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Jiang J, Zhang Z, Bai Y, Wang X, Dou Y, Geng R, Wu C, Zhang H, Lu C, Gu L, Gao J. Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1087-1105. [PMID: 38051011 DOI: 10.1111/jipb.13592] [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: 09/13/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023]
Abstract
Dendrocalamus brandisii (Munro) Kurz is a sympodial bamboo species with inimitable taste and flavorful shoots. Its rapid growth and use as high-quality material make this bamboo species highly valued for both food processing and wood applications. However, genome information for D. brandisii is lacking, primarily due to its polyploidy and large genome size. Here, we assembled a high-quality genome for hexaploid D. brandisii, which comprises 70 chromosomes with a total size of 2,756 Mb, using long-read HiFi sequencing. Furthermore, we accurately separated the genome into its three constituent subgenomes. We used Oxford Nanopore Technologies long reads to construct a transcriptomic dataset covering 15 tissues for gene annotation to complement our genome assembly, revealing differential gene expression and post-transcriptional regulation. By integrating metabolome analysis, we unveiled that well-balanced lignin formation, as well as abundant flavonoid and fructose contents, contribute to the superior quality of D. brandisii shoots. Integrating genomic, transcriptomic, and metabolomic datasets provided a solid foundation for enhancing bamboo shoot quality and developing efficient gene-editing techniques. This study should facilitate research on D. brandisii and enhance its use as a food source and wood material by providing crucial genomic resources.
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Affiliation(s)
- Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Xiaojing Wang
- School of Life Science, Peking University, Beijing, 100871, China
| | - Yuping Dou
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Ruiman Geng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Hangxiao Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cunfu Lu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lianfeng Gu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, 100102, China
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Chen J, Bi YY, Wang QQ, Liu DK, Zhang D, Ding X, Liu ZJ, Chen SP. Genome-wide identification and analysis of anthocyanin synthesis-related R2R3-MYB genes in Cymbidium goeringii. FRONTIERS IN PLANT SCIENCE 2022; 13:1002043. [PMID: 36247626 PMCID: PMC9554442 DOI: 10.3389/fpls.2022.1002043] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
The MYB gene family plays a vital regulatory role in plant metabolism, stress response, and floral color. The R2R3-MYB gene family of C. goeringii was identified, and its expression was analyzed using bioinformatics in this article. The R2R3-MYB genes of Arabidopsis thaliana were used as a reference to determine 104 CgMYB genes and categorize them into 22 subfamilies. Exon/intron organizations and conserved motif analysis revealed that the majority of CgMYB genes were highly conserved, and chromosome localization and collinearity analysis provided evidence of tandem duplication and segmental duplication events, indicating the phenomenon of gene family expansion and contraction. The function of CgMYB genes was analyzed by cis-acting element and gene ontology (GO) enrichment. In addition, we selected CgMYB91 and CgMYB32 for RT-qPCR, suggesting that CgMYB91 and CgMYB32 are associated with anthocyanin formation. In short, this study provides a comprehensive and specific function of the R2R3-MYB transcription factors (TFs) in orchids.
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Affiliation(s)
- Jiating Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan-Yang Bi
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian-Qian Wang
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiangqing Ding
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shi-Pin Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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Ajayi OO, Held MA, Showalter AM. Glucuronidation of type II arabinogalactan polysaccharides function in sexual reproduction of Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:164-181. [PMID: 34726315 DOI: 10.1111/tpj.15562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Arabinogalactan proteins (AGPs) are complex, hyperglycosylated plant cell wall proteins with little known about the biological roles of their glycan moieties in sexual reproduction. Here, we report that GLCAT14A, GLCAT14B, and GLCAT14C, three enzymes responsible for the addition of glucuronic acid residues to AGPs, function in pollen development, polytubey block, and normal embryo development in Arabidopsis. Using biochemical and immunolabeling techniques, we demonstrated that the loss of function of the GLCAT14A, GLCAT14B, and GLCAT14C genes resulted in disorganization of the reticulate structure of the exine wall, abnormal development of the intine layer, and collapse of pollen grains in glcat14a/b and glcat14a/b/c mutants. Synchronous development between locules within the same anther was also lost in some glcat14a/b/c stamens. In addition, we observed excessive attraction of pollen tubes targeting glcat14a/b/c ovules, indicating that the polytubey block mechanism was compromised. Monosaccharide composition analysis revealed significant reductions in all sugars in glcat14a/b and glcat14a/b/c mutants except for arabinose and galactose, while immunolabeling showed decreased amounts of AGP sugar epitopes recognized by glcat14a/b and glcat14a/b/c mutants compared with the wild type. This work demonstrates the important roles that AG glucuronidation plays in Arabidopsis sexual reproduction and reproductive development.
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Affiliation(s)
- Oyeyemi O Ajayi
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
| | - Michael A Held
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Allan M Showalter
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
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Ajayi OO, Held MA, Showalter AM. Three β-Glucuronosyltransferase Genes Involved in Arabinogalactan Biosynthesis Function in Arabidopsis Growth and Development. PLANTS 2021; 10:plants10061172. [PMID: 34207602 PMCID: PMC8227792 DOI: 10.3390/plants10061172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/21/2022]
Abstract
Arabinogalactan proteins (AGPs) contain arabinogalactan (AG) polysaccharides that are biologically relevant to plant growth processes. Here, the biochemical and physiological roles of three Golgi localized β-glucuronosyltransferase genes (GLCAT14A, GLCAT14B and GLCAT14C) in Arabidopsis thaliana, responsible for the addition of glucuronic acid to AG chains, were further investigated using single, double and triple glcat14 mutant plants. These proteins were localized to the Golgi apparatus when transiently expressed in Nicotiana benthamiana. Sugar analysis of AGP extracts from Arabidopsis stem, leaf and siliques showed a consistent reduction in glucuronic acid in glcat14 mutants relative to wild type, with concomitant effects resulting in tissue-specific alterations, especially in arabinose and galactose sugars. Although we observed defects in trichome branching in glca14a/b and glca14a/b/c mutants, scanning electron microscope analysis/energy dispersive microanalysis (SEM/EDX) showed no difference in the calcium content of trichomes in these mutants relative to wild type. Immunoblot analyses of the stem and leaf showed a reduction in AGPs as detected with the LM2 antibody in glcat14a/b and glcat14a/b/c mutants relative to wild type. The current work exemplifies the possibility of conducting structure-function assessment of cell wall biosynthetic genes to identify their physiological roles in plant growth and development.
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Affiliation(s)
- Oyeyemi O. Ajayi
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA;
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
| | - Michael A. Held
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Allan M. Showalter
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA;
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Correspondence:
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Narciso JO, Zeng W, Ford K, Lampugnani ER, Humphries J, Austarheim I, van de Meene A, Bacic A, Doblin MS. Biochemical and Functional Characterization of GALT8, an Arabidopsis GT31 β-(1,3)-Galactosyltransferase That Influences Seedling Development. FRONTIERS IN PLANT SCIENCE 2021; 12:678564. [PMID: 34113372 PMCID: PMC8186459 DOI: 10.3389/fpls.2021.678564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/21/2021] [Indexed: 05/31/2023]
Abstract
Arabinogalactan-proteins (AGPs) are members of the hydroxyproline-rich glycoprotein (HRGP) superfamily, a group of highly diverse proteoglycans that are present in the cell wall, plasma membrane as well as secretions of almost all plants, with important roles in many developmental processes. The role of GALT8 (At1g22015), a Glycosyltransferase-31 (GT31) family member of the Carbohydrate-Active Enzyme database (CAZy), was examined by biochemical characterization and phenotypic analysis of a galt8 mutant line. To characterize its catalytic function, GALT8 was heterologously expressed in tobacco leaves and its enzymatic activity tested. GALT8 was shown to be a β-(1,3)-galactosyltransferase (GalT) that catalyzes the synthesis of a β-(1,3)-galactan, similar to the in vitro activity of KNS4/UPEX1 (At1g33430), a homologous GT31 member previously shown to have this activity. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmed the products were of 2-6 degree of polymerisation (DP). Previous reporter studies showed that GALT8 is expressed in the central and synergid cells, from whence the micropylar endosperm originates after the fertilization of the central cell of the ovule. Homozygous mutants have multiple seedling phenotypes including significantly shorter hypocotyls and smaller leaf area compared to wild type (WT) that are attributable to defects in female gametophyte and/or endosperm development. KNS4/UPEX1 was shown to partially complement the galt8 mutant phenotypes in genetic complementation assays suggesting a similar but not identical role compared to GALT8 in β-(1,3)-galactan biosynthesis. Taken together, these data add further evidence of the important roles GT31 β-(1,3)-GalTs play in elaborating type II AGs that decorate AGPs and pectins, thereby imparting functional consequences on plant growth and development.
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Affiliation(s)
- Joan Oñate Narciso
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Wei Zeng
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Kris Ford
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Edwin R. Lampugnani
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - John Humphries
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Ingvild Austarheim
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Allison van de Meene
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Antony Bacic
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Monika S. Doblin
- ARC Centre of Excellence on Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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