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Fu N, Xu Y, Jin L, Xiao TW, Song F, Yan HF, Chen YS, Ge XJ. Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer. BMC PLANT BIOLOGY 2024; 24:445. [PMID: 38778277 PMCID: PMC11112886 DOI: 10.1186/s12870-024-05073-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer. RESULT Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer. CONCLUSION Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.
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Affiliation(s)
- Ning Fu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Xu
- Conghua Middle School, Guangzhou, 510920, China
| | - Lu Jin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - You-Sheng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Yunrui X, Rui S, Xing Y, Zhe Z, Keqin Z, Nanyi Z. Comparative transcriptomic analysis reveals differences in MADS-box genes of different hypericum in Changbai Mountains. Ecol Evol 2023; 13:e10196. [PMID: 37325719 PMCID: PMC10261973 DOI: 10.1002/ece3.10196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/13/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023] Open
Abstract
To explore the differences between the hypericum in the Changbai Mountains, we carried out a transcriptome analysis of two common hypericums in the area, which was Hypericum attenuatum Choisy and Hypericum longistylum Oliv. We screened the MADS-box genes to analyze divergence time and evolutionary selection expression, and determine their expression levels. The results showed that we detected 9287 differentially expressed genes in the two species, of which shared 6044 genes by the two species. Analysis of the selected MADS genes revealed that the species was in an environment adapted to its natural evolution. The divergence time estimation showed that the segregation of these genes in the two species was related to the changes of external environment and genome replication events. The results of relative expression showed that the later flowering period of Hypericum attenuatum Choisy was related to the higher expression of the SVP (SHORT VEGETATIVE PHASE) and the AGL12 (AGAMOUS LIKE 12), while the lower expression of the FUL (FRUITFULL).
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Affiliation(s)
- Xia Yunrui
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Song Rui
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Yang Xing
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Zhao Zhe
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Zhang Keqin
- Jilin Agricultural Science and Technology UniversityJilinJilin ProvinceChina
| | - Zhang Nanyi
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
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Zhang L, Huang YW, Huang JL, Ya JD, Zhe MQ, Zeng CX, Zhang ZR, Zhang SB, Li DZ, Li HT, Yang JB. DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes. Mol Ecol Resour 2023; 23:424-439. [PMID: 36219539 DOI: 10.1111/1755-0998.13719] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 01/04/2023]
Abstract
Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopted and the identification rate increased to 72%. It appears that nuclear genome data have a vital role in species identification and are expected to be used as next-generation nuclear barcodes.
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Affiliation(s)
- Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yi-Wei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meng-Qing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Ren W, Liu C, Yan S, Jiang Z, Wang T, Wang Z, Zhang M, Liu M, Sun J, Gao J, Ma W. Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus. Front Genet 2022; 13:849182. [PMID: 35910210 PMCID: PMC9329572 DOI: 10.3389/fgene.2022.849182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity.
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Affiliation(s)
- Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Chi Liu
- Faculty of Electrical Engineering and Information Technology, Technical University of Chemnitz, Chemnitz, Germany
| | - Song Yan
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhehui Jiang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Tianhao Wang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Zhen Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Meiqi Zhang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Meiqi Liu
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jiaying Sun
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jinhui Gao
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
- *Correspondence: Jinhui Gao, ; Wei Ma,
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, China
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang, China
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, China
- *Correspondence: Jinhui Gao, ; Wei Ma,
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