Application of chloroplast phylogenomics to resolve species relationships within the plant genus Amaranthus

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dc.contributor.author Viljoen, Erika
dc.contributor.author Odeny, Damaris A.
dc.contributor.author Coetzee, Martin Petrus Albertus
dc.contributor.author Berger, David Kenneth
dc.contributor.author Rees, David J.G.
dc.date.accessioned 2018-12-06T13:04:26Z
dc.date.issued 2018-04
dc.description.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. en_ZA
dc.description.department Forestry and Agricultural Biotechnology Institute (FABI) en_ZA
dc.description.department Genetics en_ZA
dc.description.department Plant Production and Soil Science en_ZA
dc.description.embargo 2019-04-01
dc.description.librarian hj2018 en_ZA
dc.description.sponsorship 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. en_ZA
dc.description.uri https://link.springer.com/journal/239 en_ZA
dc.identifier.citation Viljoen, E., Odeny, D.A., Coetzee, M.P.A. et al. Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. Journal of Molecular Evolution (2018) 86: 216-239. https://doi.org/10.1007/s00239-018-9837-9. en_ZA
dc.identifier.issn 0022-2844 (print)
dc.identifier.issn 1432-1432 (online)
dc.identifier.other 10.1007/s00239-018-9837-9
dc.identifier.uri http://hdl.handle.net/2263/68047
dc.language.iso en en_ZA
dc.publisher Springer en_ZA
dc.rights © Springer Science+Business Media, LLC, part of Springer Nature 2018. The original publication is available at : https://link.springer.com/journal/239 en_ZA
dc.subject Phylogenomics en_ZA
dc.subject Chloroplast en_ZA
dc.subject Amaranthus en_ZA
dc.subject Barcode en_ZA
dc.subject Plastid genomes en_ZA
dc.subject Fragment length polymorphism en_ZA
dc.subject African leafy vegetables en_ZA
dc.subject Maximum likelihood en_ZA
dc.subject Genetic diversity en_ZA
dc.subject Genome sequences en_ZA
dc.subject South Africa (SA) en_ZA
dc.subject Phylogenetic relationship en_ZA
dc.subject Angiosperm phylogeny en_ZA
dc.subject Evolutionary history en_ZA
dc.title Application of chloroplast phylogenomics to resolve species relationships within the plant genus Amaranthus en_ZA
dc.type Postprint Article en_ZA


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