Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

Abstract

The Chenopodium genus comprises ~150 species, including Chenopodium quinoa and Chenopodium album, two important crops with high nutritional value. To elucidate the phylogenetic relationship between the two species, the complete chloroplast (cp) genomes of these species were obtained by next generation sequencing. We performed comparative analysis of the sequences and, using InDel markers, inferred phylogeny and genetic diversity of the Chenopodium genus. The cp genome is 152,099 bp (C. quinoa) and 152,167 bp (C. album) long. In total, 119 genes (78 protein-coding, 37 tRNA, and 4 rRNA) were identified. We found 14 (C. quinoa) and 15 (C. album) tandem repeats (TRs); 14 TRs were present in both species and C. album and C. quinoa each had one species-specific TR. The trnI-GAU intron sequences contained one (C. quinoa) or two (C. album) copies of TRs (66 bp); the InDel marker was designed based on the copy number variation in TRs. Using the InDel markers, we detected this variation in the TR copy number in four species, Chenopodium hybridum, Chenopodium pumilio, Chenopodium ficifolium, and Chenopodium koraiense, but not in Chenopodium glaucum. A comparison of coding and non-coding regions between C. quinoa and C. album revealed divergent sites. Nucleotide diversity >0.025 was found in 17 regions—14 were located in the large single copy region (LSC), one in the inverted repeats, and two in the small single copy region (SSC). A phylogenetic analysis based on 59 protein-coding genes from 25 taxa resolved Chenopodioideae monophyletic and sister to Betoideae. The complete plastid genome sequences and molecular markers based on divergence hotspot regions in the two Chenopodium taxa will help to resolve the phylogenetic relationships of Chenopodium.

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., ). 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., ).…”

Characterization of the complete plastome of Dysphania botrys, a candidate plant for cancer treatment

“…Chenopodioideae, together with Betoideae formed a sister clade to the three subfamilies (Salicornioideae, Suaedoideae, and Salsoloideae), and this sister clade formed an evolutionary sister clade to Amaranthoideae. This result was similar to the most recent phylogenetic studies of Amaranthaceae, but with much higher bootstrap support (Fuentes-Bazan et al 2012;Hong et al 2017). Overall, we firstly report the complete chloroplast of genera Dysphania, and our data will largely enrich the genetic information of D. botrys and facilitate future studies on its evolutionary status.…”

Biological and Molecular Characterization of Chenopodium quinoa Mitovirus 1 Reveals a Distinct Small RNA Response Compared to Those of Cytoplasmic RNA Viruses

“…7). Availability of C. quinoa chloroplast (32) and nuclear (27) genomes, and our own selection of a number of mitochondrial genes from our transcriptome data, allowed us to check the read distribution lengths of host sRNA mapping to those genomes. sRNA mapping onto the chloroplast genome had a major peak at 27 nt (22%), whereas the second peak is at 22 nt; in the case of sRNA mapping to mitochondrial genes (in this case only the putative coding sequences were used), a sharp peak is present for 16 nt (67% of the sRNA).…”