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An expanded nuclear phylogenomic PCR toolkit for Sapindales.

ABSTRACT: We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16-90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon. Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation.

SUBMITTER: Collins ES

PROVIDER: S-EPMC5238699 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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An expanded nuclear phylogenomic PCR toolkit for Sapindales.

Collins Elizabeth S ES Gostel Morgan R MR Weeks Andrea A

Applications in plant sciences 20161207 12

<h4>Premise of the study</h4>We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for <i>Bursera simaruba</i> (Burseraceae).<h4>Methods and results</h4>Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from <i>B. simaruba</i>. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16-90). <i>Arabidopsis thaliana</i> (Brassicales), by contrast, yielded product for two ...[more]

PMID: 28101434

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Project description:Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

Dataset Information

An expanded nuclear phylogenomic PCR toolkit for Sapindales.

Publications

An expanded nuclear phylogenomic PCR toolkit for Sapindales.

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