Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions
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Abstract
Background
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 >1,000 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 article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project.
Results
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 walk-through 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 dataset.
Conclusions
We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.
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Now published in GigaScience doi: 10.1093/gigascience/giaa004
Zheng Li Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zheng LiMichael S Barker Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael S Barker
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa004 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102092 Reviewer 2: http://dx.do…
Now published in GigaScience doi: 10.1093/gigascience/giaa004
Zheng Li Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zheng LiMichael S Barker Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael S Barker
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa004 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102092 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102093
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