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Han F, Bi C, Zhao Y, Gao M, Wang Y, Chen Y. Unraveling the complex evolutionary features of the Cinnamomum camphora mitochondrial genome. PLANT CELL REPORTS 2024; 43:183. [PMID: 38922445 DOI: 10.1007/s00299-024-03256-1] [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: 04/07/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024]
Abstract
KEY MESSAGE We reported the mitochondrial genome of Cinnamomum camphora for the first time, revealing frequent rearrangement events in the non-coding regions of Magnoliids mitochondrial genomes. As one of the representative species in the Lauraceae family of Magnoliids, Cinnamomum camphora holds significant economic and ecological value. In this study, the mitochondrial genome (mitogenome) of C. camphora was complete assembled and annotated using PacBio HiFi sequencing. The C. camphora mitogenome is characterized by a branch structure, spans 900,894 bp, and contains 43 protein-coding genes (PCGs), 24 tRNAs, and 3 rRNAs. Most of these PCGs are under purifying selection, with only two (ccmFc and rps7) exhibiting signs of positive selection. The C. camphora mitogenome contains numerous repetitive sequences and intracellular gene transfers, with a total of 36 mitochondrial plastid DNAs, amounting to a combined length of 23,816 bp. Comparative analysis revealed that the non-coding regions of Magnoliids mitogenomes have undergone frequent rearrangements during evolution, but the coding sequences remain highly conserved (more than 98% similarity for protein-coding sequences). Furthermore, a maximum-likelihood phylogenetic tree was reconstructed based on 25 PCGs from 23 plant mitogenomes. The analysis supports the closest relationship between C. camphora and C. chekiangense, consistent with the APG IV classification system. This study elucidates the unique evolutionary features of the C. camphora mitogenome, which will provide valuable insights into the study of genetics and evolution of the family Lauraceae.
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Affiliation(s)
- Fuchuan Han
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Changwei Bi
- State Key Laboratory of Tree Genetics and Breeding, Co-innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Yunxiao Zhao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Ming Gao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Yangdong Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Yicun Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China.
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Huang XZ, Gong SD, Shang XH, Gao M, Zhao BY, Xiao L, Shi PL, Zeng WD, Cao S, Wu ZD, Song JM, Chen LL, Yan HB. High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus. DNA Res 2024; 31:dsae017. [PMID: 38809753 PMCID: PMC11149379 DOI: 10.1093/dnares/dsae017] [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: 06/26/2023] [Revised: 04/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024] Open
Abstract
Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.
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Affiliation(s)
- Xuan-Zhao Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Shao-Da Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Xiao-hong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Ping-li Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Wen-dan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Zheng-dan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Hua-bing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
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Ling Q, Zhang B, Wang Y, Xiao Z, Hou J, Liu Q, Zhang J, Xiao C, Jin Z, Liu Y. Identification of key genes controlling monoterpene biosynthesis of Citral-type Cinnamomum bodinieri Levl. Based on transcriptome and metabolite profiling. BMC Genomics 2024; 25:540. [PMID: 38822238 PMCID: PMC11141066 DOI: 10.1186/s12864-024-10419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 05/15/2024] [Indexed: 06/02/2024] Open
Abstract
The citral-type is the most common chemotype in Cinnamomum bodinieri Levl (C. bodinieri), which has been widely used in the daily necessities, cosmetics, biomedicine, and aromatic areas due to their high citral content. Despite of this economic prospect, the possible gene-regulatory roles of citral biosynthesis in the same geographic environment remains unknown. In this study, the essential oils (EOs) of three citral type (B1, B2, B3) and one non-citral type (B0) varieties of C. bodinieri were identified by GC-MS after hydrodistillation extraction in July. 43 components more than 0.10% were identified in the EOs, mainly composed of monoterpenes (75.8-91.84%), and high content citral (80.63-86.33%) were identified in citral-type. Combined transcriptome and metabolite profiling analysis, plant-pathogen interaction(ko04626), MAPK signaling pathway-plant(ko04016), starch and sucrose metabolism(ko00500), plant hormone signal transduction(ko04075), terpenoid backbone biosynthesis (ko00900) and monoterpenoid biosynthesis (ko00902) pathways were enriched significantly. The gene expression of differential genes were linked to the monoterpene content, and the geraniol synthase (CbGES), alcohol dehydrogenase (CbADH), geraniol 8-hydroxylase-like (CbCYP76B6-like) and 8-hydroxygeraniol dehydrogenase (Cb10HGO) were upregulated in the citral-type, indicating that they were associated with high content of geraniol and citral. The activities of CbGES and CbADH in citral type were higher than in non-citral type, which was corroborated by enzyme-linked immunosorbent assay (ELISA). This study on the accumulation mechanism of citral provides a theoretical basis for the development of essential oil of C. bodinieri.
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Affiliation(s)
- Qingyan Ling
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
- College of Forestry, Jiangxi Agricultural University, Jiangxi Key Laboratory of Subtropical Forest Resources Cultivation, Nanchang, China
| | - Beihong Zhang
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
| | - Yanbo Wang
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
| | - Zufei Xiao
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
| | - Jiexi Hou
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
| | - Qingqing Liu
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
| | - Jie Zhang
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
| | - Changlong Xiao
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China
| | - Zhinong Jin
- School of Soil and Water Conservation, Nanchang Institute of Technology, Jiangxi Provincial Engineering Research Center For Seed-Breeding and Utilization of Camphor Trees, Nanchang, China.
| | - Yuanqiu Liu
- College of Forestry, Jiangxi Agricultural University, Jiangxi Key Laboratory of Subtropical Forest Resources Cultivation, Nanchang, China.
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Zhao Y, Chen Y, Gao M, Wang Y. Alcohol dehydrogenases regulated by a MYB44 transcription factor underlie Lauraceae citral biosynthesis. PLANT PHYSIOLOGY 2024; 194:1674-1691. [PMID: 37831423 DOI: 10.1093/plphys/kiad553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023]
Abstract
Lineage-specific terpenoids have arisen throughout the evolution of land plants and are believed to play a role in interactions between plants and the environment. Species-specific gene clusters in plants have provided insight on the evolution of secondary metabolism. Lauraceae is an ecologically important plant family whose members are also of considerable economic value given their monoterpene contents. However, the gene cluster responsible for the biosynthesis of monoterpenes remains yet to be elucidated. Here, a Lauraceae-specific citral biosynthetic gene cluster (CGC) was identified and investigated using a multifaceted approach that combined phylogenetic, collinearity, and biochemical analyses. The CGC comprises MYB44 as a regulator and 2 alcohol dehydrogenases (ADHs) as modifying enzymes, which derived from species-specific tandem and proximal duplication events. Activity and substrate divergence of the ADHs has resulted in the fruit of mountain pepper (Litsea cubeba), a core Lauraceae species, consisting of more than 80% citral. In addition, MYB44 negatively regulates citral biosynthesis by directly binding to the promoters of the ADH-encoding genes. The aggregation of citral biosynthetic pathways suggests that they may form the basis of important characteristics that enhance adaptability. The findings of this study provide insights into the evolution of and the regulatory mechanisms involved in plant terpene biosynthesis.
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Affiliation(s)
- Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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Li D, Lin HY, Wang X, Bi B, Gao Y, Shao L, Zhang R, Liang Y, Xia Y, Zhao YP, Zhou X, Zhang L. Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes. BMC Biol 2023; 21:192. [PMID: 37697363 PMCID: PMC10496300 DOI: 10.1186/s12915-023-01692-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/25/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Lauraceae is well known for its significant phylogenetic position as well as important economic and ornamental value; however, most evergreen species in Lauraceae are restricted to tropical regions. In contrast, camphor tree (Cinnamomum camphora) is the most dominant evergreen broadleaved tree in subtropical urban landscapes. RESULTS Here, we present a high-quality reference genome of C. camphora and conduct comparative genomics between C. camphora and C. kanehirae. Our findings demonstrated the significance of key genes in circadian rhythms and phenylpropanoid metabolism in enhancing cold response, and terpene synthases (TPSs) improved defence response with tandem duplication and gene cluster formation in C. camphora. Additionally, the first comprehensive catalogue of C. camphora based on whole-genome resequencing of 75 accessions was constructed, which confirmed the crucial roles of the above pathways and revealed candidate genes under selection in more popular C. camphora, and indicated that enhancing environmental adaptation is the primary force driving C. camphora breeding and dominance. CONCLUSIONS These results decipher the dominance of C. camphora in subtropical urban landscapes and provide abundant genomic resources for enlarging the application scopes of evergreen broadleaved trees.
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Affiliation(s)
- Danqing Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Han-Yang Lin
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Xiuyun Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bo Bi
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yuan Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lingmei Shao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Runlong Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuwei Liang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun-Peng Zhao
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Sanya, China.
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Shen Z, Ding X, Cheng J, Wu F, Yin H, Wang M. Phylogenetic studies of magnoliids: Advances and perspectives. FRONTIERS IN PLANT SCIENCE 2023; 13:1100302. [PMID: 36726671 PMCID: PMC9885158 DOI: 10.3389/fpls.2022.1100302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Magnoliids are the largest flowering plant clades outside of the eudicots and monocots, which are distributed worldwide and have high economic, ornamental and ecological values. Eudicots, monocots and magnoliids are the three major clades of Mesangiospermae, and their phylogenetic relationship is one of the most interesting issues. In recent years, with the continuous accumulation of genomic information, the evolutionary status of magnoliids has become a hot spot in plant phylogenetic research. Although great efforts have been made to study the evolution of magnoliids using molecular data from several representative species such as nuclear genome, plastid genome, mitochondrial genome, and transcriptome, the results of current studies on the phylogenetic status of magnoliids are inconsistent. Here, we systematically describe the current understanding of the molecular research on magnoliid phylogeny and review the differences in the evolutionary state of magnoliids. Understanding the research approaches and limitations of magnoliid phylogeny can guide research strategies to further improve the study of the phylogenetic evolution of magnoliids.
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Affiliation(s)
- Zhiguo Shen
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Xin Ding
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Jianming Cheng
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Fangfang Wu
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Minyan Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
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Genome-Scale Identification, Classification, and Expression Profiling of MYB Transcription Factor Genes in Cinnamomum camphora. Int J Mol Sci 2022; 23:ijms232214279. [PMID: 36430756 PMCID: PMC9693371 DOI: 10.3390/ijms232214279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
The camphor tree (Cinnamomum camphora (L.) Presl.) is the representative species of subtropical evergreen broadleaved forests in eastern Asia and an important raw material for essential oil production worldwide. Although MYBs have been comprehensively characterized and their functions have been partially resolved in many plants, it has not been explored in C. camphora. In this study, 121 CcMYBs were identified on 12 chromosomes in the whole genome of C. camphora and found that CcMYBs were mainly expanded by segmental duplication. They were divided into 28 subgroups based on phylogenetic analysis and gene structural characteristics. In the promoter regions, numerous cis-acting elements were related to biological processes. Analysis of RNA sequencing data from seven tissues showed that CcMYBs exhibited different expression profiles, suggesting that they have various roles in camphor tree development. In addition, combined with the correlation analysis of structural genes in the flavonoid synthesis pathway, we identified CcMYBs from three subgroups that might be related to the flavonoid biosynthesis pathway. This study systematically analyzed CcMYBs in C. camphora, which will set the stage for subsequent research on the functions of CcMYBs during their lifetime and provide valuable insights for the genetic improvement of camphor trees.
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