The generation and analysis of genomic resources information are essential to understand genomic features of crops. Even though medicinal component and its effect of Panax ginseng was well studied, the genomic study has been recently started. The ginseng genome has been known to undergo two rounds of whole genome duplication (WGD), therefore we investigated an evidence of WGD in ginseng draft sequence for understanding current ginseng genome structure. Four paralogous gene-rich genome blocks were found, consisted by eight scaffolds, using about 3.0 Gb whole genome draft sequence and 48,821 unigenes of P. ginseng generated by whole genome shotgun sequencing. The eight scaffold sequences were ordered and connected into four genomic blocks, using zig-zag extension within scaffold sequences recently duplicated. The paralogous scaffold pairs that were recently duplicated showed high sequence conservation in genic and non-genic regions. However, paleo duplicated paralogue scaffold sequences showed little conservation only in genic regions. Finally, a total of 110 paralogous gene pairs and its expression were identified from recently and paleo duplicated scaffold pairs, which were co-linear among four genomic blocks. This study provides the first insight into duplicated genome structure of ginseng and will be a valuable information for further ginseng genomics including improvement of draft sequence quality, chromosome anchoring of scaffolds, and genetic mapping.

Chloroplasts are plant-specific organelles, which have their own genome. Most of the plant chloroplast genomes (CP genome) are highly conserved in terms of its gene contents and genome structures, and they exist in cells with abundant copy numbers. Because of numerous copy numbers, the complete chloroplast sequence assembly pipeline with small amount of whole genome resequencing data, produced by NGS technique, was established in our laboratory. From 14 accessions of cabbage (Brassica oleracea L.) resequencing data produced by Illumina Hi-seq 2000, CP genomes were assembled and compared to each other. 18 sequence variance regions were detected, and 6 HRM(High Resolution Melting curves) markers were developed. Approximately 1 Gb of whole genome sequencing data of 10 Brassica rapa and 2 Brassica napus were also obtained from Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science. With these resequencing data, all CP genomes from these accessions were assembled. Total 27 complete CP genomes of B.oleracea, B.rapa, B.napus, and brassico-raphanus which is a novel allotetraploid species between B.rapa and Raphanus sativus, were compared in sequence level. Phylogenetic analysis based on the comparison revealed that B.rapa could be the maternal species when rapeseeds and brassico-raphanus became allotetraploid species. Additionally, CP genome of B.napus cv.M083 is closer to B.rapa accessions than the other B.napus accessions, thus B.napus could have several different origins.

Mitochondria are essential organelles of eukaryotic cells and plant cells contain varying numbers of mitochondrial genome sequences. Sizes and shapes of mitochondria differ within a tissue or in the same cells. Previously sequenced complete mitochondrial genome (NC_016118) of Brassica oleracea size was 360,271 bp, where segmental duplication (repeat block) was 141,800 bp. In this study, we resequenced this whole mitochondrial genome by using WGS (whole genome sequencing) and assembled organelles genome method (unpublished). Newly sequenced mitochondrial genome length was 219,975 bp and circle form. A new sequence segment of approximately 4,800 bp was obtained compared to the previous genome sequence without any large repeat block. Newly obtained mitochondria genome sequence was compared with recently reported mitochondria genome sequences of various species (B. oleracea, B. juncea, B. rapa, B. napus and B. carinata) and subspecies (cabbage, cauliflower, brussels sprouts, kohlrabi, broccoli and kale) by PCR using primers specifying different region of genome sequences. PCR analysis results have also confirmed the variation between previous and newly sequenced mitochondrial genome circles form. Thus, the results suggest new B. oleracea mitotype, including evolutionary events such as inheritance, rearrangement, genome compaction, and diversity

Genetic map provides basic and important informations for breeding. Therefore, genetic map construction is a essential process in plant research. Panax ginseng is one of the most famous medical plant in the world. However, genetic informations of this medical plant for breeding are not enough. Because of little informations, genetic map construction of panax ginseng provides very useful information for breeding. Using Solexa next generation sequencing (NGS) technology, we have been produced a lot of expressed sequence tags (ESTs) and whole genome sequences from Chunpoong (368 Gb) and Yunpoong (6 Gb) cultivar. To develop large amount of DNA markers and thus construct high resolution genetic map, we inspect large scale of SSR motif and putative SNP sites which can be used as dCAPs markers using produced ginseng’s sequence data. As a result, we can find a number of DNA markers that have polymorphism between Yunpoong and Chunpoong cultivar. These developed DNA markers were analyzed for F2 population of Yunpoong x Chunpoong to find markers showing Mendelian segregation ratio 1:2:1.

Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetables and widely cultivated in Asia countries including Korea and China. Recently, whole genome sequence and full-length cDNA information of this species became available, which are encouraging genetic studies of this species to characterize agricultural important traits. Orange-colored (Or) cultivar of Chinese cabbage has inner leaves in orange, whereas other cultivars generally cultivated have yellow (Ye)- or white-colored inner leaves. In this study, we investigated phenotypes and carotenoid biosynthesis genes related to color variation in the Or cultivar. Firstly we compared the carotenoid content and composition between the Or and Ye cultivars by HPLC analysis. The inner leaves of Or cultivar contained approximately 9-fold high β-carotene content, whereas content of both lutein and violaxanthin was decreased to less than 30%, compared to Ye cultivar. Or cultivar was segregated with ratio of 3:1 in F2 population derived from crossing between Or and Ye inbred lines, indicating that Or phenotype is controlled by single recessive gene. To identify this gene, we investigated the expression of several genes involved in carotenoid biosynthesis by RT-PCR analysis. Among genes tested, two encoding putative carotenoid isomerase (CRTISO) and phytoene desaturase (PDS) were identified to show different expression between Or and Ye cultivars. Through further analysis of genomic DNA regions of these two genes, we could expect that several mutations such as InDel and base-substitution occurred and then affected expression of these genes in Or cultivar. In this presentation, I will introduce more detailed results for Or cultivars.