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Feng M, Kong H, Lin M, Zhang R, Gong W. The complete plastid genome provides insight into maternal plastid inheritance mode of the living fossil plant Ginkgo biloba. PLANT DIVERSITY 2023; 45:752-756. [PMID: 38197005 PMCID: PMC10772217 DOI: 10.1016/j.pld.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 01/11/2024]
Abstract
In the current research, we focus on uniparental inheritance of chloroplast genome of the living fossil plant, Ginkgo biloba L., one of the gymnosperms, using genomic data.•Our results provide strong genomic evidence to support plastid maternal inheritance mode of G. biloba, which is different from most other gymnosperms.•The combination of manually genetic crosses and genomic data is proved to be an efficient way to investigate the inheritance mode of chloroplasts genome in land plants.•The current research also provides a case study for further research of plastid inheritance in gymnosperms using genomic techniques, which will contribute to a better understanding of cytologically uniparental inheritance mode and evolutionary mechanism of plastids in both gymnosperms and angiosperms.
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Affiliation(s)
- Mengxue Feng
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Meixiu Lin
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
| | - Rongjing Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
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Nam DE, Cha MJ, Kim YD, Awasthi M, Do Y, Kong SG, Chung KW. Microsatellite Dataset for Cultivar Discrimination in Spring Orchid ( Cymbidium goeringii). Genes (Basel) 2023; 14:1610. [PMID: 37628661 PMCID: PMC10454716 DOI: 10.3390/genes14081610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Cymbidium goeringii Reichb. fil., locally known as the spring orchid in the Republic of Korea, is one of the most important and popular horticultural species in the family Orchidaceae. C. goeringii cultivars originated from plants with rare phenotypes in wild mountains where pine trees commonly grow. This study aimed to determine the cultivar-specific combined genotypes (CGs) of short sequence repeats (SSRs) by analyzing multiple samples per cultivar of C. goeringii. In this study, we collected more than 4000 samples from 67 cultivars and determined the genotypes of 12 SSRs. Based on the most frequent combined genotypes (CG1s), the average observed allele number and combined matching probability were 11.8 per marker and 3.118 × 10-11, respectively. Frequencies of the CG1 in 50 cultivars (n ≥ 10) ranged from 40.9% to 100.0%, with an average of 70.1%. Assuming that individuals with the CG1 are genuine in the corresponding cultivars, approximately 30% of C. goeringii on the farms and markets may be not genuine. The dendrogram of the phylogenetic tree and principal coordinate analysis largely divided the cultivars into three groups according to their countries of origin; however, the genetic distances were not great among the cultivars. In conclusion, this dataset of C. goeringii cultivar-specific SSR profiles could be used for ecogenetic studies and forensic authentication. This study suggests that genetic authentication should be introduced for the sale of expensive C. goeringii cultivars. We believe that this study will help establish a genetic method for the forensic authentication of C. goeringii cultivars.
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Affiliation(s)
- Da Eun Nam
- Department of Biological Sciences and BK21 Team for Field-Oriented BioCore Human Resources Development, Kongju National University, 56 Gongjudaehak-ro, Gongju 32588, Republic of Korea
| | - Min Ju Cha
- Department of Biological Sciences and BK21 Team for Field-Oriented BioCore Human Resources Development, Kongju National University, 56 Gongjudaehak-ro, Gongju 32588, Republic of Korea
| | - Yae Dam Kim
- Department of Biological Sciences and BK21 Team for Field-Oriented BioCore Human Resources Development, Kongju National University, 56 Gongjudaehak-ro, Gongju 32588, Republic of Korea
| | - Manisha Awasthi
- Department of Biological Sciences and BK21 Team for Field-Oriented BioCore Human Resources Development, Kongju National University, 56 Gongjudaehak-ro, Gongju 32588, Republic of Korea
| | - Yuno Do
- Department of Biological Sciences and BK21 Team for Field-Oriented BioCore Human Resources Development, Kongju National University, 56 Gongjudaehak-ro, Gongju 32588, Republic of Korea
| | - Sam-Geun Kong
- Department of Biological Sciences and BK21 Team for Field-Oriented BioCore Human Resources Development, Kongju National University, 56 Gongjudaehak-ro, Gongju 32588, Republic of Korea
| | - Ki Wha Chung
- Department of Biological Sciences and BK21 Team for Field-Oriented BioCore Human Resources Development, Kongju National University, 56 Gongjudaehak-ro, Gongju 32588, Republic of Korea
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Kim YK, Jo S, Cheon SH, Joo MJ, Hong JR, Kwak M, Kim KJ. Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences. FRONTIERS IN PLANT SCIENCE 2020; 11:22. [PMID: 32153600 PMCID: PMC7047749 DOI: 10.3389/fpls.2020.00022] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/10/2020] [Indexed: 05/08/2023]
Abstract
In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Forty-two of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera (Amitostigma, Bulbophyllum, Dactylorhiza, Dipodium, Galearis, Gymnadenia, Hetaeria, Oreorchis, and Sedirea)-are new in this study. All orchid plastomes, except Aphyllorchis montana, Epipogium aphyllum, and Gastrodia elata, have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the A. montana and G. elata plastomes. The SSC is lost in the E. aphyllum plastome. The smallest plastome size was 19,047 bp, in E. roseum, and the largest plastome size was 178,131 bp, in Cypripedium formosanum. The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of rpl (14, 16, and 36), seven subunits of rps (2, 3, 4, 7, 8, 11, and 14), three subunits of rrn (5, 16, and 23), trnC-GCA, and clpP genes. Three stages of gene loss were observed among the orchid plastomes. The first was ndh gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes (atp, pet, psa, and psb) and rpo gene subunits, which are restricted to Aphyllorchis, Hetaeria, Hexalectris, and some species of Corallorhiza and Neottia. The third stage was gene loss related to prokaryotic gene expression (rpl, rps, trn, and others), which was observed in Epipogium, Gastrodia, Lecanorchis, and Rhizanthella. In addition, an intermediate stage between the second and third stage was observed in Cyrtosia (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in rpl16, rps16, and clpP(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of 124 orchid species confirmed the relationship of {Apostasioideae [Vanilloideae (Cypripedioideae (Orchidoideae, Epidendroideae))]} at the subfamily level and the phylogenetic relationships of 17 tribes were also established. Molecular clock analysis based on the whole plastome sequences suggested that Orchidaceae diverged from its sister family 99.2 mya, and the estimated divergence times of five subfamilies are as follows: Apostasioideae (79.91 mya), Vanilloideae (69.84 mya), Cypripedioideae (64.97 mya), Orchidoideae (59.16 mya), and Epidendroideae (59.16 mya). We also released the first nuclear ribosomal (nr) DNA unit (18S-ITS1-5.8S-ITS2-28S-NTS-ETS) sequences for the 42 species of Orchidaceae. Finally, the phylogenetic tree based on the nrDNA unit sequences is compared to the tree based on the 42 identical plastome sequences, and the differences between the two datasets are discussed in this paper.
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Affiliation(s)
- Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Sangjin Jo
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Min-Jung Joo
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Ja-Ram Hong
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Myounghai Kwak
- Department of Plant Resources, National Institute of Biological Resources, Incheon, South Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
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Wang H, Park SY, Song SH, San ML, Kim YC, Ham TH, Kim DY, Kim TS, Lee J, Kwon SW. Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii. 3 Biotech 2020; 10:29. [PMID: 32015946 PMCID: PMC6944737 DOI: 10.1007/s13205-019-2020-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/18/2019] [Indexed: 01/16/2023] Open
Abstract
The complete chloroplast genome sequence of Korean Cymbidium goeringii acc. smg222 was analyzed. Based on a comparison with Chinese C. goeringii, losses of nine ndh subunits (ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhH, ndhJ, and ndhK), three protein-coding genes (ycf 1-like, ycf 15, and ycf 68), six transfer RNAs, and one conserved open reading frame (orf 42). In addition, 219 InDels (insertion or deletion) and 171 simple sequence repeats were observed. Twenty-Five of which InDel markers have been evaluated, that useful for distinguishing Korean and Chinese Cymbidium associations based on the polymorphisms of chloroplast genomes between Korean Cymbidium goeringii acc. smg222 and Chinese C. goeringii and evaluation of genetic diversity. Finally, the phylogenetic relationships of the 39 Korean and 22 Chinese species was constructed based on the five InDel markers of them and obtained high support, indicating that our data may be useful in resolving relationships in this genus. The information about chloroplast DNA structure and gene variants of C. goeringii acc. smg222 chloroplast genome will provide sufficient phylogenetic information for resolving evolutionary relationships. The molecular markers developed in here will contribute to further research of Cymbidium species and conservation of endemic Cymbidium species.
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Affiliation(s)
- Heng Wang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - So-Yeon Park
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Su-Hyang Song
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Mar-Lar San
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Yong-Chul Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Tae-Ho Ham
- Department of Applied Bioscience, Konkuk University, Seoul, 05029 Republic of Korea
- Department of Agricultural Science, Korea National Open University, Seoul, 03087 Republic of Korea
| | - Dong-Yong Kim
- Saemangeum BioCenter Co, 1044 Heomi-ro, Daeya-myeon, Gunsan, 54061 Republic of Korea
| | - Tae-Sung Kim
- Department of Agricultural Science, Korea National Open University, Seoul, 03087 Republic of Korea
| | - Joohyun Lee
- Department of Applied Bioscience, Konkuk University, Seoul, 05029 Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
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Liu W, Kong H, Zhou J, Fritsch PW, Hao G, Gong W. Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae. Int J Mol Sci 2018; 19:E1286. [PMID: 29693617 PMCID: PMC5983592 DOI: 10.3390/ijms19051286] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 11/17/2022] Open
Abstract
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.
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Affiliation(s)
- Wanzhen Liu
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Juan Zhou
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107, USA.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
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