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Dynamic evolution of Panax species
Hyeonah Shim,Nomar Espinosa Waminal,Hyun Hee Kim,Tae‑Jin Yang 한국유전학회 2021 Genes & Genomics Vol.43 No.3
Background Panax ginseng is one of the most valuable medicinal plants in Korea. However, deciphering its full genome sequence information for crop improvement has been hampered due to its complex genomic, genetic, and growth characteristics. Many eforts have been made in the past decade to overcome these limitations and understand the genome structure and the evolutionary history of P. ginseng. Methods This review aims to discuss the current status of genomic studies on P. ginseng and related species, and the experimental clues suggesting phylogenetic classifcation and evolutionary history of the genus Panax. Conclusion The development of sequencing technologies made genome sequencing of the large P. ginseng genome possible, providing fundamental information to deciphering the evolutionary history of P. ginseng and related species. P. ginseng went through two rounds of whole genome duplication events after diverging from the closest family Apiaceae, which was unveiled from complete whole genome sequences. Further in-depth comparative genome analysis with other related species and genera will uncover the evolutionary history as well as important morphological and ecological characteristics of Panax species.
[PA-0025] Plastid Phylogenomics and Evolution of Araliaceae
Jong-Soo Kang(Jong-Soo Kang),Vo Ngoc Linh Giang(Vo Ngoc Linh Giang ),Hyunjin Koo(Hyunjin Koo),Hyeonah Shim(Hyeonah Shim),Woohyeon Cho(Woohyeon Cho),Young Ju Oh(Young Ju Oh),Hye Ji Lee(Hye Ji Lee),Jee 한국육종학회 2022 한국육종학회 공동학술발표집 Vol.2022 No.-
Genomic Signature for Stem Swollen of Kohlrabi Morphotype in Brassica oleracea
( Hyunjin Koo ),( Hyeonah Shim ),( Sampath Perumal ),( Ho Jun Joh ),( Tae-jin Yang ) 한국육종학회 2021 Plant Breeding and Biotechnology Vol.9 No.1
Brassica oleracea contains various morphotypes within the species, but genomic signatures differentiating each morphotype have been poorly understood of. Here, we utilized whole genome sequence data of 44 B. oleracea collections including those of seven different morphotypes such as cabbage, broccoli, cauliflower, kailan, kale, brussels sprout, and kohlrabi to elucidate the genomic signature of B. oleracea morphotypes. Molecular structure analysis divided the 44 B. oleracea lines into two groups: group I represents broccoli, cauliflower, kailan; group II represents other B. oleracea subspecies. Kohlrabi has admixed genomic structure through genetic admixture analysis. Based on the population stratification result, we have investigated genetic signatures that offer the possible evolutionary processes for the kohlrabi morphotype. Several statistical analyses were implemented to identify selective regions and explore 45 candidate loci that may contribute to stem swollen in kohlrabi. Above all, we identified two kohlrabi-unique genes, LOC106333915 and LOC106308097, showing kohlrabi-unique non-synonymous mutations, which might be candidate genes for stem swollen in kohlrabi.
Origin and evolution of Korean ginseng revealed by genome sequence
Cho, Woohyeon,Shim, Hyeonah,Yang, Tae-Jin The Korean Society of Ginseng 2021 인삼문화 Vol.3 No.-
인삼은 세계에서 가장 중요한 약용식물 중 하나이다. 본 연구실에서는 국립종자원에 최초로 등록된 인삼 품종 '천풍'을 이용하여 대략 3Gbp의 완성도 높은 유전체 서열과 60,000여개의 유전자를 동정하여 공개하였다. 인삼속 근연종들과의 비교유전체연구를 통해 종의 분화 시기 등을 추정하였고, 이를 통해 고려인삼의 기원과 두 번의 대륙이동을 통한 인삼속의 진화와 분포모델을 확립하였다. 인삼속 18종 중 2종 (고려인삼, 화기삼)은 24쌍의 염색체를 가지는 사배체 식물이며 나머지 16종은 12쌍의 염색체를 가지는 이배체 식물이다. 인삼속과 두릅나무속은 두릅나무과에 속하는 가장 가까운 식물로서 약 8백만년 전에 분화하였다. 인삼속은 약 6백만년 전 베트남 등의 동남아시아에서 러시아와 같은 동북아시아에 이르는 지역의 깊은 숲 속 서늘한 기후와 숲 속의 음지조건에 적응하며 음지식물로 진화했다. 그 기간은 빙하기와 간빙기가 반복되는 시기로 월동 능력이 없는 이배체 인삼종은 대부분 동북아시아 지역에서 멸종하였고 이 과정에 이배체간 종간 교잡종인 이질사배체가 약 2백만년전 만들어졌으며 한반도를 위시한 동북아시아를 중심으로 월동능력을 가진 고려인삼이 태동되었다고 추정된다. 북미에 분포하는 화기삼은 동북아시아 전역에 분포하던 고려인삼이 약 1백만년전에 빙하의 이동과 더불어 대륙간 이주를 통해 새로운 생태 환경에 적응하면서 분화되었다고 판단된다. 반면 대부분의 이배체 인삼종은 고온을 견디지 못하고 월동능력도 없어 동남아시아 지역에서 1,600미터 이상의 고산 지역으로 쫓겨 올라가 연중 서늘한 기후에서 생존하고 있다. 유전체 해독 정보는 인삼의 기원과 진화기작을 추정하는 학문적 성과 뿐 아니라 인삼산업을 보호하고 우수 인삼을 개발하기 위한 실용적인 분자육종 수단에도 매우 효율적으로 활용될 수 있다. Panax ginseng (Ginseng or Korean ginseng) is one of the most important medicinal herbs in the world. We made a high-quality whole genome sequence of P. ginseng using 'Chunpoong' cultivar, which is the first cultivar registered in Korea Seed and Variety Service (KSVS) with relatively similar genotypes and superior phenotypes, representing approximately 3 Gbp and 60,000 genes. Genome sequence analyses of P. ginseng and related speciesrevealed the origin of Korean ginseng and the ecological adaptation of 18 Panax species around the world. Korean ginseng and American ginseng (P. quinquefolius) are tetraploid species having 24 chromosome pairs, while the other 16 species are diploid species with 12 chromosome pairs. Panax and Aralia are the closest genera belonging to the Araliaceae family that diverged approximately 8 million years ago (MYA). All Panax species evolved as shade plants adapting to cool climates and low light conditions under the canopy of deep forests from Southeast Asia such as Vietnam to Northeast Asia such as Russia approximately 6 MYA. However, through recurrent ice ages and global warming, most diploid Panax species disappeared due to the freezing winter, while tetraploid P. ginseng may have appeared by allotetraploidization, which contributed to the adaptation to cold temperaturesin Northeast Asian countries including the Korea peninsula approximately 2 MYA. American ginseng evolved by the adaptation of P. ginseng in Northeast America after the intercontinental migration 1 MYA. Meanwhile, most of diploid Panax species survived in high-altitude mountains over 1,600 meters in Southeast Asia because they could not endure the hot temperature and freezing cold. The genome sequence provides good basisto unveil the origin and evolution of ginseng and also supports practical gene chips which is useful for breeding and the ginseng industry.
이준기,강신재,Hyeonah Shim,이상춘,김남훈,장우종,박지영,강정화,이완희,Taek Joo Lee,Gyoungju Nah,양태진 한국육종학회 2019 Plant Breeding and Biotechnology Vol.7 No.1
Although genomics provides useful tools for crops, most wild resource plants still lack molecular data. To retrieve useful genomic data and thus provide fundamental information for a resource plant, we established a multi-directional approach using two low coverage whole-genome shotgun sequence (WGS) data of Euonymus hamiltonianus, which is a wild resource plant with potential as a medicinal and ornamental plant. We assembled complete chloroplast genome and nuclear ribosomal DNA (nrDNA) sequences and analyzed polymorphic simple sequence repeats (pSSRs) in the nuclear genome based on the comparison of WGS data between two different phenotypes. We developed a bioinformatics pipeline to identify pSSR motifs by systematic comparison of two WGS datasets. The pipeline is composed of multiple steps including end-joining of paired reads, isolation of joined reads harboring SSR motifs derived from unique non-repetitive regions, identification of pSSR via in silico comparison with counterpart WGS reads, design of pSSR primer sets, and validation. The pipeline was applied to WGS data of E. hamiltonianus and identified 161 contigs with pSSR motifs between the two different phenotypes. Based on the pSSR motifs, 20 primer pairs were designed, of which seven were successfully validated as real pSSR markers. We expect this information to be applicable to genomic resources of E. hamiltonianus.