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Aizawa M, Worth JRP. Phylogenetic origin of two Japanese Torreya taxa found in two regions with strongly contrasting snow depth. JOURNAL OF PLANT RESEARCH 2021; 134:907-919. [PMID: 33866439 DOI: 10.1007/s10265-021-01301-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The Japanese archipelago exhibits a notable difference in snow depth in winter, deep snow on the Sea of Japan side and low snow cover on the Pacific Ocean side. This contrasting pattern has shaped the distribution of infraspecific taxon pairs in a range of woody plants, with taxa found on the Sea of Japan side typically exhibiting a stunted shrub form with multiple decumbent stems. The phylogenetic origin of these taxon pairs is unknown, i.e., whether the two taxa diverged from the same species or if they have different origins. This study aimed to reveal the phylogenetic origin of two varieties of Torreya nucifera (Taxaceae); var. nucifera is a tree found on the Pacific Ocean side, whereas var. radicans is a shrub found on the Sea of Japan side. We examined the phylogenetic relationships of the two varieties and worldwide Torreya taxa using whole chloroplast genomes, chloroplast DNA fragments, and the nuclear ribosomal internal transcribed spacer (ITS). The whole chloroplast genome phylogeny indicated that T. nucifera var. radicans was a sister taxon to Chinese T. grandis, rather than to var. nucifera. In contrast, the nuclear ITS phylogeny indicated that while several haplotypes of T. nucifera var. radicans were closely related to T. grandis, most haplotypes of T. nucifera var. radicans formed a single clade with those of var. nucifera. This implies that the homogenization of the ITS has occurred between the two taxa, while taxon-specific chloroplast DNA haplotypes were retained. These discordant phylogenies suggested that the two taxa have different phylogenetic origins, but have an intricate evolutionary history, involving inter-taxa hybridization and gene flow, possibly when their distributions were confined to sympatric refugia. Given the genetic evidence and distinct difference in growth form, we propose that T. nucifera var. radicans should be taxonomically treated as a distinct species, T. fruticosa.
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Affiliation(s)
- Mineaki Aizawa
- Department of Forest Science, School of Agriculture, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi, 321-8505, Japan.
| | - James R P Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
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Li H, Liang YR, Chen SX, Wang WX, Zou Y, Nuryyeva S, Houk KN, Xiong J, Hu JF. Amentotaxins C-V, Structurally Diverse Diterpenoids from the Leaves and Twigs of the Vulnerable Conifer Amentotaxus argotaenia and Their Cytotoxic Effects. JOURNAL OF NATURAL PRODUCTS 2020; 83:2129-2144. [PMID: 32633512 DOI: 10.1021/acs.jnatprod.0c00064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A phytochemical investigation of the MeOH extract of the leaves and twigs of Amentotaxus argotaenia, a relict vulnerable coniferous species endemic to China, led to the isolation and characterization of 35 diterpenoids/norditerpenoids. Twenty of these are new, including 11 ent-kaurane-type (amentotaxins C-M, 1-11, respectively), three icetexane-type [= 9(10→20)abeo-abietane-type (amentotaxins N-P, 12-14, respectively)], four ent-labdane-type (amentotaxins Q-T, 15-18, respectively), and two isopimarane-type [amentotaxins U (19) and V (20)] compounds. Their structures were elucidated on the basis of spectroscopic data, single-crystal X-ray diffraction, the modified Mosher's method, and electronic circular dichroism data analyses. Compounds 1-9 are rare 18-nor-ent-kaurane-type diterpenoids featuring a 4β,19-epoxy ring. All the isolates were evaluated for their cytotoxic effects against a small panel of cultured human cancer cell lines (HeLa, A-549, MDA-MB-231, SKOV3, Huh-7, and HCT-116), and some of them exhibited cytotoxicities with IC50 values ranging from 1.5 to 10.0 μM.
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Affiliation(s)
- Hao Li
- School of Pharmacy, Fudan University, No. 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Yu-Ru Liang
- School of Pharmacy, Fudan University, No. 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Shao-Xin Chen
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, No. 285 Gebaini Road, Shanghai 201203, People's Republic of China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Tongzipolu 172, Changsha 410013, People's Republic of China
| | - Yike Zou
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Selbi Nuryyeva
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - K N Houk
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Juan Xiong
- School of Pharmacy, Fudan University, No. 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Jin-Feng Hu
- School of Pharmacy, Fudan University, No. 826 Zhangheng Road, Shanghai 201203, People's Republic of China
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Zhang Y, Xu Y, Chen H, Wang L, Yin K, Du FK. Comparative Genomic Analysis Reveals the Mechanism Driving the Diversification of Plastomic Structure in Taxaceae Species. Front Genet 2020; 10:1295. [PMID: 32010180 PMCID: PMC6971195 DOI: 10.3389/fgene.2019.01295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/25/2019] [Indexed: 11/20/2022] Open
Abstract
Inverted repeat (IR) regions in the plastomes from land plants induce homologous recombination, generating isomeric plastomes. While the plastomes of Taxaceae species often lose one of the IR regions, considerable isomeric plastomes were created in Taxaceae species with a hitherto unclarified mechanism. To investigate the detailed mechanism underpinning the IR-independent genesis of plastomic diversity, we sequenced four Taxaceae plastomes, including Taxus cuspidata Siebold & Zuccarini, Taxus fauna Nan Li & R. R. Mill, and two individuals of Taxus wallichiana Zuccarini. Then we compared these structures with those of previously reported Taxaceae plastomes. Our analysis identified four distinct plastome forms that originated from the rearrangements of two IR-flanking inverted fragments. The presence of isomeric plastomes was then verified in T. cuspidata individuals. Both rearrangement analyses and phylogenetic results indicated that Taxaceae were separated into two clades, one including Taxus and Pseudotaxus and another formed by Amentotaxus and Torreya. Our reconstructed scenario suggests that the minimum number of inversion events required for the transformation of the plastome of Cephalotaxus oliveri Masters into the diversified Taxaceae plastomes ranged from three to six. To sum up, our study reveals a distinct pattern and the mechanism driving the structural diversification of Taxaceae plastomes, which will advance our understanding of the maintenance of plastomic diversity and complexity in conifers.
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Affiliation(s)
- Yue Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yang Xu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hao Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States
| | - Kangquan Yin
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Fang K. Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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Zhang J, Cao ZP, Li S, Liu MM, Huo XW. The complete chloroplast genome sequence of Amentotaxus yunnanensis (Taxaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2477-2478. [PMID: 33365590 PMCID: PMC7687433 DOI: 10.1080/23802359.2019.1637293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The complete chloroplast genome sequence of Amentotaxus yunnanensis has been defined in this study. The genome is 138,604 bp in length and one of the large inverted repeats found till date. The overall GC content of the genome is 35.1%. The A. yunnanensis chloroplast genome contains 118 unique genes, including 81 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Nine protein-coding genes and 6 tRNA contain a single intron, while another species (ycf3) has a couple of introns. A neighbor-joining phylogenetic analysis suggested that A. yunnanensis is closely related to A. argotaenia and A. formosana within the Taxaceae family.
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Affiliation(s)
- Jun Zhang
- College of Pharmaceutical Science, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, China
| | - Ze-Peng Cao
- College of Pharmaceutical Science, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, China
| | - Shuo Li
- College of Traditional Chinese Medicine, Hebei University, Baoding, China
| | - Meng-Meng Liu
- College of Traditional Chinese Medicine, Hebei University, Baoding, China.,Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiao-Wei Huo
- College of Pharmaceutical Science, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, China
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Zhang YY, Shi E, Yang ZP, Geng QF, Qiu YX, Wang ZS. Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China. FRONTIERS IN PLANT SCIENCE 2018; 9:246. [PMID: 29545814 PMCID: PMC5838013 DOI: 10.3389/fpls.2018.00246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/12/2018] [Indexed: 05/14/2023]
Abstract
Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units.
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Affiliation(s)
- Yun-Yan Zhang
- College of Life Sciences, Nanjing University, Nanjing, China
| | - En Shi
- College of Life Sciences, Nanjing University, Nanjing, China
| | - Zhao-Ping Yang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Life Sciences, Tarim University, Alaer, China
| | - Qi-Fang Geng
- College of Life Sciences, Nanjing University, Nanjing, China
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
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Li JH, Cheng HX, Liu LL, Wang XY, Pan T, Hong X. The complete chloroplast genome sequence of an endangered plant Torreya jackii (Pinales, Taxaceae). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0855-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tao K, Gao L, Li J, Chen S, Su Y, Wang T. The complete chloroplast genome of Torreya fargesii (Taxaceae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3512-3. [PMID: 27158868 DOI: 10.3109/19401736.2015.1074195] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast genome sequence of Torreya fargesii (Taxaceae), a relic plant endemic to China, is presented in this study. The genome is 137 075 bp in length, with 35.47% average GC content. One copy of the large inverted repeats is lost from this genome. The T. fargesii chloroplast genome encodes 118 unique genes, in which trnI-CAU, trnQ-UUG, trnN-GUU are duplicated. Protein-coding, tRNA and rRNA genes represent 54.7%, 1.9% and 3.4% of the genome, respectively. There are 17 intron-containing genes, of which 6 are tRNA genes. A maximum likelihood phylogenetic analysis revealed a strong sister relationship between Torreya and Amentotaxus.
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Affiliation(s)
- Ke Tao
- a CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan , Hubei , China .,b University of Chinese Academy of Sciences , Beijing , China
| | - Lei Gao
- a CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan , Hubei , China
| | - Jia Li
- a CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan , Hubei , China .,b University of Chinese Academy of Sciences , Beijing , China
| | - Shanshan Chen
- a CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan , Hubei , China .,b University of Chinese Academy of Sciences , Beijing , China
| | - Yingjuan Su
- c State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University , Guangzhou , Guangdong , China .,d Institute for Technology Research and Innovation, Sun Yat-sen University , Zhuhai , Guangdong , China , and
| | - Ting Wang
- a CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan , Hubei , China .,e College of Life Sciences, South China Agricultural University , Guangzhou , Guangdong , China
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