Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus

Viljoen, E and Odeny, D A and Coetzee, M P A and Berger, D K and Rees, D J G (2018) Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. Journal of Molecular Evolution (TSI). pp. 1-24. ISSN 0022-2844

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Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.

Item Type: Article
Divisions: Research Program : East & Southern Africa
Uncontrolled Keywords: Phylogenomics, Chloroplast, Amaranthus, Barcode, Amaranthus species, Vegetable food , Barcoding genes, Amaranthus accessions, Breeding
Subjects: Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 27 Mar 2018 05:58
Last Modified: 27 Mar 2018 05:58
Official URL:
Acknowledgement: The authors wish to thank the Department of Science and Technology of South Africa, the National Research Foundation and the Professional Development Program of the Agricultural Research Council (ARC) in South Africa for providing funding for the PhD study from where this work originated. The authors also thank Dr Charles Hefer at the ARC for bioinformatics support. The authors thank Mr Willem Jansen van Rensburg and his staff at the ARC Vegetable and Ornamental Plant Institute for providing the Amaranthus germplasm set (SAG) as well as plant maintenance. The authors thank the Core Facility team at the ARC Biotechnology Platform for DNA sequencing.
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