Omics · dataset · 2021
Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae
Listed in Borealis and Agri-environmental Research Data Dataverse — shown once because both records carry DOI 10.5683/sp2/j1dsdn
Description
Abstract
Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae.
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We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
Usage notes
COS alignment files Alignments from all COS loci COS_alignment_files_NEW.zip COS_sequence_length&number_of_sequences List of COS sequences with alignment length and number of sequences in each alignment. tree file in newick format for the concatenation of all COS loci, as run in Garli 763_loci_tree_newick Concatenation_of_all_763_ COS_alignments Concatenated alignment file. Concatenation_of_all_763_COS_alignments_NEW.fasta
Links
Where it is published
- Dataverse dataset page borealisdata.ca/dataset.xhtml?persistentId=doi%3A10.5683%2FSP2%2FJ1DSDN ↗
landing page · from borealisdata ca
- DOI doi.org/10.5683/sp2/j1dsdn ↗
DOI / persistent id · from borealisdata ca
Catalogue records · 1
- Dataverse API borealisdata.ca/api/datasets/:persistentId/?persistentId=doi%3A10.5683%2FSP2%2… ↗
metadata API · from borealisdata ca
Topics
- From keywords
- Chemistry · Computer Science & AI · Earth & Environmental Science · Economics & Finance · Engineering · Humanities · Life Sciences · Mathematics & Statistics · Medicine & Health · Ocean & Atmospheric Science · Sequencing · Sequencing · Social Science
- Inferred from text
- Plant and fungus systematics and taxonomy 79%
Provenance · 2 source records, 22 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Borealis | doi:10.5683/SP2/J1DSDN | 12 d ago | JSON v1 |
| Agri-environmental Research Data Dataverse | doi:10.5683/SP2/J1DSDN | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:field:310411 | enrichment · borealisdata ca | taxonomy-embedding@1.0.0 | title+keywords+description (79%) |
| concepts[field].dataverse_subject:other | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /subjects |
| concepts[field].dataverse_subject:other | source · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:computer-science-ai | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:earth-environmental | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:economics-finance | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:mathematics-statistics | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:ocean-atmospheric | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[modality].local:modality:sequencing | mapping · borealisdata ca | vocabulary-mapper@1.0.0 | keywords['Next-generation sequencing'] |
| concepts[modality].local:modality:sequencing | mapping · borealisdata ca dataverse | vocabulary-mapper@1.0.0 | keywords['Next-generation sequencing'] |
| created_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| description | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /description |
| publication_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| title | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /name |
| updated_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| version_label | source · borealisdata ca | connector:borealisdata_ca@1.0.0 |