Abstract
BackgroundChloroplast genome sequences are extremely informative about species-interrelationships owing to its non-meiotic and often uniparental inheritance over generations. The subject of our study, Fagopyrum esculentum, is a member of the family Polygonaceae belonging to the order Caryophyllales. An uncertainty remains regarding the affinity of Caryophyllales and the asterids that could be due to undersampling of the taxa. With that background, having access to the complete chloroplast genome sequence for Fagopyrum becomes quite pertinent.ResultsWe report the complete chloroplast genome sequence of a wild ancestor of cultivated buckwheat, Fagopyrum esculentum ssp. ancestrale. The sequence was rapidly determined using a previously described approach that utilized a PCR-based method and employed universal primers, designed on the scaffold of multiple sequence alignment of chloroplast genomes. The gene content and order in buckwheat chloroplast genome is similar to Spinacia oleracea. However, some unique structural differences exist: the presence of an intron in the rpl2 gene, a frameshift mutation in the rpl23 gene and extension of the inverted repeat region to include the ycf1 gene. Phylogenetic analysis of 61 protein-coding gene sequences from 44 complete plastid genomes provided strong support for the sister relationships of Caryophyllales (including Polygonaceae) to asterids. Further, our analysis also provided support for Amborella as sister to all other angiosperms, but interestingly, in the bayesian phylogeny inference based on first two codon positions Amborella united with Nymphaeales.ConclusionComparative genomics analyses revealed that the Fagopyrum chloroplast genome harbors the characteristic gene content and organization as has been described for several other chloroplast genomes. However, it has some unique structural features distinct from previously reported complete chloroplast genome sequences. Phylogenetic analysis of the dataset, including this new sequence from non-core Caryophyllales supports the sister relationship between Caryophyllales and asterids.
Highlights
Chloroplast genome sequences are extremely informative about speciesinterrelationships owing to its non-meiotic and often uniparental inheritance over generations
Overall structure and gene content of buckwheat chloroplast genome The GenBank accession number for the nucleotide sequence reported in this study is EU254477
Complete chloroplast genome of Fagopyrum esculentum ssp. ancestrale is composed of 159599 nucleotide bases
Summary
Chloroplast genome sequences are extremely informative about speciesinterrelationships owing to its non-meiotic and often uniparental inheritance over generations. With that background, having access to the complete chloroplast genome sequence for Fagopyrum becomes quite pertinent. Chloroplasts are hypothesized to have evolved from ancient endosymbiotic cyanobacteria. They are semiautonomous possessing their own genome that codes for a set of proteins, which orchestrate the process of photosynthesis and other house-keeping functions. The nonmeiotic and mostly uniparental inheritance of chloroplast genes render them as most informational entities in plant phylogenetic studies. Despite the availability of these datasets, complete chloroplast genome sequence-based phylogenies are prone to artifacts caused by incomplete taxon sampling [2,3,4]. Availability of complete chloroplast genome sequences from additional taxa is highly desirable for robust phylogenetic studies
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