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Yan Y, da Fonseca RR, Rahbek C, Borregaard MK, Davis CC. A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia. Mol Phylogenet Evol 2024; 196:108089. [PMID: 38679302 DOI: 10.1016/j.ympev.2024.108089] [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: 04/23/2023] [Revised: 03/08/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.
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Affiliation(s)
- Yujing Yan
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA.
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Life Sciences, Imperial College London, Silkwood Park campus, Ascot SL5 7PY, UK; Danish Institute for Advanced Study, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michael K Borregaard
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA
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Zhang F, Feng LY, Lin PF, Jia JJ, Gao LZ. Chromosome-scale genome assembly of oil-tea tree Camellia crapnelliana. Sci Data 2024; 11:599. [PMID: 38849406 PMCID: PMC11161624 DOI: 10.1038/s41597-024-03459-x] [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: 02/13/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024] Open
Abstract
Camellia crapnelliana Tutch., belonging to the Theaceae family, is an excellent landscape tree species with high ornamental values. It is particularly an important woody oil-bearing plant species with high ecological, economic, and medicinal values. Here, we first report the chromosome-scale reference genome of C. crapnelliana with integrated technologies of SMRT, Hi-C and Illumina sequencing platforms. The genome assembly had a total length of ~2.94 Gb with contig N50 of ~67.5 Mb, and ~96.34% of contigs were assigned to 15 chromosomes. In total, we predicted 37,390 protein-coding genes, ~99.00% of which could be functionally annotated. The chromosome-scale genome of C. crapnelliana will become valuable resources for understanding the genetic basis of the fatty acid biosynthesis, and greatly facilitate the exploration and conservation of C. crapnelliana.
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Affiliation(s)
- Fen Zhang
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education; Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou, 570228, China
| | - Li-Ying Feng
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education; Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou, 570228, China
| | - Pei-Fan Lin
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education; Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou, 570228, China
| | - Ju-Jin Jia
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education; Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou, 570228, China
| | - Li-Zhi Gao
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education; Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou, 570228, China.
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3
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Hu Z, Fan Z, Li S, Wang M, Huang M, Ma X, Liu W, Wang Y, Yu Y, Li Y, Sun Y, Li X, Li J, Yin H. Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia. BMC Biol 2024; 22:50. [PMID: 38414012 PMCID: PMC10900828 DOI: 10.1186/s12915-024-01851-y] [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: 07/25/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The formation and domestication of ornamental traits are influenced by various aspects, such as the recognition of esthetic values and cultural traditions. Camellia japonica is widely appreciated and domesticated around the world mainly due to its rich variations in ornamental traits. Ornamental camellias have a diverse range of resources, including different bud variations from Camellia spp. as well as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking. RESULTS Here, we report the chromosomal-level reference genome of C. japonica through combining multiple DNA-sequencing technologies and obtain a high-density genetic linkage map of 4255 markers by sequencing 98 interspecific F1 hybrids between C. japonica and C. chekiangoleosa. We identify two whole-genome duplication events in C. japonica: one is a shared ancient γ event, and the other is revealed to be specific to genus Camellia. Based on the micro-collinearity analysis, we find large-scale segmental duplication of chromosome 8, resulting to two copies of the AGAMOUS loci, which may play a key role in the domestication of floral shapes. To explore the regulatory mechanisms of seasonal flowering, we have analyzed year-round gene expression patterns of C. japonica and C. azalea-a sister plant of continuous flowering that has been widely used for cross breeding. Through comparative analyses of gene co-expression networks and annual gene expression patterns, we show that annual expression rhythms of some important regulators of seasonal growth and development, including GIGANTEA and CONSTANS of the photoperiod pathway, have been disrupted in C. azalea. Furthermore, we reveal that the distinctive expression patterns of FLOWERING LOCUS T can be correlated with the seasonal activities of flowering and flushing. We demonstrate that the regulatory module involved in GIGANTEA, CONSTANS, and FLOWERING LOCUS T is central to achieve seasonality. CONCLUSIONS Through the genomic and comparative genomics characterizations of ornamental Camellia spp., we propose that duplication of chromosomal segments as well as the establishment of gene expression patterns has played a key role in the formation of ornamental traits (e.g., flower shape, flowering time). This work provides a valuable genomic platform for understanding the molecular basis of ornamental traits.
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Affiliation(s)
- Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Zhengqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Sijia Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Minyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Mingchuan Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Weixin Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Yifan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yaxuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yingkun Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xinlei Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
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Liu D, Zhang Z, Hao Y, Li M, Yu H, Zhang X, Mi H, Cheng L, Zhao Y. Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae. BMC Genomics 2024; 25:114. [PMID: 38273225 PMCID: PMC10811901 DOI: 10.1186/s12864-024-10016-8] [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: 09/02/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history. RESULT We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae. CONCLUSIONS We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.
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Affiliation(s)
- Daliang Liu
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
| | - Zhihan Zhang
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
- College of Engineering and Technology, Northeast Forestry University, Harbin, 150040, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Present address: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xingruo Zhang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yiyong Zhao
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China.
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China.
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5
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Gao Q, Tong W, Li F, Wang Y, Wu Q, Wan X, Xia E. TPIA2: an updated tea plant information archive for Camellia genomics. Nucleic Acids Res 2024; 52:D1661-D1667. [PMID: 37650644 PMCID: PMC10767884 DOI: 10.1093/nar/gkad701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
The genus Camellia consists of about 200 species, which include many economically important species widely used for making tea, ornamental flowers and edible oil. Here, we present an updated tea plant information archive for Camellia genomics (TPIA2; http://tpia.teaplants.cn) by integrating more novel large-scale genomic, transcriptomic, metabolic and genetic variation datasets as well as a variety of useful tools. Specifically, TPIA2 hosts all currently available and well assembled 10 Camellia genomes and their comprehensive annotations from three major sections of Camellia. A collection of 15 million SNPs and 950 950 small indels from large-scale genome resequencing of 350 diverse tea accessions were newly incorporated, followed by the implementation of a novel 'Variation' module to facilitate data retrieval and analysis of the functionally annotated variome. Moreover, 116 Camellia transcriptomes were newly assembled and added, leading to a significant extension of expression profiles of Camellia genes to 13 developmental stages and eight abiotic/biotic treatments. An updated 'Expression' function has also been implemented to provide a comprehensive gene expression atlas for Camellia. Two novel analytic tools (e.g. Gene ID Convert and Population Genetic Analysis) were specifically designed to facilitate the data exchange and population genomics in Camellia. Collectively, TPIA2 provides diverse updated valuable genomic resources and powerful functions, and will continue to be an important gateway for functional genomics and population genetic studies in Camellia.
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Affiliation(s)
- Qijuan Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- School of Computer and Artificial Intelligence, Hefei Normal University, Hefei 230061, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- School of Science, Anhui Agricultural University, Hefei 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
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Wang Y, Li J, Guo P, Liu Q, Ren S, Juan L, He J, Tan X, Yan J. Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase gene increased plant height and promoted secondary cell walls deposition in Arabidopsis. PLANTA 2023; 258:65. [PMID: 37566145 DOI: 10.1007/s00425-023-04222-z] [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: 12/13/2022] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
MAIN CONCLUSION Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase 1 caused a taller phenotype, promoted secondary cell wall deposition, leaf enlargement, and early flowering, and reduced chlorophyll and anthocyanin accumulation and seed enlargement phenotype in Arabidopsis. Plant height and secondary cell wall (SCW) deposition are important plant traits. Gibberellins (GAs) play important roles in regulating plant height and SCWs deposition. Gibberellin 20-oxidase (GA20ox) is an important enzyme involved in GA biosynthesis. In the present study, we identified a GA synthesis gene in Camellia oleifera. The total length of the CoGA20ox1 gene sequence was 1146 bp, encoding 381 amino acids. Transgenic plants with CoGA20ox1 had a taller phenotype; a seed enlargement phenotype; promoted SCWs deposition, leaf enlargement, and early flowering; and reduced chlorophyll and anthocyanin accumulation. Genetic analysis showed that the mutant ga20ox1-3 Arabidopsis partially rescued the phenotype of CoGA20ox1 overexpression plants. The results showed that CoGA20ox1 participates in the growth and development of C. oleifera. The morphological changes in CoGA20ox1 overexpressed plants provide a theoretical basis for further exploration of GA biosynthesis and analysis of the molecular mechanism in C. oleifera.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Jian'an Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
| | - Purui Guo
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Qian Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Shuangshuang Ren
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Lemei Juan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Jiacheng He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
| | - Jindong Yan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, Changsha, 410004, China.
- Yuelu Mountain Laboratory Non-Wood Forests Variety Innovation Center, Changsha, 410004, China.
- Key Laboratory of Breeding and Cultivation of Economic Forest, State Forestry and Grassland Administration, Changsha, 410004, China.
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7
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Lin Z, Huang LJ, Yu P, Chen J, Du S, Qin G, Zhang L, Li N, Yuan D. Development of a protoplast isolation system for functional gene expression and characterization using petals of Camellia Oleifera. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107885. [PMID: 37437343 DOI: 10.1016/j.plaphy.2023.107885] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/17/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
Protoplasts preparation and purification have been frequently used in plant genetics and breeding studies, whereas application of protoplasts in woody plants is still in its infancy. Although transient gene expression using purified protoplasts is well-documented and widely used in model plants and agriculture crops, no instance of either stable transformation or transient gene expression in the woody plant Camellia Oleifera has as of yet been reported. Here, we developed a protoplast preparation and purification method using C. oleifera petals by optimizing osmotic condition with D-mannitol and polysaccharide-degrading enzyme concentrations for petal cell wall digestion, to reach a high efficiency of protoplast productivity and viability. The achieved protoplasts yield was approximately 1.42 × 107 cells per gram of petal material and the viability of protoplasts was up to 89%. In addition, we explored influencing factors of protoplast transformation, including concentrations of PEG4000 and plasmid DNA. The transformation efficiency of 81% could be reached under the optimized condition. This protoplast isolation and transient expression system were deployed to further identify the functional regulation of C. oleifera related genes and the subcellular distribution of their encoded products. In summary, the protoplast isolation and transient expression system we established using oil-tea tree petals is an efficient, versatile and time-saving system, being suitable for gene function characterization and molecular mechanism analysis.
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Affiliation(s)
- Zeng Lin
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Li-Jun Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha, China.
| | - Peiyao Yu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Jiali Chen
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Shenxiu Du
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, China
| | - Guannan Qin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Ning Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha, China.
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Chen J, Han X, Liu L, Yang B, Zhuo R, Yao X. Genome-Wide Detection of SPX Family and Profiling of CoSPX-MFS3 in Regulating Low-Phosphate Stress in Tea-Oil Camellia. Int J Mol Sci 2023; 24:11552. [PMID: 37511309 PMCID: PMC10380294 DOI: 10.3390/ijms241411552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Camellia oleifera a member of the family Theaceae, is a phosphorus (P) tolerator native to southern China. The SPX gene family critically regulates plant growth and development and maintains phosphate (Pi) homeostasis. However, the involvement of SPX genes in Pi signaling in Tea-Oil Camellia remains unknown. In this work, 20 SPX genes were identified and categorized into four subgroups. Conserved domains, motifs, gene structure, chromosomal location and gene duplication events were also investigated in the SPX gene family. Defense and stress responsiveness cis-elements were identified in the SPX gene promoters, which participated in low-Pi stress responses. Based on transcriptome data and qRT-PCR results, nine CoSPX genes had similar expression patterns and eight genes (except CoPHO1H3) were up-regulated at 30 days after exposure to low-Pi stress. CoSPX-MFS3 was selected as a key candidate gene by WGCNA analysis. CoSPX-MFS3 was a tonoplast protein. Overexpression of CoSPX-MFS3 in Arabidopsis promoted the accumulation of total P content and decreased the anthocyanin content. Overexpression of CoSPX-MFS3 could enhance low-Pi tolerance by increased biomass and organic acid contents in transgenic Arabidopsis lines. Furthermore, the expression patterns of seven phosphate starvation genes were higher in transgenic Arabidopsis than those in the wild type. These results highlight novel physiological roles of the SPX family genes in C. oleifera under low-Pi stress, and lays the foundation for a deeper knowledge of the response mechanism of C. oleifera to low-Pi stress.
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Affiliation(s)
- Juanjuan Chen
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Forestry Faculty, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaojiao Han
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Linxiu Liu
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Bingbing Yang
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Renying Zhuo
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiaohua Yao
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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Zhang W, Xiong T, Ye F, Chen JH, Chen YR, Cao JJ, Feng ZG, Zhang ZB. The lineage-specific evolution of the oleosin family in Theaceae. Gene 2023; 868:147385. [PMID: 36958508 DOI: 10.1016/j.gene.2023.147385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/04/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Oleosins play essential roles in stabilization of lipid droplets (LDs) and seed oil production. However, evolution of this gene family has not been reported in Theaceae, a large plant family that contains many important tea and oil tea species. In this study, a total of 65 oleosin genes were identified in nine genome-sequenced Theaceae species. Among these genomes, the gene number of oleosin showed significant difference, with Camellia sinensis var. sinensis cv. Shuchazao and Camellia lanceoleosa displayed more oleosin numbers than other species. Phylogenetic analyses revealed that Theaceae oleosin genes were classified into three clades (U, SL, SH) respectively. Proteins within the same clade had similar gene structure and motif composition. Segmental duplication was the primary driving force for the evolution of oleosin genes in Shuchazao (SCZ), Huangdan (HD), C.lanceoleosa (Cla), and wild tea (DASZ). Synteny analysis showed that most oleosin genes displayed inter-species synteny among tea and oil tea species. Expression analysis demonstrated that oleosin genes were specifically expressed in seed and kernel of Huangdan (HD) and C.lanceoleosa. Moreover, expression divergence was observed in paralogous pairs and ∼1-2 oleosin genes in each clade have become activate. This study leads to a comprehensive understanding of evolution of oleosin family in Theaceae, and provides a rich resource to further address the functions of oleosin in tea and oil tea species.
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Affiliation(s)
- Wei Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China; Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Fan Ye
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jia-Hui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jia-Jia Cao
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Zhi-Guo Feng
- School of Science, Qiongtai Normal University, Hainan, China.
| | - Zai-Bao Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China; Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China.
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Ye C, He Z, Peng J, Wang R, Wang X, Fu M, Zhang Y, Wang A, Liu Z, Jia G, Chen Y, Tian B. Genomic and genetic advances of oiltea-camellia ( Camellia oleifera). FRONTIERS IN PLANT SCIENCE 2023; 14:1101766. [PMID: 37077639 PMCID: PMC10106683 DOI: 10.3389/fpls.2023.1101766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Oiltea-camellia (C. oleifera) is a widely cultivated woody oil crop in Southern China and Southeast Asia. The genome of oiltea-camellia was very complex and not well explored. Recently, genomes of three oiltea-camellia species were sequenced and assembled, multi-omic studies of oiltea-camellia were carried out and provided a better understanding of this important woody oil crop. In this review, we summarized the recent assembly of the reference genomes of oiltea-camellia, genes related to economic traits (flowering, photosynthesis, yield and oil component), disease resistance (anthracnose) and environmental stress tolerances (drought, cold, heat and nutrient deficiency). We also discussed future directions of integrating multiple omics for evaluating genetic resources and mining key genes of important traits, and the application of new molecular breeding and gene editing technologies to accelerate the breeding process of oiltea-camellia.
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Affiliation(s)
- Changrong Ye
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Zhilong He
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Jiayu Peng
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Rui Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Xiangnan Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Mengjiao Fu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Ying Zhang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Ai Wang
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Zhixian Liu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Gaofeng Jia
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Yongzhong Chen
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Bingchuan Tian
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
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Chang Y, Gong W, Xu J, Gong H, Song Q, Xiao S, Yuan D. Integration of semi- in vivo assays and multi-omics data reveals the effect of galloylated catechins on self-pollen tube inhibition in Camellia oleifera. HORTICULTURE RESEARCH 2023; 10:uhac248. [PMID: 36643738 PMCID: PMC9832949 DOI: 10.1093/hr/uhac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/04/2022] [Indexed: 05/02/2023]
Abstract
Camellia oil extracted from the seeds of Camellia oleifera Abel. is a popular and high-quality edible oil, but its yield is limited by seed setting, which is mainly caused by self-incompatibility (SI). One of the obvious biological features of SI plants is the inhibition of self-pollen tubes; however, the underlying mechanism of this inhibition in C. oleifera is poorly understood. In this study, we constructed a semi-in vivo pollen tube growth test (SIV-PGT) system that can screen for substances that inhibit self-pollen tubes without interference from the genetic background. Combined with multi-omics analysis, the results revealed the important role of galloylated catechins in self-pollen tube inhibition, and a possible molecular regulatory network mediated by UDP-glycosyltransferase (UGT) and serine carboxypeptidase-like (SCPL) was proposed. In summary, galloylation of catechins and high levels of galloylated catechins are specifically involved in pollen tube inhibition under self-pollination rather than cross-pollination, which provides a new understanding of SI in C. oleifera. These results will contribute to sexual reproduction research on C. oleifera and provide theoretical support for improving Camellia oil yield in production.
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Affiliation(s)
- Yihong Chang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Wenfang Gong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Jinming Xu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Han Gong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Qiling Song
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Shixin Xiao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
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12
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Zhu Y, Liang D, Song Z, Tan Y, Guo X, Wang D. Genetic Diversity Analysis and Core Germplasm Collection Construction of Camellia oleifera Based on Fruit Phenotype and SSR Data. Genes (Basel) 2022; 13:genes13122351. [PMID: 36553618 PMCID: PMC9777545 DOI: 10.3390/genes13122351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Many Camellia oleifera germplasm resources were collected from Guizhou Province, but the fruit morphological variation and genetic diversity of C. oleifera germplasm resources remain unclear. The genetic diversity of C. oleifera germplasms resources in Guizhou was studied based on fruit traits and simple sequence repeat (SSR) molecular markers to build a core collection. This paper aims to provide a scientific basis for the collection, management, development, and utilization of C. oleifera resources in Guizhou province. The variation coefficients among and within varieties of seven fruit phenotypic traits of C. oleifera ranged from 11.79% to 61.76% and from 8.15% to 42.31%, respectively, showing rich phenotypic variation. Furthermore, 12 SSR markers were used to analyze the genetic diversity. These primers generated 214 polymorphic bands, and the average number was 17.833. The average number of effective alleles (Ne), Shannon's information index (I), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and major allele frequency (MAF) were 8.999, 2.301, 0.965, 0.50, 0.836, and 0.238, respectively. The results showed that 12 SSR markers had high polymorphism, and the genetic diversity of 167 C. oleifera germplasm resources was high. Based on SSR molecular marker information and fruit traits clustering, 167 C. oleifera germplasm resources were divided into three groups. When constructing core collections based on fruit traits and molecular marker information, the PowerCore-25 of core collections greatly preserves fruit traits and improves genetic diversity. This paper can provide a reference for the genetic diversity and fruit traits variation of C. camellia germplasm resources in Guizhou Province. It is significant for establishing a core collection, thus promoting germplasm innovation and the development of the oil tea industry in Guizhou.
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Affiliation(s)
- Yunzheng Zhu
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Deyang Liang
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Zejun Song
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Yi Tan
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Xiaolan Guo
- College of Life Sciences, Huizhou University, Huizhou 516007, China
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang 550025, China
- Correspondence:
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13
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Transcriptome Analysis Reveals Putative Induction of Floral Initiation by Old Leaves in Tea-Oil Tree (Camellia oleifera ‘changlin53’). Int J Mol Sci 2022; 23:ijms232113021. [PMID: 36361817 PMCID: PMC9655362 DOI: 10.3390/ijms232113021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Floral initiation is a major phase change in the spermatophyte, where developmental programs switch from vegetative growth to reproductive growth. It is a key phase of flowering in tea-oil trees that can affect flowering time and yield, but very little is known about the molecular mechanism of floral initiation in tea-oil trees. A 12-year-old Camellia oleifera (cultivar ‘changlin53’) was the source of experimental materials in the current study. Scanning electron microscopy was used to identify the key stage of floral initiation, and transcriptome analysis was used to reveal the transcriptional regulatory network in old leaves involved in floral initiation. We mined 5 DEGs related to energy and 55 DEGs related to plant hormone signal transduction, and we found floral initiation induction required a high level of energy metabolism, and the phytohormones signals in the old leaves regulate floral initiation, which occurred at stage I and II. Twenty-seven rhythm-related DEGs and 107 genes associated with flowering were also identified, and the circadian rhythm interacted with photoperiod pathways to induce floral initiation. Unigene0017292 (PSEUDO-RESPONSE REGULATOR), Unigene0046809 (LATE ELONGATED HYPOCOTYL), Unigene0009932 (GIGANTEA), Unigene0001842 (CONSTANS), and Unigene0084708 (FLOWER LOCUS T) were the key genes in the circadian rhythm-photoperiod regulatory network. In conjunction with morphological observations and transcriptomic analysis, we concluded that the induction of floral initiation by old leaves in C. oleifera ‘changlin53’ mainly occurred during stages I and II, floral initiation was completed during stage III, and rhythm–photoperiod interactions may be the source of the main signals in floral initiation induced by old leaves.
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14
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The CfSnt2-Dependent Deacetylation of Histone H3 Mediates Autophagy and Pathogenicity of Colletotrichum fructicola. J Fungi (Basel) 2022; 8:jof8090974. [PMID: 36135699 PMCID: PMC9506038 DOI: 10.3390/jof8090974] [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: 07/18/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 12/12/2022] Open
Abstract
Camellia oleifera is one of the most valuable woody edible-oil crops, and anthracnose seriously afflicts its yield and quality. We recently showed that the CfSnt2 regulates the pathogenicity of Colletotrichum fructicola, the dominant causal agent of anthracnose on C. oleifera. However, the molecular mechanisms of CfSnt2-mediated pathogenesis remain largely unknown. Here, we found that CfSnt2 is localized to the nucleus to regulate the deacetylation of histone H3. The further transcriptomic analysis revealed that CfSnt2 mediates the expression of global genes, including most autophagy-related genes. Furthermore, we provided evidence showing that CfSnt2 negatively regulates autophagy and is involved in the responses to host-derived ROS and ER stresses. These combined functions contribute to the pivotal roles of CfSnt2 on pathogenicity. Taken together, our studies not only illustrate how CfSnt2 functions in the nucleus, but also link its roles on the autophagy and responses to host-derived stresses with pathogenicity in C. fructicola.
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Yan J, He J, Li J, Ren S, Wang Y, Zhou J, Tan X. Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods. BMC PLANT BIOLOGY 2022; 22:435. [PMID: 36089577 PMCID: PMC9465947 DOI: 10.1186/s12870-022-03798-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Camellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera's ability to adapt to different photoperiods. RESULTS Our results indicate that the photoperiod can significantly impact flowering time in C. oleifera. We grew a total of nine samples under the short day condition (SD), middle day condition (MD) and long day condition (LD). Transcriptome analysis yielded 66.94 Gb of high-quality clean reads, with an average of over 6.73 Gb of reads for per sample. Following assembly, a total of 120,080 transcripts were obtained and 94,979 unigenes annotated. A total of 3475 differentially expressed genes (DEGs) were identified between the SD_MD, SD_LD, and MD_LD gene sets. Moreover, WGCNA identified ten gene modules. Genes in pink module (92 genes) were positively correlated with SD, and negatively correlated with both MD and LD. Genes in the magenta module (42 genes) were positively correlated with MD and negatively correlated with both LD and SD. Finally, genes in the yellow module (1758 genes) were positively correlated with both SD and MD, but negatively correlated with LD. KEGG enrichment analysis revealed that genes in the pink, magenta, and yellow modules were involved in flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism and circadian rhythm pathways. Additionally, eight hub genes (GI, AP2, WRKY65, SCR, SHR, PHR1, ERF106, and SCL3) were obtained through network analysis. The hub genes had high connectivity with other photoperiod-sensitive DEGs. The expression levels of hub genes were verified by qRT-PCR analysis. CONCLUSION An increase in light duration promotes earlier flowering of C. oleifera. Flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, and circadian rhythm pathways may function in the photoperiodic flowering pathway of C. oleifera. We also identified eight hub genes that may play a role in this pathway. Ultimately, this work contributes to our understanding of the photoperiodic flowering pathway of C. oleifera and further informs molecular breeding programs on the plant's photoperiodic sensitivity.
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Affiliation(s)
- Jindong Yan
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Jiacheng He
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Jian'an Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China.
| | - Shuangshuang Ren
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Ying Wang
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Junqin Zhou
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China.
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Histone Acetyltransferase CfGcn5-Mediated Autophagy Governs the Pathogenicity of Colletotrichum fructicola. mBio 2022; 13:e0195622. [PMID: 35975920 PMCID: PMC9600425 DOI: 10.1128/mbio.01956-22] [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] [Indexed: 11/20/2022] Open
Abstract
Camellia oleifera is a woody edible-oil plant in China, and anthracnose occurs wherever it is grown, causing serious losses each year. We previously identified that the histone acetyltransferase CfGcn5 orchestrates growth, development, and pathogenicity in Colletotrichum fructicola, the major causal agent of anthracnose on C. oleifera. To elucidate the underlying mechanism, we conducted a transcriptome analysis and found that CfGcn5 is mainly involved in ribosomes, catalytic and metabolic processes, primary metabolism, and autophagy. In addition, we provided evidence showing that CfGcn5 serves as an autophagy repressor to mediate the expression of many autophagy-related genes (ATG) and undergoes degradation during autophagy. Moreover, we found that the CfATG8 and CfATG9 gene-deletion mutants had defects in mitosis and autophagy, resulting in their decreased appressoria formation rates and lower turgor pressure. These combined effects caused the failure of their appressoria functions and caused defects on their pathogenicity, revealing the importance of autophagy in pathogenicity. Taken together, our study illustrates that the autophagy repressor CfGcn5 undergoes degradation in order to regulate autophagy-dependent pathogenicity in C. fructicola.
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Cheng L, Li M, Han Q, Qiao Z, Hao Y, Balbuena TS, Zhao Y. Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity. BIOLOGY 2022; 11:biology11071007. [PMID: 36101388 PMCID: PMC9311850 DOI: 10.3390/biology11071007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary The Theaceae includes more than 300 species of great morphological diversity and has immense economic, cultural, and ornamental values. However, the evolutionary history of this family remains elusive. We integrated 91 genomes and transcriptome datasets of Theaceae and successfully resolved the phylogeny of Theaceae including relatives of cultivated tea plants from both extensive low-copy and multi-copy nuclear gene markers. Bayes-based molecular dating revealed that the ancestor of the tea family originated slightly earlier than the K-Pg boundary (Mass extinction events including the extinction of dinosaurs) with early diversification of three tribes associated with the Early Eocene Climatic Optimum. Further speciation analysis suggested a sole significant diversification shift rate in the common ancestor of Camellia associated with the Mid-Miocene Climatic Optimum. Collectively, polyploidy events, and key morphological innovation characters, such as pericarp with seed coat hardening, could possibly contribute to the Theaceae species diversity. Abstract Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed. Our results maximumly supported that the tribes Stewartieae and Gordonieae are successive sister groups to the tribe Theeae from both coalescent and super matrix ML tree analyses. Moreover, in the most evolved tribe, Theeae, the monophyletic genera Pyrenaria, Apterosperma, and Polyspora are the successive sister groups of Camellia. We also yield a well-resolved relationship of Camellia, which contains the vast majority of Theaceae species richness. Molecular dating suggests that Theaceae originated in the late L-Cretaceous, with subsequent early radiation under the Early Eocene Climatic Optimal (EECO) for the three tribes. A diversification rate shift was detected in the common ancestors of Camellia with subsequent acceleration in speciation rate under the climate optimum in the early Miocene. These results provide a phylogenetic framework and new insights into factors that likely have contributed to the survival of Theaceae, especially a successful radiation event of genus Camellia members to subtropic/tropic regions. These novel findings will facilitate the efficient conservation and utilization of germplasm resources for breeding cultivated tea and oil-tea. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Theaceae.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal 14884-900, Brazil;
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence:
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18
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Wu Q, Tong W, Zhao H, Ge R, Li R, Huang J, Li F, Wang Y, Mallano AI, Deng W, Wang W, Wan X, Zhang Z, Xia E. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:406-421. [PMID: 35510493 DOI: 10.1111/tpj.15799] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Camellia plants include more than 200 species of great diversity and immense economic, ornamental, and cultural values. We sequenced the transcriptomes of 116 Camellia plants from almost all sections of the genus Camellia. We constructed a pan-transcriptome of Camellia plants with 89 394 gene families and then resolved the phylogeny of genus Camellia based on 405 high-quality low-copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We provide strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavily accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found that some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web-accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards a breeding program for cultivated tea, camellia, and oil-tea plants.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjie Wang
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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19
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Quan W, Wang A, Gao C, Li C. Applications of Chinese Camellia oleifera and its By-Products: A Review. Front Chem 2022; 10:921246. [PMID: 35685348 PMCID: PMC9171030 DOI: 10.3389/fchem.2022.921246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Camellia oleifera is a woody oil tree species unique to China that has been cultivated and used in China for more than 2,300 years. Most biological research on C. oleifera in recent years has focused on the development of new varieties and breeding. Novel genomic information has been generated for C. oleifera, including a high-quality reference genome at the chromosome level. Camellia seeds are used to process high-quality edible oil; they are also often used in medicine, health foods, and daily chemical products and have shown promise for the treatment and prevention of diseases. C. oleifera by-products, such as camellia seed cake, saponin, and fruit shell are widely used in the daily chemical, dyeing, papermaking, chemical fibre, textile, and pesticide industries. C. oleifera shell can also be used to prepare activated carbon electrodes, which have high electrochemical performance when used as the negative electrode of lithium-ion batteries. C. oleifera is an economically valuable plant with diverse uses, and accelerating the utilization of its by-products will greatly enhance its industrial value.
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Affiliation(s)
- Wenxuan Quan
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China.,Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Institute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang, China
| | - Anping Wang
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
| | - Chao Gao
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Institute for Forest Resources and Environment of Guizhou, Guizhou University, Guiyang, China
| | - Chaochan Li
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
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