Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum) and Comparative Analysis with Common Buckwheat (F. esculentum)

May Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum) and Comparative Analysis with Common Buckwheat (F. esculentum) Kwang-Soo Cho 0 1 Bong-Kyoung Yun 0 1 Young-Ho Yoon 0 1 Su-Young Hong 0 1 Manjulatha Mekapogu 0 1 Kyung-Hee Kim 0 1 Tae-Jin Yang 0 1 0 1 Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration , Pyeongchang , South Korea , 2 Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University , Seoul , South Korea , 3 Phygen Genomics Institute , Gwanak Century Tower, Kwanak-gu, Seoul , South Korea 1 Academic Editor: Berthold Heinze, Austrian Federal Research Centre for Forests BFW , AUSTRIA We report the chloroplast (cp) genome sequence of tartary buckwheat (Fagopyrum tataricum) obtained by next-generation sequencing technology and compared this with the previously reported common buckwheat (F. esculentum ssp. ancestrale) cp genome. The cp genome of F. tataricum has a total sequence length of 159,272 bp, which is 327 bp shorter than the common buckwheat cp genome. The cp gene content, order, and orientation are similar to those of common buckwheat, but with some structural variation at tandem and palindromic repeat frequencies and junction areas. A total of seven InDels (around 100 bp) were found within the intergenic sequences and the ycf1 gene. Copy number variation of the 21-bp tandem repeat varied in F. tataricum (four repeats) and F. esculentum (one repeat), and the InDel of the ycf1 gene was 63 bp long. Nucleotide and amino acid have highly conserved coding sequence with about 98% homology and four genes-rpoC2, ycf3, accD, and clpP-have high synonymous (Ks) value. PCR based InDel markers were applied to diverse genetic resources of F. tataricum and F. esculentum, and the amplicon size was identical to that expected in silico. Therefore, these InDel markers are informative biomarkers to practically distinguish raw or processed buckwheat products derived from F. tataricumand F. esculentum. - Funding: This study was supported by a grant from the Cooperative Research Program for Agriculture Science and Technology Development, (Project Title: Development of DNA markers linked to agricultural traits for buckwheat breeding, Project No. PJ009246), Rural Development Administration, Republic of Korea. The funders had no role in study Chloroplasts are essential organelles in plant cells that perform photosynthesis, in addition to other functions including synthesizing sugars, pigments, and certain amino acids. The chloroplast (cp) is considered to have originated from an ancestral endosymbiotic cyanobacteria. In addition to the larger dominant genome located in the nucleus of plant cell, chloroplasts design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. contain their own independent genome encoding a specific set of proteins. The non-recombinant nature of the cp genome makes it a potentially useful tool in genomics and evolutionary studies. Although the cp genome is highly conserved in vascular plants, evolutionary hotspots such as single nucleotide polymorphisms [SNPs] and insertion/deletions [In/Dels] resulting from inversions, translocations, rearrangements and copy number variation of tandem repeats have been found in many plants [1]. As such, these SNPs and In/Dels are useful as molecular markers as the cp genome is highly conserved within the species. Further, cp DNA can be easily extracted from samples because of the high copy number. The small size of the cp genome makes it suitable for complete sequencing and the data can be further applied to phylogeny construction [2], DNA bar coding [3], and transplastomic studies [4]. Complete cp DNA sequencing began in 1991 [5] and to date cp genomes of various algae and plants, including crop species, have been reported (CpBase: http://chloroplasr.ocean.washington.edu). Until recently, cp genome sequencing was a costly and time-consuming process. The majority of such research, therefore, has been limited to sequencing a small portion of the cp genome, which in many cases is insufficient for determining evolutionary relationships, thereby limiting its utility for plant evolutionary and genomic studies. As complete cp genome sequences harbor sufficient information, sequencing of whole cp genomes is essential for the comparison and analyses of diversifications among plant species. The advent of next-generation sequencing (NGS) has made it considerably cheaper and easier to sequence complete cp genomes. NGS is advantageous as it provides extremely high yield and the opportunity for multiplexing when investigating whole-cp genomes, rather than targeting individual regions [6,7]. NGS allows potentially hundreds of flowering plant cp genomes to be sequenced simultaneously, significantly reducing the per-sample cost of cp genome sequencing [8]. Buckwheat (Fagopyrum species) belonging to Polygonaceae, a member of knotgrass is an annual herbaceous plant. Buckwheat is classified into twenty species, is largely centered in the Eurasian region, and is mainly grown in the highlands [9,10]. It is divided into two groups cymosum and urophyllum, based on the morphology and cp genome [11]. The cymosum group comprises F. esculentum, F. tataricum, F. cymosum, and F. homotropicum, which are characterized according to the flowering calyx (persistent perianth) and achene. The urophyllum group comprises F. urophyllum, which is characterized by a glossy calyx. Among these, common buckwheat (F. esculentum) and tartary buckwheat (also known as bitter buckwheat (F. tataricum), are used in various dietary preparations and are mainly grown in South Korea, Japan, and China [12]. Because of the nutritional value of tartary buckwheat, the cultivated area in South Korea has increased in recent years [13]. Bitter buckwheat is a particularly rich source of rutin compared to common buckwheat, which helps reduce intra-vascular cholesterol, high blood pressure, and diabetes. Rutin is also reported to have a crucial role in pharmaceutical research [14,15,16]. The complete cp genome of Fagopyrum may provide useful information for phylogenetic comparisons with the related species. To date there have been few cp genome sequencing studies performed in buckwheat. The complete cp genome sequence of a wild ancestor of cultivated buckwheat F. esculentum spp. ancestrale was reported using amplification, sequencing, and annotation (ASAP) method [17]. Here, we present the complete cp genome sequence of tartary buckwheat (F. tataricum) by using NGS and comparative analysis with common buckwheat (F. esculentum). To the best of our knowledge, this is the first report of the complete cp genome sequence of tartary buckwheat. Comparative analysis between two Fagopyrum species could reveal the evolution of each species and provi (...truncated)