Supporting data for "Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions"

Dataset type: Genomic, Transcriptomic
Data released on January 10, 2020

Li Z; Barker MS (2020): Supporting data for "Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions" GigaScience Database. http://dx.doi.org/10.5524/100691

DOI10.5524/100691

Polyploidy or whole genome duplications (WGDs) repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced over 1000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this paper provides expanded methodological details, results validation, and descriptions of newly released data sets that will aid researchers that wish to use the extended data generated by the 1KP project. In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walkthrough examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole genome synteny analyses and our total evidence approach may minimize the false positive rate throughout the data set. Given these resources will be useful for many future analyses on gene and genome evolution in green plants, we release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 32043527)

Additional information:

https://bitbucket.org/barkerlab/1kp/src/master/

Projects:






File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataTEXT155.63 KB2019-12-21
Mixed archivearchive848.04 MB2019-12-21
ReadmeTEXT2.82 KB2020-01-10
Tabular dataTEXT35.81 KB2019-12-21
Displaying 1-4 of 4 File(s).
Funding body Awardee Award ID Comments
Division of Integrative Organismal Systems M S Barker IOS‐1339156
Division of Emerging Frontiers M S Barker EF‐1550838
Date Action
January 10, 2020 Dataset publish
January 18, 2020 Manuscript Link added : 10.1093/gigascience/giaa004
October 7, 2022 Manuscript Link updated : 10.1093/gigascience/giaa004