Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

Version 1.0

Hodgins, Kathryn A.; Lai, Zhao; Oliveira, Luiz O.; Still, David W.; Scascitelli, Moira; Barker, Michael S.; Kane, Nolan C.; Dempewolf, Hannes; Kozik, Alex; Kesseli, Richard V.; Burke, John M.; Michelmore, Richard W.; Rieseberg, Loren H., 2013, "Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives", https://doi.org/10.5683/SP2/DVELSY, Borealis, V1

Learn about Data Citation Standards.

Contact Owner

Dataset Metrics

0 Downloads

Description	Abstract Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared to the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of post-zygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values. (2020-06-24) Usage notes The 15 reference transcriptome assemblies of Compositae crops and their wild relativesdryad_submission.tar (2020-06-24)
Subject	Other
Keyword	Echinacea angustifolia, Cichorium intybus, Glebionis segetum, Smallanthus sonchifolius, Iva annua, Helianthus tuberosus, Guizotia scabra, Transcriptomics, Leontodon taraxacoides and Glebionis segetum, Parthenium argentatum, Agriculture, Stevia rebaudiana, Dahlia hybrida, Cichorium endivia
Related Publication	Article
Notes	Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/gtcaggztBWzvSL7Tasx2QCJ3A9usrqiWuqt8S3zvBqU Storage size: 754721881 Visibility: public
License/Data Use Agreement	Custom Dataset Terms

Filter by

	1 to 3 of 3 Files	Download
	dryad_cp723.json Plain Text - 6.1 KB Published May 19, 2021 0 Downloads MD5: 785aa1735d572faefedd74aa7d3a9cb3 Original JSON from Dryad DocumentationCode	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	dryad_submission.tar TAR Archive - 719.6 MB Published May 19, 2021 0 Downloads MD5: 22fb6cb9bcba287d864550b60acc147b	Access File File Access Public Download Options TAR Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	README_for_dryad_submission.docx MS Word - 96.0 KB Published May 19, 2021 0 Downloads MD5: 6917deecc1fb877b5daf780f53ac4d78	Access File File Access Public Download Options MS Word Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.5683/SP2/DVELSY
Publication Date	2021-05-19
Citation Date
Title	Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives
Other Identifier	Dryad: doi:10.5061/dryad.cp723
Author	Hodgins, Kathryn A. (University of British Columbia) Lai, Zhao (Indiana University Bloomington) Oliveira, Luiz O. (University of Massachusetts Boston) Still, David W. (University of British Columbia) Scascitelli, Moira (University of British Columbia) Barker, Michael S. (University of Arizona) Kane, Nolan C. (University of Colorado Boulder) Dempewolf, Hannes (University of British Columbia) Kozik, Alex (University of California, Davis) Kesseli, Richard V. (University of Massachusetts Amherst) Burke, John M. (University of Georgia) Michelmore, Richard W. (University of British Columbia) Rieseberg, Loren H. (University of British Columbia)
Point of Contact	Use email button above to contact. UBC Library Research Data Team
Description	Abstract Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared to the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of post-zygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values. (2020-06-24) Usage notes The 15 reference transcriptome assemblies of Compositae crops and their wild relativesdryad_submission.tar (2020-06-24)
Subject	Other
Keyword	Echinacea angustifolia (Dryad) Cichorium intybus (Dryad) Glebionis segetum (Dryad) Smallanthus sonchifolius (Dryad) Iva annua (Dryad) Helianthus tuberosus (Dryad) Guizotia scabra (Dryad) Transcriptomics (Dryad) Leontodon taraxacoides and Glebionis segetum (Dryad) Parthenium argentatum (Dryad) Agriculture (Dryad) Stevia rebaudiana (Dryad) Dahlia hybrida (Dryad) Cichorium endivia (Dryad)
Related Publication	Article doi: https://doi.org/10.1111/1755-0998.12163
Notes	Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/gtcaggztBWzvSL7Tasx2QCJ3A9usrqiWuqt8S3zvBqU Storage size: 754721881 Visibility: public
Distribution Date	2013-08-19
Deposit Date	2020-06-24

Geospatial Metadata

Geographic Coverage

Pakistan
Garden origin West Coast Seeds B.C. Canada
Jimma. Ethiopia. 5km from Jimma on the way to Bonga 1775m evolution. Latitude 7.626 Longitude 36.760
Ohio United States Hwy. 81W 16.8km west of Ada Allen County. Latitude 40.733 Longitude -84.017
Krasnodar Russian Federation (latitude 45.033 longitude 35.977)
Cleden-cap-Sizun Finistere France Porto Portugal (Between Lordelo do Ouro and Porto Douro Litoral Province Latitude 41.15 Longitude -8.633)
Granite City IL Latitude 38.804 Longitude 90.114
Oregon Benton Cty OSU campus vacant lot at corner of SW 11th St and Washington
Oklahoma United States Section 24 T19N R2W Logan County 36.1 -97.367
Peru
Germany

Dataset Terms

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom Dataset Terms — the following Custom Dataset Terms have been defined for this dataset.

This dataset is made available under a Creative Commons CC0 license with the following additional/modified terms and conditions: CC0 Waiver

Dataset Version	Summary	Contributors	Published on
No records found.

Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Request Access

Enable access request

You must enable request access or add terms of access to restrict file access.

Terms of Access for Restricted Files

Save Changes

Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.

Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.

Restricted Files Selected

The selected file(s) may not be downloaded because you have not been granted access.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 4.7 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

Click Continue to download the files you have access to download.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Private URL

Private URL can only be used with unpublished versions of datasets.

Unpublished Dataset Private URL

Are you sure you want to disable the Private URL? If you have shared the Private URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? The selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? It will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details

Version:
Last Updated:

Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

You need to Sign Up or Log In to request access.

Dataset Terms

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom terms specific to this dataset Custom Dataset Terms — the following Custom Dataset Terms have been defined for this dataset.

Terms of Use This dataset is made available under a Creative Commons CC0 license with the following additional/modified terms and conditions: CC0 Waiver

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Guestbook Name

Collected Data

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

Download URL

https://borealisdata.ca/api/access/datafile/

Request Access

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

Compute Batch

Clear Batch

Dataset	Persistent Identifier	Change Compute Batch

Compute Batch

Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Minor Release (1.1)

Major Release (2.0)

Publish Dataset

This dataset cannot be published until UBC Dryad2Dataverse is published by its administrator.

Publish Dataset

This dataset cannot be published until UBC Dryad2Dataverse and UBC Dataverse Collection are published.

Return to Author

Return this dataset to contributor for modification.