Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.)

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.

The genome of Chenopodium pallidicaule: An emerging Andean super grain

“…). Twenty‐one genes were located in each IR, including a pseudogene previously characterized in other Amaranthaceae species as rpl23 (Park et al., ; Maughan et al., ). With a length of 151,799 bp, the cañahua plastid genome is of a similar size to quinoa, which has been reported for multiple quinoa accessions ranging in size from 152,079–152,282 bp, with an average length of 152,134 bp (Hong et al., ; Maughan et al., ).…”

“…Twenty‐one genes were located in each IR, including a pseudogene previously characterized in other Amaranthaceae species as rpl23 (Park et al., ; Maughan et al., ). With a length of 151,799 bp, the cañahua plastid genome is of a similar size to quinoa, which has been reported for multiple quinoa accessions ranging in size from 152,079–152,282 bp, with an average length of 152,134 bp (Hong et al., ; Maughan et al., ). Due to the lack of recombination in chloroplast genomes and the relatively recent allotetraploidization event leading to quinoa (3.3–6.3 mya; Jarvis et al., ), the high degree of similarity between the cañahua and quinoa chloroplasts supports the hypothesis that the maternal parent in the polyploidization event that led to modern quinoa was an A‐genome species (Maughan et al., ).…”

“…A reference‐guided assembly of the cañahua chloroplast genome was constructed by the Assembly by Reduced Complexity (ARC) assembler version 1.1.4 (Hunter et al., ) using a subset of six million whole‐genome, paired‐end Illumina reads with the quinoa chloroplast genome (Maughan et al., ) as a target. The ARC algorithm uses Bowtie2 (Langmead and Salzberg, ) with relaxed parameters to map reads against targets, extract mapped reads from each target, and assemble mapped reads using the SPAdes assembler (Bankevich et al., ).…”

“…A circularized contig representing the complete plastid genome was constructed using the circularize tool from Geneious (version 11.1.5; https://www.geneious.com/), then the assembly was polished with the same six million paired‐end Illumina reads as used in the initial assembly. Annotation of the cañahua chloroplast genome was performed using GeSeq version 1.65 (Tillich et al., ) with the quinoa chloroplast annotation (Maughan et al., ) and the Max Planck Institute of Molecular Plant Physiology (MPI‐MP) chloroplast database as references. ARAGORN version 1.2.3 and HMMER profile searches were enabled, the latter using the embryophyta chloroplast (CDS + rRNA) database.…”

Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

“…Due to the ability to grow on marginal soils in short vegetation periods, the high tolerance for abiotic stresses such as cold and UV radiation, and the high nutritional value of its grains, quinoa is ranked as a "high potential" crop with priority for sustainable agriculture (www.fao.org, Zurita-Silva et al, 2014). Having an allotetraploid origin with 2n=4x=36 chromosomes, quinoa was derived from hybridisation of a female American Chenopodium diploid (A genome) with a male Old World diploid (B genome), dating back 3.3 to 6.3 million years (Kolano et al, 2012, Štorchová et al, 2015, Walsh et al, 2015, Maughan et al, 2019. Potential diploid progenitors with B genomes have approximately 30 % larger genomes than A genome species (approximately 0.6 and 0.9 Gb; Kolano et al, 2016).…”