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Guo L, Chen T, Chu X, Sun K, Yu F, Que F, Ahmad Z, Wei Q, Ramakrishnan M. Anatomical and Transcriptome Analyses of Moso Bamboo Culm Neck Growth: Unveiling Key Insights. PLANTS (BASEL, SWITZERLAND) 2023; 12:3478. [PMID: 37836218 PMCID: PMC10574802 DOI: 10.3390/plants12193478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
The Moso bamboo culm neck, connected with the rhizome and the shoot bud, is an important hub for connecting and transporting the aboveground and belowground systems of bamboo for the shoot bud development and rapid growth. Our previous study revealed that the culm neck generally undergoes six different developmental stages (CNS1-CNS6), according to the primary thickening growth of the underground shoot bud. However, the molecular mechanism of the culm neck development remains unknown. The present study focused on the developmental process of the CNS3-CNS5 stages, representing the early, middle, and late elongation stages, respectively. These stages are densely packed with vascular tissues and consist of epidermis, hypodermis, cortex, and ground tissue. Unlike the hollow structure of the culms, the culm necks are solid structures. As the culm neck continues to grow, the lignin deposition increases noticeably, contributing to its progressive strengthening. For the transcriptome analysis, a total of 161,160 transcripts with an average length of 2373 were obtained from these stages using both PacBio and Illumina sequencing. A total of 92.2% of the reads mapped to the Moso bamboo reference genome. Further analysis identified a total of 5524 novel genes and revealed a dynamic transcriptome. Secondary-metabolism- and transport-related genes were upregulated particularly with the growth of the culm neck. Further analysis revealed the molecular processes of lignin accumulation in the culm neck, which include differentially expressed genes (DEGs) related to cell wall loosening and remodeling and secondary metabolism. Moreover, the upregulations of transcription factors such as MYBH and RSM in the MYB family play crucial roles during critical transitions in the culm neck development, such as changes in the angle between the rhizome and the culm neck. Our new findings provide essential insights into the cellular roadmaps, transcriptional networks, and key genes involved in the culm neck development.
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Affiliation(s)
- Lin Guo
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Tianguo Chen
- Changzhou Agricultural Technology Extension Center, Changzhou 213000, China
| | - Xue Chu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Kai Sun
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Fen Yu
- Changzhou Agricultural Technology Extension Center, Changzhou 213000, China
| | - Feng Que
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang 330045, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
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Wei L, Zhao X, Gu X, Peng J, Song W, Deng B, Cao Y, Hu S. Genome-Wide Identification and Expression Analysis of Dendrocalamus farinosus CCoAOMT Gene Family and the Role of DfCCoAOMT14 Involved in Lignin Synthesis. Int J Mol Sci 2023; 24:8965. [PMID: 37240316 PMCID: PMC10219071 DOI: 10.3390/ijms24108965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/07/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
As the main component of plant cell walls, lignin can not only provide mechanical strength and physical defense for plants, but can also be an important indicator affecting the properties and quality of wood and bamboo. Dendrocalamus farinosus is an important economic bamboo species for both shoots and timber in southwest China, with the advantages of fast growth, high yield and slender fiber. Caffeoyl-coenzyme A-O-methyltransferase (CCoAOMT) is a key rate-limiting enzyme in the lignin biosynthesis pathway, but little is known about it in D. farinosus. Here, a total of 17 DfCCoAOMT genes were identified based on the D. farinosus whole genome. DfCCoAOMT1/14/15/16 were homologs of AtCCoAOMT1. DfCCoAOMT6/9/14/15/16 were highly expressed in stems of D. farinosus; this is consistent with the trend of lignin accumulation during bamboo shoot elongation, especially DfCCoAOMT14. The analysis of promoter cis-acting elements suggested that DfCCoAOMTs might be important for photosynthesis, ABA/MeJA responses, drought stress and lignin synthesis. We then confirmed that the expression levels of DfCCoAOMT2/5/6/8/9/14/15 were regulated by ABA/MeJA signaling. In addition, overexpression of DfCCoAOMT14 in transgenic plants significantly increased the lignin content, xylem thickness and drought resistance of plants. Our findings revealed that DfCCoAOMT14 can be a candidate gene that is involved in the drought response and lignin synthesis pathway in plants, which could contribute to the genetic improvement of many important traits in D. farinosus and other species.
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Affiliation(s)
- Lixian Wei
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
| | - Xin Zhao
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
| | - Xiaoyan Gu
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
| | - Jiahui Peng
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
| | - Wenjuan Song
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
| | - Bin Deng
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
| | - Ying Cao
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
| | - Shanglian Hu
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China
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Li L, Zhou B, Liu D, Wu H, Shi Q, Lin S, Yao W. Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo. Int J Mol Sci 2023; 24:ijms24087425. [PMID: 37108588 PMCID: PMC10138756 DOI: 10.3390/ijms24087425] [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: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm-the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.
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Affiliation(s)
- Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Binao Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Dong Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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Li T, Wang H, Zhang Y, Wang H, Zhang Z, Liu X, Zhang Z, Liu K, Yang D, Zhang H, Gu L. Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots. PLANT PHYSIOLOGY 2023; 191:1017-1035. [PMID: 36417282 PMCID: PMC9922427 DOI: 10.1093/plphys/kiac525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 11/17/2022] [Indexed: 05/13/2023]
Abstract
The fast growth of Moso bamboo (Phyllostachys edulis) shoots is caused by the rapid elongation of each internode. However, the key underlying cellular processes and epigenetic mechanisms remain largely unexplored. We used microscopy and multi-omics approaches to investigate two regions (bottom and middle) of the 18th internode from shoots of two different heights (2 and 4 m). We observed that internode cells become longer, and that lignin biosynthesis and glycosyltransferase family 43 (GT43) genes are substantially upregulated with shoot height. Nanopore direct RNA sequencing (DRS) revealed a higher N6-methyladenine (m6A) modification rate in 2-m shoots than in 4-m shoots. In addition, different specific m6A modification sites were enriched at different growth stages. Global DNA methylation profiling indicated that DNA methylation levels are higher in 4-m shoots than in 2-m shoots. We also detected shorter poly(A) tail lengths (PALs) in 4-m shoots compared with 2-m shoots. Genes showing differential PAL were mainly enriched in the functional terms of protein translation and vesicle fusion. An association analysis between PALs and DNA methylation strongly suggested that gene body CG methylation levels are positively associated with PAL. This study provides valuable information to better understand post-transcriptional regulations responsible for fast-growing shoots in Moso bamboo.
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Affiliation(s)
- Tao Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huihui Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaxin Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeyu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zekun Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Wang H, Guo L, Zha R, Gao Z, Yu F, Wei Q. Histological, metabolomic and transcriptomic analyses reveal mechanisms of cold acclimation of the Moso bamboo (Phyllostachys edulis) leaf. TREE PHYSIOLOGY 2022; 42:2336-2352. [PMID: 35723499 DOI: 10.1093/treephys/tpac064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
The Moso bamboo (Phyllostachys edulis) leaf copes well with cold winters in southeastern China. However, until now, there has been almost no research on its adaptation mechanisms to cold weather. Herein, we found that the Moso bamboo leaf has evolved several anatomical structures that may play a role in enhancing its cold tolerance. These structures include fewer fusiform cells, smaller bulliform cells, lower stomata density and many more trichomes, as well as lower relative water content than in the leaf of a cold-sensitive bamboo species, Bambusa ventricosa. Untargeted metabolomic analysis revealed that the winter leaf of Moso bamboo had 10- to 1000-fold higher stress-resistant metabolites such as glutathione, trehalose and ascorbic acid than the leaf of B. ventricosa on both warm and cold days. In contrast to the leaves that grew on a warm day, some metabolites such as glutathione and trehalose increased dramatically in the leaves of Moso bamboo that grew on a cold day. However, they unexpectedly decreased in the leaf of B. ventricosa growing at cold temperatures. Transcriptome analysis revealed a cold stress response network that includes trehalose, glutathione, flavonoid metabolism, DNA repair, reactive oxygen species degradation, stress-associated genes and abiotic stress-related plant hormones such as jasmonic acid, abscisic acid and ethylene. The potential mediator transcription factors, such as EREBP, HSF, MYB, NAC and WRYK, were also significantly upregulated in Moso bamboo leaves growing at cold temperatures. Interestingly, many newly identified genes were involved in the transcriptome of the winter leaf of the Moso bamboo. Most of these new genes have not even been annotated yet. The above results indicate that the Moso bamboo leaf has evolved special histological structures, metabolic pathways and a cold stress-tolerant transcriptome to adapt to the cold weather in its distribution areas.
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Affiliation(s)
- Haiyue Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
- International Education College, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
| | - Ruofei Zha
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
| | - Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, College of Forestry, 1101 Zhimin Road, Nanchang, Jiangxi 330045, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, College of Forestry, 1101 Zhimin Road, Nanchang, Jiangxi 330045, China
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Jiang J, Gao Z, Xiang Y, Guo L, Zhang C, Que F, Yu F, Wei Q. Characterization of anatomical features, developmental roadmaps, and key genes of bamboo leaf epidermis. PHYSIOLOGIA PLANTARUM 2022; 174:e13822. [PMID: 36335549 DOI: 10.1111/ppl.13822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The exact developmental roadmaps of bamboo leaf epidermis and the regulating genes are largely unknown. In this study, we comprehensively investigated the morphological features of the leaf epidermis of bamboo, Pseudosasa japonica. We also established the developmental roadmaps of the abaxial epidermis along the linearly growing leaf. A variant of P. japonica, P. japonica var. tsutsumiana, with smaller stomata and higher stomata density, was identified. Further analysis revealed that the higher stomata density of the variant was due to the abnormal increase in stomata columns within the single stomata band. This abnormal development of stomata bands was observed as early as the guard mother cell stage in the leaf division zone (DZ). Interestingly, the developmental pattern of the single stomata was similar in P. japonica and the variant. Molecular data showed that PjDLT (Dwarf and Low Tillering) was significantly downregulated in leaves DZ of the variant. Overexpression of PjDLT in Arabidopsis and rice results in smaller plants with lower stomata density, whereas downregulation or mutation of OsDLT results in increased stomata density. Our results highlight the morphological features and developmental schedule of the leaf epidermis of bamboo and provide evidence that DLT plays an important role in regulating stomata in bamboo and rice.
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Affiliation(s)
- Jiawen Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yu Xiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Chuzheng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- International Education College, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Feng Que
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, China
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Chen M, Guo L, Ramakrishnan M, Fei Z, Vinod KK, Ding Y, Jiao C, Gao Z, Zha R, Wang C, Gao Z, Yu F, Ren G, Wei Q. Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors. THE PLANT CELL 2022; 34:3577-3610. [PMID: 35766883 PMCID: PMC9516176 DOI: 10.1093/plcell/koac193] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 05/09/2023]
Abstract
Moso bamboo (Phyllostachys edulis) shows remarkably rapid growth (114.5 cm/day), but the underlying biological mechanisms remain unclear. After examining more than 12,750 internodes from more than 510 culms from 17 Moso populations, we identified internode 18 as a representative internode for rapid growth. This internode includes a 2-cm cell division zone (DZ), a cell elongation zone up to 12 cm, and a secondary cell wall (SCW) thickening zone. These zones elongated 11.8 cm, produced approximately 570,000,000 cells, and deposited ∼28 mg g-1 dry weight (DW) lignin and ∼44 mg g-1 DW cellulose daily, far exceeding vegetative growth observed in other plants. We used anatomical, mathematical, physiological, and genomic data to characterize development and transcriptional networks during rapid growth in internode 18. Our results suggest that (1) gibberellin may directly trigger the rapid growth of Moso shoots, (2) decreased cytokinin and increased auxin accumulation may trigger cell DZ elongation, and (3) abscisic acid and mechanical pressure may stimulate rapid SCW thickening via MYB83L. We conclude that internode length involves a possible tradeoff mediated by mechanical pressure caused by rapid growth, possibly influenced by environmental temperature and regulated by genes related to cell division and elongation. Our results provide insight into the rapid growth of Moso bamboo.
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Affiliation(s)
- Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Kunnummal K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | | | - Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ruofei Zha
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chunyue Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhimin 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
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
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Guo L, Wang C, Chen J, Ju Y, Yu F, Jiao C, Fei Z, Ding Y, Wei Q. Cellular differentiation, hormonal gradient, and molecular alternation between the division zone and the elongation zone of bamboo internodes. PHYSIOLOGIA PLANTARUM 2022; 174:e13774. [PMID: 36050899 DOI: 10.1111/ppl.13774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/20/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Bamboo differentiates a cell division zone (DZ) and a cell elongation zone (EZ) to promote internode elongation during rapid growth. However, the biological mechanisms underlying this sectioned growth behavior are still unknown. Using histological, physiological, and genomic data, we found that the cell wall and other subcellular organelles such as chloroplasts are more developed in the EZ. Abundant hydrogen peroxide accumulated in the pith cells of the EZ, and stomata formed completely in the EZ. In contrast, most cells in the DZ were in an undifferentiated state with wrinkled cell walls and dense cytoplasm. Hormone detection revealed that the levels of gibberellin, auxin, cytokinin, and brassinosteroid were higher in the DZ than in the EZ. However, the levels of salicylic acid and jasmonic acid were higher in the EZ than in the DZ. Transcriptome analysis with qRT-PCR quantification revealed that the transcripts for cell division and primary metabolism had higher expression in the DZ, whereas the genes for photosynthesis, cell wall growth, and secondary metabolism were dramatically upregulated in the EZ. Overexpression of a MYB transcription factor, BmMYB83, promotes cell wall lignification in transgenic plants. BmMYB83 is specifically expressed in cells that may have lignin deposits, such as protoxylem vessels and fiber cells. Our results indicate that hormone gradient and transcriptome reprogramming, as well as specific expression of key genes such as BmMYB83, may lead to differentiation of cell growth in the bamboo internode.
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Affiliation(s)
- Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Chunyue Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Jin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ye Ju
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, China
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9
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Cheng Q, Sun L, Qiao H, Li Z, Li M, Cui X, Li W, Liu S, Wang H, Yang W, Shen H. Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome. iScience 2022; 25:104565. [PMID: 35784787 PMCID: PMC9240803 DOI: 10.1016/j.isci.2022.104565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/23/2022] [Accepted: 06/06/2022] [Indexed: 10/26/2022] Open
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10
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Li Y, Zhang D, Zhang S, Lou Y, An X, Jiang Z, Gao Z. Transcriptome and miRNAome analysis reveals components regulating tissue differentiation of bamboo shoots. PLANT PHYSIOLOGY 2022; 188:2182-2198. [PMID: 35157078 PMCID: PMC8968251 DOI: 10.1093/plphys/kiac018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/17/2021] [Indexed: 05/27/2023]
Abstract
Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. This study identified a total of 58,652 genes and 150 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild-type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis "Pachyloen") at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 14,029 (65.17%) differentially expressed genes and 68 (45.33%) differentially expressed miRNAs were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations, each between two successive stages (WTS2/TWS2_versus_WTS1/TWS1, WTS3/TWS3_versus_WTS2/TWS2, WTS4/TWS4_versus_WTS3/TWS3, and WTS5/TWS5_versus_WTS4/TWS4), and the WTTW group was composed of five combinations, each between two relative stages (TWS1-5_versus_WTS1-5). Additionally, among the phytohormones, zeatin showed more remarkable changes in concentrations than indole-3-acetic acid, gibberellic acid, and abscisic acid throughout the five stages in the WT and the TW groups. Moreover, 125 cleavage sites were identified for 387 miRNA-mRNA pairs via degradome sequencing (P < 0.05). The dual-luciferase reporter assay confirmed that 13 miRNAs bound to 12 targets. Fluorescence in situ hybridization localized miR166 and miR160 in the shoot apical meristem and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.
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Affiliation(s)
- Ying Li
- National State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuqin Zhang
- National State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China
| | - Yongfeng Lou
- Jiangxi Academy of Forestry, Jiangxi 330032, China
| | - Xinmin An
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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11
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Gao Z, Guo L, Ramakrishnan M, Xiang Y, Jiao C, Jiang J, Vinod KK, Fei Z, Que F, Ding Y, Yu F, Chen T, Wei Q. Cellular and molecular characterizations of the irregular internode division zone formation of a slow-growing bamboo variant. TREE PHYSIOLOGY 2022; 42:570-584. [PMID: 34633049 DOI: 10.1093/treephys/tpab129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/01/2021] [Accepted: 09/24/2021] [Indexed: 05/16/2023]
Abstract
The key molecular mechanisms underlying the sectionalized growth within bamboo or other grass internodes remain largely unknown. Here, we genetically and morphologically compared the culm and rhizome internode division zones (DZs) of a slow-growing bamboo variant (sgv) having dwarf internodes, with those of the corresponding wild type (WT). Histological analysis discovers that the sgv has an irregular internode DZ. However, the shoot apical meristems in height, width, outside shape, cell number and cell width of the sgv and the WT were all similar. The DZ irregularities first appeared post apical meristem development, in 1-mm sgv rhizome internodes. Thus, the sgv is a DZ irregularity bamboo variant, which has been first reported in bamboo according to our investigation. Transcriptome sequencing analysis finds that a number of cell wall biogenesis and cell division-related genes are dramatically downregulated in the sgv DZ. Interestingly, both transcriptomic and brassinosteroid (BR) contents detection, as well as quantitative real-time PCR analyses show that these irregularities have resulted from the BR signaling pathway defects. Brassinosteroid defect might also cause the erect leaves and branches as well as the irregular epidermis of the sgv. These results suggest that BR signaling pathway plays critical roles in bamboo internode DZ and leaf development from a mutant perspective and also explain the upstream mechanisms causing the dwarf internode of the sgv bamboo.
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Affiliation(s)
- Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Yu Xiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
- College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Jiaweng Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Kunnummal K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Sahyadri Ave New Delhi, 110012, India
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
| | - Feng Que
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, College of Forestry, 1101 Zhimin Road, Nanchang, Jiangxi 330045, China
| | - Tianguo Chen
- Changzhou Agricultural Technology Extension Center, 289-1 Changjiang Middle Road, Changzhou, Jiangsu 213000, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, College of Forestry, 1101 Zhimin Road, Nanchang, Jiangxi 330045, China
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12
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Zheng Y, Yang D, Rong J, Chen L, Zhu Q, He T, Chen L, Ye J, Fan L, Gao Y, Zhang H, Gu L. Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:649-670. [PMID: 34990066 DOI: 10.1111/jipb.13217] [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: 11/22/2021] [Accepted: 01/04/2022] [Indexed: 05/25/2023]
Abstract
Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele-aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2, 737 Mb) for hexaploid D. latiflorus using both single-molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi-C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135 231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA-Seq and PacBio single-molecule real-time long-read isoform sequencing revealed highly differential alternative splicing (AS) between non-abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.
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Affiliation(s)
- Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jundong Rong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liguang Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiang Zhu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tianyou He
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingyan Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Ye
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lili Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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13
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Wang J, Hou Y, Wang Y, Zhao H. Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis). BMC Genomics 2021; 22:638. [PMID: 34479506 PMCID: PMC8417995 DOI: 10.1186/s12864-021-07953-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Background LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive. Results For comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding. Conclusions We provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07953-z.
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Affiliation(s)
- Jiongliang Wang
- 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 Centre for Bamboo and Rattan, 100102, Beijing, China
| | - Yinguang Hou
- 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 Centre for Bamboo and Rattan, 100102, Beijing, China
| | - Yu Wang
- 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 Centre for Bamboo and Rattan, 100102, Beijing, China
| | - Hansheng Zhao
- 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 Centre for Bamboo and Rattan, 100102, Beijing, China.
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14
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Gao Z, Guo L, Chen M, Yu F, Wei Q. Characterization of the development dynamics within the linear growth bamboo leaf. PHYSIOLOGIA PLANTARUM 2021; 172:1518-1534. [PMID: 33502764 DOI: 10.1111/ppl.13346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
The leaf is the main photosynthetic organ in plants, such as bamboo. Leaves from bamboo are used as a food additive. However, according to our investigation, to date there have been no reports concerning the leaf development of bamboo. By measuring over 7500 parenchymal cells, we discovered that the linear leaf growth of Pseudosasa japonica could be divided into three growth sections. The first one is a roughly 1-cm long division zone (DZ), containing about 1580 cells, located at the bottom of the leaf; the second one is an about 3-cm long elongation zone (EZ), with ~1905 cells, located above the DZ; and the last is a mature zone (MZ) in which cell elongation is completed. The cell production rate of the DZ was 25.33-35.81 cells per hour, with an average of 29.73; and the cell division rate was ~0.45 cells per cell every 24 h. PacBio and Illumina transcriptome sequencing found 21 933 unigenes expressed in these zones. Further analysis revealed a dynamic transcriptome, with transcripts for cell division in the DZ changing to transcripts for cell elongation, photosynthetic development, secondary metabolism, stress resistance, and nutrition transport toward the leaf distal. Those transcriptome transformations correlated well with the changes of relative water content, biomass accumulation, and cellulose crystal degree and were supported by quantitative polymerase chain reaction data. These results revealed a developmental gradient of the bamboo linear growth leaf, which offers a foundation to elucidate and engineer leaf development in bamboo, an economically valuable plant.
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Affiliation(s)
- Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, China
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15
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Ma X, Zhao H, Yan H, Sheng M, Cao Y, Yang K, Xu H, Xu W, Gao Z, Su Z. Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data. Comput Struct Biotechnol J 2021; 19:2708-2718. [PMID: 34093986 PMCID: PMC8131310 DOI: 10.1016/j.csbj.2021.04.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 01/07/2023] Open
Abstract
Bamboo, one of the most crucial nontimber forest resources worldwide, has the capacity for rapid growth. In recent years, the genome of moso bamboo (Phyllostachys edulis) has been decoded, and a large amount of transcriptome data has been published. In this study, we generated the genome-wide profiles of the histone modification H3K4me3 in leaf, stem, and root tissues of bamboo. The trends in the distribution patterns were similar to those in rice. We developed a processing pipeline for predicting novel transcripts to refine the structural annotation of the genome using H3K4me3 ChIP-seq data and 29 RNA-seq datasets. As a result, 12,460 novel transcripts were predicted in the bamboo genome. Compared with the transcripts in the newly released version 2.0 of the bamboo genome, these novel transcripts are tissue-specific and shorter, and most have a single exon. Some representative novel transcripts were validated by semiquantitative RT-PCR and qRT-PCR analyses. Furthermore, we put these novel transcripts back into the ChIP-seq analysis pipeline and discovered that the percentages of H3K4me3 in genic elements were increased. Overall, this work integrated transcriptomic data and epigenomic data to refine the annotation of the genome in order to discover more functional genes and study bamboo growth and development, and the application of this predicted pipeline may help refine the structural annotation of the genome in other species.
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Affiliation(s)
- Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hansheng Zhao
- 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
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.,College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Minghao Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kebin Yang
- 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
| | - Hao Xu
- 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
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhimin 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
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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16
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Chen M, Ju Y, Ahmad Z, Yin Z, Ding Y, Que F, Yan J, Chu J, Wei Q. Multi-analysis of sheath senescence provides new insights into bamboo shoot development at the fast growth stage. TREE PHYSIOLOGY 2021; 41:491-507. [PMID: 33079187 DOI: 10.1093/treephys/tpaa140] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 05/16/2023]
Abstract
Sheath senescence is an important part of bamboo shoot development during the fast growth stage. However, no information has been reported about this distinctive process until now. Using multiple approaches, we found that sheath senescence is a complex process that occurs sequentially with chloroplast corruption, chlorophyll degradation and water loss. Reactive oxygen species (ROS), salicylic acid and abscisic acid also accumulate in the senescing sheath. Transcriptome analysis showed that NAC and WRKY transcription factors, such as NAC2 and WRKY75, as well as their possible downstream target genes, such as those involved in ROS production, proteolysis and nutrition recycling, constitute the gene network of the bamboo sheath senescence process. Furthermore, the initiation of sheath senescence might be triggered by hexokinase genes, such as HXK6, which is localized to the mitochondrion and could promote leaf senescence when overexpressed in Arabidopsis. Sheath senescence occurs after the growth decrease of the internodes, which provides assimilates. The slowing of internode growth possibly results in sugar accumulation, such as glucose, in the sheath, which finally upregulates hexokinase genes and initiates sheath senescence. These findings reveal that sheath senescence is a multilevel regulation process and has a close link to the corresponding internode growth, which provides new insights into the shoot development of bamboo during the fast growth stage.
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Affiliation(s)
- Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ye Ju
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zengfang Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Feng Que
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jijun Yan
- National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China
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Wang X, Yan X, Li S, Jing Y, Gu L, Zou S, Zhang J, Liu B. Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots. BMC Genomics 2021; 22:45. [PMID: 33423665 PMCID: PMC7798191 DOI: 10.1186/s12864-020-07290-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 11/28/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. RESULT In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. CONCLUSION Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.
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Affiliation(s)
- Xiaqin Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, 311300, Hangzhou, China
| | - Xinyang Yan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shubin Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yun Jing
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, 311300, Hangzhou, China.
| | - Bobin Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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18
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Gene Set Subtraction Reveals 633 Candidate Genes for Bamboo Culm Wall Thickening. FORESTS 2020. [DOI: 10.3390/f11121331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Abundant research has been conducted on the physiological, biochemical, and anatomical aspects of bamboo culm wall thickening, but its molecular mechanism has not yet been investigated. In this study, we performed whole-genome resequencing of Phyllostachys edulis ‘Pachyloen’, Phyllostachys nidularia f. farcta, Phyllostachys heteroclada f. solida with significantly thicker culm walls, and Schizostachyum dumetorum var. xinwuense with extremely thin culm walls. Moreover, we pioneered the innovative use of gene set subtraction to explore candidate genes that regulate bamboo culm wall thickening. A candidate gene set, containing 633 genes, was obtained by eliminating shared genes that help maintain physiological processes after alignment with the P. edulis reference genome. Starch and sucrose, oxidative phosphorylation, and ribosome were the three most important pathways enriched by differentially expressed genes. Although it cannot be used for hyperfine localization of bamboo wall thickness-regulatory genes, gene set reduction narrows down the range of candidate genes at minimal cost and provides new clues for the application of bioinformatics in plant research.
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19
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Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
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20
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Abstract
Many natural shapes exhibit surprising symmetry and can be described by the Gielis equation, which has several classical geometric equations (for example, the circle, ellipse and superellipse) as special cases. However, the original Gielis equation cannot reflect some diverse shapes due to limitations of its power-law hypothesis. In the present study, we propose a generalized version by introducing a link function. Thus, the original Gielis equation can be deemed to be a special case of the generalized Gielis equation (GGE) with a power-law link function. The link function can be based on the morphological features of different objects so that the GGE is more flexible in fitting the data of the shape than its original version. The GGE is shown to be valid in depicting the shapes of some starfish and plant leaves.
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21
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Wang Y, Sun X, Ding Y, Fei Z, Jiao C, Fan M, Yao B, Xin P, Chu J, Wei Q. Cellular and molecular characterization of a thick-walled variant reveal a pivotal role of shoot apical meristem in transverse development of bamboo culm. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3911-3926. [PMID: 31037305 DOI: 10.1093/jxb/erz201] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/17/2019] [Indexed: 05/27/2023]
Abstract
Little is known about the mechanisms underlying the development of bamboo culm. Using anatomical, mathematical modeling, and genomics methods, we investigated the role of shoot apical meristem (SAM) in the development of the transverse morphology of bamboo culm and explored the underlying cellular and molecular processes. We discovered that maintenance of SAM morphology that can produce circular culm and increase in SAM cell numbers, especially corpus cells, is the means by which bamboo makes a larger culm with a regular pith cavity and culm wall during development. A less cellular form of SAM with a lower proportion of corpus cells causes an abnormal higher ratio of wall component cells to pith cells, which breaks the balance of their interaction and triggers the random invasion of wall component cells into pith tissues during development, and finally results in the various thick culm walls of Phyllostachys nidularia f. farcta. The smaller SAM also results in a lower level of hormones such as cytokinin and auxin, and down-regulates hormone signaling and the downstream functional genes such as those related to metabolism, which finally results in a dwarf and smaller diameter culm with lower biomass. These results provide an important perspective on the culm development of bamboo, and support a plausible mechanism causing the size-reduced culm and various thick culm walls of P. nidularia f. farcta.
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Affiliation(s)
- Yujun Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xuepeng Sun
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Chen Jiao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Mingyuan Fan
- International Education College, Nanjing Forestry University, Nanjing, Jiangsu, China
| | | | - Peiyong Xin
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
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22
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Wei Q, Guo L, Jiao C, Fei Z, Chen M, Cao J, Ding Y, Yuan Q. Characterization of the developmental dynamics of the elongation of a bamboo internode during the fast growth stage. TREE PHYSIOLOGY 2019; 39:1201-1214. [PMID: 31135922 DOI: 10.1093/treephys/tpz063] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/26/2019] [Accepted: 05/17/2019] [Indexed: 05/16/2023]
Abstract
Previous studies on the fast growth of bamboo shoots mainly focused on the entire culm. No work about the fast elongation of a single internode, which is the basic unit for the fast growth of bamboo shoots, has been reported so far according to our knowledge. In this study, we have systematically investigated the regulating mechanisms underlying the fast growth of a single bamboo internode of Bambusa multiplex (Lour.) Raeusch. ex Schult. We discovered that the growth of the internode displays a logistic pattern, and the two sections located in the bottom of the internode, one for cell division and, another for cell elongation, each with an ~1-cm length, comprise the effective zones for the internode growth. RNA-Seq analysis identified a number of genes potentially involved in regulating the fast growth of bamboo internode such as those that have positive roles in promoting cell growth or division, which were dramatically down-regulated in the internode at fast growth decreasing stage. Further analysis revealed that sugar plays an important role in promoting the fast growth of bamboo internodes through inhibition of BmSnf1. Mechanical stress is found to be involved in the triggering of the internode growth decrease through activation of the generation of reactive oxygen species by upregulating Calmodulins. These results provide systematic insight into the biological mechanisms underlying the fast growth of bamboo shoots based on the behavior of a single internode.
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Affiliation(s)
- Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Junjie Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Qisen Yuan
- International Education College, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
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