands, enabled us to pinpoint proteins associated with virulence/avirulence phenotypes. There was relatively little impact of host genotype, whereas large numbers of transcripts and proteins were differentially expressed between parental aphids, likely a reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer transcripts intersected with the equivalent differential expression patterns in the bulked F1 progeny, providing an effective filter for removing genomic background effects. Overall, there were more upregulated genes detected in the F1 avirulent dataset compared with the virulent one. Some of the differentially expressed transcripts were also found in the differentially expressed proteomes, with aminopeptidase N proteins being the most frequent differentially expressed family. In addition, a substantial proportion (26%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered.  




Conclusions. Especially when combined with tightly controlled genetics of both insect and host, multi-omic approaches are powerful tools for revealing and filtering candidate lists down to plausible genes for further functional analysis as putative aphid effectors.
DOI: 10.15468/dl.akqrcz
title: Occurrence Download

description: A dataset containing 9525 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Quercus garryana Douglas ex Hook."
 ]
}

 The dataset includes 9525 records from 135 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163871-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f9pwmg
title: Occurrence Download

description: A dataset containing 766 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vireolanius melitophrys Bonaparte, 1850",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 766 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004788-150316153013904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7t3pgd
title: Occurrence Download

description: A dataset containing 8093 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Pomatorhinus ruficollis Hodgson, 1836"
 ]
}

 The dataset includes 8093 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000114-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p46p7j
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lobelia bridgesii Hook. & Arn."
 ]
}

 The dataset includes 101 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163892-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gd0zwx
title: Occurrence Download

description: A dataset containing 224176 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salmo trutta sp. caspius Kessler, 1877"
 ]
}

 The dataset includes 224176 records from 240 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004788-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wk4fk5
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Smithia purpurea Hook."
 ]
}

 The dataset includes 33 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163873-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wn45fm
title: Occurrence Download

description: A dataset containing 182 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centrosema platycarpum Benth."
 ]
}

 The dataset includes 182 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004788-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sxtuhk
title: Occurrence Download

description: A dataset containing 220688 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Branta canadensis (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2005",
 "Year is less than or equal to 2014",
 "Month is December",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 220688 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029055-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ihrekb
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anodontostoma selangkat (Bleeker, 1852)"
 ]
}

 The dataset includes 23 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004788-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ksbxtw
title: Occurrence Download

description: A dataset containing 946 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Registros del inventario y monitoreo de la Biodiversidad en la Jurisdicción de la Corporación Autónoma Regional de Cundinamarca CAR"
 ]
}

 The dataset includes 946 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163899-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5mdnx
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Wiese und Weide am Waldrand von Gusterath"
 ]
}

 The dataset includes 99 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004788-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qa9gmu
title: Occurrence Download

description: A dataset listing the 10563 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is EOD – eBird Observation Dataset"
 ]
}

 The dataset's 10563 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032257-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fg98om
title: Occurrence Download

description: A dataset containing 28838 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is River Biologists' Database (EPA)"
 ]
}

 The dataset includes 28838 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004788-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rseywo
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "InstitutionCode is Herbario de la Universidad Industrial de Santander",
 "TaxonKey is Plantae",
 "HasCoordinate is TRUE",
 {
 "or" : [
 "Country is Albania",
 "Country is Austria",
 "Country is Bosnia and Herzegovina",
 "Country is Belgium",
 "Country is Bulgaria",
 "Country is Belarus",
 "Country is Switzerland",
 "Country is Cyprus",
 "Country is Czechia",
 "Country is Germany",
 "Country is Denmark",
 "Country is Estonia",
 "Country is Spain",
 "Country is Finland",
 "Country is France",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Country is Greece",
 "Country is Croatia",
 "Country is Hungary",
 "Country is Ireland",
 "Country is Iceland",
 "Country is Italy",
 "Country is Lithuania",
 "Country is Luxembourg",
 "Country is Latvia",
 "Country is Moldova, Republic of",
 "Country is Montenegro",
 "Country is Malta",
 "Country is North Macedonia",
 "Country is Netherlands",
 "Country is Norway",
 "Country is Poland",
 "Country is Portugal",
 "Country is Romania",
 "Country is Serbia",
 "Country is Russian Federation",
 "Country is Sweden",
 "Country is Slovenia",
 "Country is Slovakia",
 "Country is Ukraine"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009976-181108115102211/datasets/export for details.
DOI: 10.15468/dl.zsf3kf
title: Occurrence Download

description: A dataset containing 549 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Damasonium bourgaei Coss."
 ]
}

 The dataset includes 549 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163879-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p6v4yu
title: Occurrence Download

description: A dataset containing 318 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tumidotheres maculatus (Say, 1818)"
 ]
}

 The dataset includes 318 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0133961-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mauaw3
title: Occurrence Download

description: A dataset containing 847 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carcharhinus altimus (Springer, 1950)"
 ]
}

 The dataset includes 847 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008718-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t4yux3
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mammillaria polythele subsp. obconella (Scheidw.) D.R.Hunt"
 ]
}

 The dataset includes 50 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114400-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmovr0
title: Occurrence Download

description: A dataset containing 558 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Fossil",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Unknown evidence",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "Year 1000-2018",
 "Geometry POLYGON((66.698 24.50115,68.10425 23.07367,68.71948 24.42114,66.82983 25.39763,66.14868 24.82064,66.698 24.50115))",
 "DatasetKey is EOD – eBird Observation Dataset",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 558 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008322-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ls30cx
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hamelia ventricosa Sw."
 ]
}

 The dataset includes 63 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008718-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3kqhwr
title: Occurrence Download

description: A dataset containing 173914 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sus scrofa Linnaeus, 1758"
 ]
}

 The dataset includes 173914 records from 615 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067058-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kd4pdh
title: Occurrence Download

description: A dataset listing the 9646 species recorded in GBIF matching the query:
{
 "GadmGid" : [
 "is COL.24_2"
 ]
}

 The dataset's 9646 records were derived from 278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013717-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xzeze9
title: Occurrence Download

description: A dataset containing 1235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.05762 -54.62402,-61.21582 -57.7002,-56.68945 -53.34961,-60.20508 -44.0332,-48.60352 -31.9043,-48.02673 -27.58118,-48.04321 -22.33521,-57.54639 -21.81885,-57.8595 -19.91272,-59.28223 -18.94043,-61.76514 -19.31396,-62.96814 -21.6925,-63.78662 -21.59912,-64.52271 -21.82983,-66.14868 -21.54419,-67.47803 -22.47803,-68.53271 -17.77588,-70.20264 -17.1167,-79.05762 -54.62402))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pappostipa (Speg.) Romasch., P.M.Peterson & Soreng"
 ]
}

 The dataset includes 1235 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071427-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8hwzdz
title: Occurrence Download

description: A dataset containing 16212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bombus lapidarius (Linnaeus, 1758)",
 "Year 2000-2010"
 ]
}

 The dataset includes 16212 records from 272 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069774-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25934/pr00004803.1
title: Available IPD datapackage for study 'A Randomized, Double-Blind, Placebo-Controlled, Parallel-Group, Multicenter Study to Evaluate the Efficacy, Safety, and Tolerability of Canagliflozin Compared With Placebo in the Treatment of Older Subjects With Type 2 Diabetes Mellitus Inadequately Controlled on Glucose Lowering Therapy'

description: The purpose of this study is to evaluate the efficacy and safety of 2 different doses of canagliflozin compared with placebo in older patients (55 to 80 years of age) with type 2 diabetes mellitus (T2DM) with inadequate control on their current diabetes treatment regimen.
DOI: 10.15468/dl.k07vjv
title: Occurrence Download

description: A dataset containing 4495 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spea hammondii (Baird, 1859)"
 ]
}

 The dataset includes 4495 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008719-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w6yqfc
title: Occurrence Download

description: A dataset containing 2592 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Soil nematodes of coniferous forests along gradient of air pollution (Komi Republic)"
 ]
}

 The dataset includes 2592 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0116503-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fvu4ky
title: Occurrence Download

description: A dataset containing 2802 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Spain",
 "Country is France",
 "Country is Italy",
 "Country is Andorra",
 "Country is Portugal"
 ]
 },
 "TaxonKey is Chorthippus biguttulus (Linnaeus, 1758)"
 ]
}

 The dataset includes 2802 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008323-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.