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Journal of Molecular Evolution

, Volume 86, Issue 3–4, pp 216–239 | Cite as

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

  • Erika Viljoen
  • Damaris A. Odeny
  • Martin P. A. Coetzee
  • Dave K. Berger
  • David J. G. Rees
Original Article

Abstract

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.

Keywords

Phylogenomics Chloroplast Amaranthus Barcode 

Notes

Acknowledgements

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.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

239_2018_9837_MOESM1_ESM.docx (333 kb)
Supplementary material 1 (DOCX 332 KB)

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Authors and Affiliations

  1. 1.Biotechnology PlatformAgricultural Research Council, OnderstepoortPretoriaSouth Africa
  2. 2.Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaHatfieldSouth Africa
  3. 3.International Crops Research Institute for the Semi-Arid TropicsNairobiKenya
  4. 4.Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaHatfieldSouth Africa
  5. 5.Department of Life and Consumer Sciences, College of Agricultural and Environmental SciencesUniversity of South AfricaFloridaSouth Africa

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