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.
Highlights
Chloroplast is a plant organelle involved in photosynthesis that has originated from an ancestral endosymbiotic cyanobacteria (Cho et al, 2015)
The complete cp genome of C. quinoa and C. album consisted of a single circular molecule with quadripartite structure (Figure 1)
The genomes contained 78 coding genes, accounting for 79,115 and 78,930 bp of the C. quinoa and C. album cp genome, respectively; of those, 62, 5, and 11 genes were located in the large single copy region (LSC), inverted repeats (IRs), and small single copy region (SSC) region, respectively (Table S3)
Summary
Chloroplast (cp) is a plant organelle involved in photosynthesis that has originated from an ancestral endosymbiotic cyanobacteria (Cho et al, 2015). This organelle plays a role in photosynthetic carbon fixation, providing essential energy to plants (Raven and Allen, 2003). The chloroplast genome consists of a circular DNA molecule with quadripartite. In addition to a quadripartite structure, the chloroplast genome contains about 100–130 genes with highly conserved order and sequences among most land plants (Smith, 2015). Sequencing of the complete cp DNA genome began in 1991 (Taberlet et al, 1991) and until present days, the cp genomes from 1,200 species of algae and plants have been sequenced (http://www.ncbi.nlm.nih.gov/ genome/organelle/)
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