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. 2019 Jan 17;9(1):185.
doi: 10.1038/s41598-018-36693-6.

Mitochondrial and Chloroplast Genomes Provide Insights Into the Evolutionary Origins of Quinoa (Chenopodium Quinoa Willd.)

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Free PMC article

Mitochondrial and Chloroplast Genomes Provide Insights Into the Evolutionary Origins of Quinoa (Chenopodium Quinoa Willd.)

Peter J Maughan et al. Sci Rep. .
Free PMC article

Abstract

Quinoa has recently gained international attention because of its nutritious seeds, prompting the expansion of its cultivation into new areas in which it was not originally selected as a crop. Improving quinoa production in these areas will benefit from the introduction of advantageous traits from free-living relatives that are native to these, or similar, environments. As part of an ongoing effort to characterize the primary and secondary germplasm pools for quinoa, we report the complete mitochondrial and chloroplast genome sequences of quinoa accession PI 614886 and the identification of sequence variants in additional accessions from quinoa and related species. This is the first reported mitochondrial genome assembly in the genus Chenopodium. Inference of phylogenetic relationships among Chenopodium species based on mitochondrial and chloroplast variants supports the hypotheses that 1) the A-genome ancestor was the cytoplasmic donor in the original tetraploidization event, and 2) highland and coastal quinoas were independently domesticated.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Structure of the mitochondrial genome in quinoa and related species. (A) Features of the mitochondrial genome assemblies in quinoa. Starting from the outside, tracks represent position (bp), annotated genes (orange, CDS; blue, tRNA; green, rRNA), predicted ORFs, RNA-seq read depth, and SNPs (black, C. pallidicaule and C. suecicum; blue, C. berlandieri; green, C. hircinum; brown, highland quinoa; orange, coastal quinoa). (B) Linear order of genes (orange, CDS; blue, tRNA; green, rRNA) in the mitochondrial genomes of quinoa and related species. Species are arranged according to the accepted organismal phylogeny, with lines connecting genes with the same annotation. Boxes are not proportional to actual gene length. (C) Dotplot visualization of nucleotide-by-nucleotide comparisons of the mitochondrial sequence from Amaranthaceae species. Axes are reported in bp. Scale bar reports percent nucleotide identity.
Figure 2
Figure 2
Structure of the chloroplast genome in quinoa and related species. (A) Features of the chloroplast genome assemblies in quinoa. Starting from the outside, tracks represent position (bp), annotated genes (orange, CDS; blue, tRNA; green, rRNA), predicted ORFs, RNA-seq read depth, SNPs (black, C. pallidicaule and C. suecicum; blue, C. berlandieri; green, C. hircinum; brown, highland quinoa; orange, coastal quinoa); and the positions of the LSC, SSC, and IR regions. (B,C) Dotplot visualization of nucleotide-by-nucleotide comparisons of the chloroplast sequence from Amaranthaceae species (B) and quinoa accessions (C). Axes are reported in bp.
Figure 3
Figure 3
Phylogenetic relationships among Chenopodium species based on variants in the mitochondria (A,B), chloroplast (C,D), and combined mitochondria/chloroplast (E,F). Networks displayed in (B), (D), and (F) are enlarged from the red-boxed regions shown in (A), (C), and (E), respectively. Black text, C. pallidicaule and C. suecicum; blue text, C. berlandieri (Cb); green text, C. hircinum (Ch); brown, highland quinoa; orange, coastal quinoa. Scale bar, 0.01 substitutions per site.

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