TY - JOUR
T1 - Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative
T2 - access to gene family phylogenies and age distributions
AU - Li, Zheng
AU - Barker, Michael S.
N1 - Funding Information:
The 1KP initiative was funded by the Alberta Ministry of Advanced Education and Alberta Innovates AITF/iCORE Strategic Chair (RES0010334) to Gane Ka-Shu Wong, Musea Ventures, The National Key Research and Development Program of China (2016YFE0122000), The Ministry of Science and Technology of the People’s Republic of China (2015BAD04B01/2015BAD04B03), the State Key Laboratory of Agricultural Genomics (2011DQ782025) and the Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application (2011A091000047). We thank Gane Ka-Shu Wong for providing the 1KP funding. Genome duplication analyses were supported by US National Science Foundation (NSF) grants IOS-1339156 and EF-1550838 to M.S.B..
Funding Information:
1KP: 1,000 Plants project; BLAST: Basic Local Alignment Search Tool; K-S: Kolmogorov-Smirnov; MAPS: MultitAxon Paleopoly-ploidy Search; NSF: National Science Foundation; PAML: Phylogenetic Analysis by Maximum Likelihood; RAxML: Randomized Axelerated Maximum Likelihood; RBH: Reciprocal Best Hit; WGD: whole-genome duplication.
Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
KW - Ancient whole-genome duplications
KW - Paleopolyploidy
KW - Phylogenomics
KW - Transcriptomes
KW - Whole-genome duplications
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U2 - 10.1093/GIGASCIENCE/GIAA004
DO - 10.1093/GIGASCIENCE/GIAA004
M3 - Article
C2 - 32043527
AN - SCOPUS:85079232024
VL - 9
JO - GigaScience
JF - GigaScience
SN - 2047-217X
IS - 2
ER -