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Liu S, Xu H, Wang G, Jin B, Cao F, Wang L. Tree Longevity: Multifaceted Genetic Strategies and Beyond. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39254418 DOI: 10.1111/pce.15146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 08/22/2024] [Accepted: 08/24/2024] [Indexed: 09/11/2024]
Abstract
Old trees are remarkable for their ability to endure for centuries or even millennia, acting as recordkeepers of historical climate and custodians of genetic diversity. The secret to their longevity has long been a subject of fascination. Despite the challenges associated with studying old trees, such as massive size, slow growth rate, long lifespan and often remote habitat, accumulating studies have investigated the mechanisms underlying tree aging and longevity over the past decade. The recent publication of high-quality genomes of long-lived tree species, coupled with research on stem cell function and secondary metabolites in longevity, has brought us closer to unlocking the secrets of arboreal longevity. This review provides an overview of the global distribution of old trees and examines the environmental and anthropogenic factors that shape their presence. We summarize the contributions of physiological characteristics, stem cell activity, and immune system responses to their extraordinary longevity. We also explore the genetic and epigenetic 'longevity code', which consists of resistance and defense genes, DNA repair genes and patterns of DNA methylation modification. Further, we highlight key areas for future research that could enhance our understanding of the mechanisms underlying tree longevity.
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Affiliation(s)
- Sian Liu
- College of Horticulture and Landscape, Yangzhou University, Yangzhou, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Biao Jin
- College of Horticulture and Landscape, Yangzhou University, Yangzhou, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Li Wang
- College of Horticulture and Landscape, Yangzhou University, Yangzhou, China
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2
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Rong J, Zheng Y, Zhang Z, Zhang J, Gu Y, Hua T, Zhao M, Fan L, Deng Z, Pan Y, Li B, Chen L, He T, Chen L, Ye J, Zhang H, Gu L. De novo Whole-Genome Assembly of the 10-Gigabase Fokienia Hodginsii Genome to Reveal Differential Epigenetic Events Between Callus and Xylem. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402644. [PMID: 39229940 DOI: 10.1002/advs.202402644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/29/2024] [Indexed: 09/05/2024]
Abstract
Fokienia hodginsii (F. hodginsii), belonging to the genus Fokienia of the Cupressaceae. F. hodginsii has significant application value due to its wood properties and great research value in evolutionary studies as a gymnosperm. However, the genome of F. hodginsii remains unknown due to the large size of gymnosperms genome. Pacific Bioscience sequencing, Hi-C mapping, whole-genome Bisulfite Sequencing (BS-Seq), long-read isoform sequencing (Iso-Seq), direct RNA sequencing (DRS), quantitative proteomics, and metabonomics analysis are employed to facilitate genome assembly, gene annotation, and investigation into epigenetic mechanisms. In this study, the 10G F. hodginsii genome is assembled into 11 chromosomes. Furthermore, 50 521 protein-coding genes are annotated and determined that 65% of F. hodginsii genome comprises repetitive sequences. It is discovered that transposable element (TE)-including introns is associated with higher expression. The DNA methylome of F. hodginsii reveals that xylem has a higher DNA methylation level compared to callus. Moreover, DRS reveals the significant alterations in RNA full-length ratio, which potentially associated with poly(A) length (PAL) and alternative polyadenylation (APA). Finally, the morphology measurement and metabonomics analysis revealed the difference of 14 cultivars. In summary, the genomes and epigenetics datasets provide a molecular basis for callus formation in the gymnosperm family.
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Affiliation(s)
- Jundong Rong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zeyu Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuying Gu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tian Hua
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengna Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lili Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiwen Deng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanmei Pan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bingjun Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liguang Chen
- College of Forestry, 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
| | - Hangxiao Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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3
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Budnick A, Franklin MJ, Utley D, Edwards B, Charles M, Hornstein ED, Sederoff H. Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus. THE PLANT GENOME 2024; 17:e20429. [PMID: 38243772 DOI: 10.1002/tpg2.20429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/21/2024]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5' site to an upstream 3' end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.
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Affiliation(s)
- Asa Budnick
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Megan J Franklin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Delecia Utley
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Brianne Edwards
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Melodi Charles
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Eli D Hornstein
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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4
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Yadav S, Meena S, Kalwan G, Jain PK. DNA methylation: an emerging paradigm of gene regulation under drought stress in plants. Mol Biol Rep 2024; 51:311. [PMID: 38372841 DOI: 10.1007/s11033-024-09243-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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5
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Goldstein RE, Jack RL, Pesci AI. How do cicadas emerge together? Thermophysical aspects of their collective decision-making. Phys Rev E 2024; 109:L022401. [PMID: 38491648 DOI: 10.1103/physreve.109.l022401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/19/2023] [Indexed: 03/18/2024]
Abstract
Periodical cicadas exhibit life cycles with durations of 13 or 17 years, and it is now accepted that large prime cycles arose to avoid synchrony with predators. Less well explored is how, in the face of intrinsic biological and environmental noise, insects within a brood emerge together in large successive swarms from underground during springtime warming. Here, we consider the decision-making process of underground cicadas experiencing random, spatially correlated thermal microclimates such as those in nature. Introducing short-range communication between insects leads to an Ising model of consensus building with a quenched, spatially correlated random magnetic field and annealed site dilution, which displays the kinds of collective swarms seen in nature. These results highlight the need for fieldwork to quantify the spatial fluctuations in thermal microclimates and their relationship to the spatiotemporal dynamics of swarm emergence.
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Affiliation(s)
- Raymond E Goldstein
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Robert L Jack
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Adriana I Pesci
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
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6
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Bush J, Webster C, Wegrzyn J, Simon C, Wilcox E, Khan R, Weisz D, Dudchenko O, Aiden EL, Frandsen P. Chromosome-Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula. Genome Biol Evol 2024; 16:evae001. [PMID: 38190231 PMCID: PMC10799293 DOI: 10.1093/gbe/evae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/09/2024] Open
Abstract
We present a high-quality assembly and annotation of the periodical cicada species, Magicicada septendecula (Hemiptera: Auchenorrhyncha: Cicadidae). Periodical cicadas have a significant ecological impact, serving as a food source for many mammals, reptiles, and birds. Magicicada are well known for their massive emergences of 1 to 3 species that appear in different locations in the eastern United States nearly every year. These year classes ("broods") emerge dependably every 13 or 17 yr in a given location. Recently, it has become clear that 4-yr early or late emergences of a sizeable portion of a population are an important part of the history of brood formation; however, the biological mechanisms by which they track the passage of time remain a mystery. Using PacBio HiFi reads in conjunction with Hi-C proximity ligation data, we have assembled and annotated the first whole genome for a periodical cicada, an important resource for future phylogenetic and comparative genomic analysis. This also represents the first quality genome assembly and annotation for the Hemipteran superfamily Cicadoidea. With a scaffold N50 of 518.9 Mb and a complete BUSCO score of 96.7%, we are confident that this assembly will serve as a vital resource toward uncovering the genomic basis of periodical cicadas' long, synchronized life cycles and will provide a robust framework for further investigations into these insects.
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Affiliation(s)
- Jonas Bush
- Huck Life Sciences Institute, The Pennsylvania State University, State College, PA, USA
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Cynthia Webster
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Edward Wilcox
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
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7
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Zhang Y, Huang D, Miao Y. Epigenetic control of plant senescence and cell death and its application in crop improvement. FRONTIERS IN PLANT SCIENCE 2023; 14:1258487. [PMID: 37965008 PMCID: PMC10642554 DOI: 10.3389/fpls.2023.1258487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Plant senescence is the last stage of plant development and a type of programmed cell death, occurring at a predictable time and cell. It involves the functional conversion from nutrient assimilation to nutrient remobilization, which substantially impacts plant architecture and plant biomass, crop quality, and horticultural ornamental traits. In past two decades, DNA damage was believed to be a main reason for cell senescence. Increasing evidence suggests that the alteration of epigenetic information is a contributing factor to cell senescence in organisms. In this review, we summarize the current research progresses of epigenetic and epitranscriptional mechanism involved in cell senescence of plant, at the regulatory level of DNA methylation, histone methylation and acetylation, chromatin remodeling, non-coding RNAs and RNA methylation. Furthermore, we discuss their molecular genetic manipulation and potential application in agriculture for crop improvement. Finally we point out the prospects of future research topics.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongmei Huang
- Department of Biochemistry and Molecular Biology, Xiamen Medical College, Xiamen, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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8
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Xi F, Zhang Z, Wu L, Wang B, Gao P, Chen K, Zhao L, Gao J, Gu L, Zhang H. Insight into gene expression associated with DNA methylation and small RNA in the rhizome-root system of Moso bamboo. Int J Biol Macromol 2023; 248:125921. [PMID: 37499707 DOI: 10.1016/j.ijbiomac.2023.125921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
Moso bamboo (Phyllostachys edulis), typically a monopodial scattering bamboo, is famous for its rapid growth. The rhizome-root system of Moso bamboo plays a crucial role in its clonal growth and spatial distribution. However, few studies have focused on rhizome-root systems. Here we collected LBs, RTs, and RGFNSs, the most important parts of the rhizome-root system, to study the molecular basis of the rapid growth of Moso bamboo due to epigenetic changes, such as DNA modifications and small RNAs. The angle of the shoot apical meristem of LB gradually decreased with increasing distance from the mother plant, and the methylation levels of LB were much higher than those of RT and RGFNS. 24 nt small RNAs and mCHH exhibited similar distribution patterns in transposable elements, suggesting a potential association between these components. The miRNA abundance of LB gradually increased with increasing distance from the mother plant, and a negative correlation was observed between gene expression levels and mCG and mCHG levels in the gene body. This study paves the way for further exploring the effects of epigenetic factors on the physiology of Moso bamboo.
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Affiliation(s)
- Feihu Xi
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin Wu
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baijie Wang
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pengfei Gao
- College of Forestry, Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Chen
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangzhen Zhao
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, China.
| | - Lianfeng Gu
- College of Forestry, Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Hangxiao Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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9
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Li J, Han F, Yuan T, Li W, Li Y, Wu HX, Wei H, Niu S. The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine. Nat Commun 2023; 14:1947. [PMID: 37029142 PMCID: PMC10082083 DOI: 10.1038/s41467-023-37684-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Epigenetics has been revealed to play a crucial role in the long-term memory in plants. However, little is known about whether the epigenetic modifications occur with age progressively in conifers. Here, we present the single-base resolution DNA methylation landscapes of the 25-gigabase Chinese pine (Pinus tabuliformis) genome at different ages. The result shows that DNA methylation is closely coupled with the regulation of gene transcription. The age-dependent methylation profile with a linearly increasing trend is the most significant pattern of DMRs between ages. Two segments at the five-prime end of the first ultra-long intron in DAL1, a conservative age biomarker in conifers, shows a gradual decline of CHG methylation as the age increased, which is highly correlated with its expression profile. Similar high correlation is also observed in nine other age marker genes. Our results suggest that DNA methylation serves as an important epigenetic signature of developmental age in conifers.
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Affiliation(s)
- Jiang Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Fangxu Han
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Tongqi Yuan
- College of Material Science and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Wei Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Yue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, SE-901 83, Umeå, Sweden
- CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT, 2601, Australia
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Shihui Niu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, PR China.
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10
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Jin Y, Wang B, Bao M, Li Y, Xiao S, Wang Y, Zhang J, Zhao L, Zhang H, Hsu YH, Li M, Gu L. Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36794821 DOI: 10.1111/jipb.13468] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Bamboo is one of the fastest growing plants among monocotyledonous species and is grown extensively in subtropical regions. Although bamboo has high economic value and produces much biomass quickly, gene functional research is hindered by the low efficiency of genetic transformation in this species. We therefore explored the potential of a bamboo mosaic virus (BaMV)-mediated expression system to investigate genotype-phenotype associations. We determined that the sites between the triple gene block proteins (TGBps) and the coat protein (CP) of BaMV are the most efficient insertion sites for the expression of exogenous genes in both monopodial and sympodial bamboo species. Moreover, we validated this system by individually overexpressing the two endogenous genes ACE1 and DEC1, which resulted in the promotion and suppression of internode elongation, respectively. In particular, this system was able to drive the expression of three 2A-linked betalain biosynthesis genes (more than 4 kb in length) to produce betalain, indicating that it has high cargo capacity and may provide the prerequisite basis for the development of a DNA-free bamboo genome editing platform in the future. Since BaMV can infect multiple bamboo species, we anticipate that the system described in this study will greatly contribute to gene function research and further promote the molecular breeding of bamboo.
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Affiliation(s)
- Yandong Jin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baijie Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingchuan Bao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yujie Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shengwu Xiao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuhua Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, School of Future Technology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, School of Future Technology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, Chung Hsing University, Taichung, 40227, China
| | - Mingjie Li
- College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, School of Future Technology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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11
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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: 6] [Impact Index Per Article: 6.0] [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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12
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Rao J, Huang Z, Chen Z, Liu H, Zhang X, Cen X, Wang X, Wu J, Miao Y, Ren Y. Identification and expression profiles of xylogen-like arabinogalactan protein (XYLP) gene family in Phyllostachys edulis in different developmental tissues and under various abiotic stresses. Int J Biol Macromol 2023; 227:1098-1118. [PMID: 36462591 DOI: 10.1016/j.ijbiomac.2022.11.290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
Xylogen-like arabinogalactan protein (XYLP) is an atypical lipid transport protein. In this study, 23 Phyllostachys edulis XYLPs were identified, and their proteins contain characteristic structures of AGP and nsLTP domain. All PeXYLPs can be divided into four clades, and their genes were unevenly distributed on 11 chromosome scaffolds. Collinear analysis revealed that segmental duplication was the main driver for PeXYLP family expansion. The cis-acting elements presented in the promoter are involved in various regulations of PeXYLPs expression. G.O. annotation revealed that PeXYLPs are mainly interested in lipid transport and synthesis and primarily function at the plasma membrane. Transcriptome analysis revealed that PeXYLPs were spatiotemporally expressed and displayed significant variability during various tissue development. Besides that, some PeXYLPs also respond to multiple phytohormones and abiotic stresses. By semi-quantitative RT-PCR, the response of some PeXYLPs to MeJA was confirmed, and the proteins were shown to localize to the plasma membrane mainly. WGCNA in defined regions of fast-growing bamboo shoots revealed that 5 PeXYLPs in 4 gene co-expression modules showed a positive module-trait relationship with three fast-growing regions. This systematic analysis of the PeXYLP family will provide a foundation for further insight into the functions of individual PeXYLP in a specific tissue or organ development, phytohormone perception, and stress responses in the future.
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Affiliation(s)
- Jialin Rao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zihong Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxian Chen
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongfei Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoting Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuexiang Cen
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaowei Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yujun Ren
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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13
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Evolutionary Landscape of Tea Circular RNAs and Its Contribution to Chilling Tolerance of Tea Plant. Int J Mol Sci 2023; 24:ijms24021478. [PMID: 36674993 PMCID: PMC9861842 DOI: 10.3390/ijms24021478] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Chilling stress threatens the yield and distribution pattern of global crops, including the tea plant (Camellia sinensis), one of the most important cash crops around the world. Circular RNA (circRNA) plays roles in regulating plant growth and biotic/abiotic stress responses. Understanding the evolutionary characteristics of circRNA and its feedbacks to chilling stress in the tea plant will help to elucidate the vital roles of circRNAs. In the current report, we systematically identified 2702 high-confidence circRNAs under chilling stress in the tea plant, and interestingly found that the generation of tea plant circRNAs was associated with the length of their flanking introns. Repetitive sequences annotation and DNA methylation analysis revealed that the longer flanking introns of circRNAs present more repetitive sequences and higher methylation levels, which suggested that repeat-elements-mediated DNA methylation might promote the circRNAs biogenesis in the tea plant. We further detected 250 differentially expressed circRNAs under chilling stress, which were functionally enriched in GO terms related to cold/stress responses. Constructing a circRNA-miRNA-mRNA interaction network discovered 139 differentially expressed circRNAs harboring potential miRNA binding sites, which further identified 14 circRNAs that might contribute to tea plant chilling responses. We further characterized a key circRNA, CSS-circFAB1, which was significantly induced under chilling stress. FISH and silencing experiments revealed that CSS-circFAB1 was potentially involved in chilling tolerance of the tea plant. Our study emphasizes the importance of circRNA and its preliminary role against low-temperature stress, providing new insights for tea plant cold tolerance breeding.
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14
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Liu R, Ma Y, Guo T, Li G. Identification, biogenesis, function, and mechanism of action of circular RNAs in plants. PLANT COMMUNICATIONS 2023; 4:100430. [PMID: 36081344 PMCID: PMC9860190 DOI: 10.1016/j.xplc.2022.100430] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded, closed RNA molecules with unique functions that are ubiquitously expressed in all eukaryotes. The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals. circRNAs mainly exert their biological functions by acting as microRNA sponges, forming R-loops, interacting with RNA-binding proteins, or being translated into polypeptides or proteins in human and animal cells. Genome-wide identification of circRNAs has been performed in multiple plant species, and the results suggest that circRNAs are abundant and ubiquitously expressed in plants. There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growth and development as well as in the responses to biotic and abiotic stress. However, compared with recent advances in human and animal systems, the roles of most circRNAs in plants are unclear at present. Here we review the identification, biogenesis, function, and mechanism of action of plant circRNAs, which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.
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Affiliation(s)
- Ruiqi Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Yu Ma
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.
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15
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Zhang P, Dai M. CircRNA: a rising star in plant biology. J Genet Genomics 2022; 49:1081-1092. [PMID: 35644325 DOI: 10.1016/j.jgg.2022.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 01/14/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding miRNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and, particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue- or development-specific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circRNA studies.
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Affiliation(s)
- Pei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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16
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Yang Z, Yan H, Wang J, Nie G, Feng G, Xu X, Li D, Huang L, Zhang X. DNA hypermethylation promotes the flowering of orchardgrass during vernalization. PLANT PHYSIOLOGY 2022; 190:1490-1505. [PMID: 35861426 PMCID: PMC9516772 DOI: 10.1093/plphys/kiac335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Vernalization, influenced by environmental factors, is an essential process associated with the productivity of temperate crops, during which epigenetic regulation of gene expression plays an important role. Although DNA methylation is one of the major epigenetic mechanisms associated with the control of gene expression, global changes in DNA methylation in the regulation of gene expression during vernalization-induced flowering of temperate plants remain largely undetermined. To characterize vernalization-associated DNA methylation dynamics, we performed whole-genome bisulfite-treated sequencing and transcriptome sequencing in orchardgrass (Dactylis glomerata) during vernalization. The results revealed that increased levels of genome DNA methylation during the early vernalization of orchardgrass were associated with transcriptional changes in DNA methyltransferase and demethylase genes. Upregulated expression of vernalization-related genes during early vernalization was attributable to an increase in mCHH in the promoter regions of these genes. Application of an exogenous DNA methylation accelerator or overexpression of orchardgrass NUCLEAR POLY(A) POLYMERASE (DgPAPS4) promoted earlier flowering, indicating that DNA hypermethylation plays an important role in vernalization-induced flowering. Collectively, our findings revealed that vernalization-induced hypermethylation is responsible for floral primordium initiation and development. These observations provide a theoretical foundation for further studies on the molecular mechanisms underlying the control of vernalization in temperate grasses.
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Affiliation(s)
| | | | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida 32611, USA
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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17
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Sota T. Life‐cycle control of 13‐ and 17‐year periodical cicadas: A hypothesis and its implication in the evolutionary process. Ecol Res 2022. [DOI: 10.1111/1440-1703.12354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Teiji Sota
- Department of Zoology, Graduate School of Science Kyoto University Kyoto Japan
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18
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Niu LZ, Xu W, Ma PF, Guo ZH, Li DZ. Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos. PLANTA 2022; 256:53. [PMID: 35913571 DOI: 10.1007/s00425-022-03962-8] [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: 01/17/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) of woody bamboos were obviously decreased, which might regulate the internode elongation during rapid shoot growth, while CHH methylation was strongly associated with shoot developmental time or age. DNA methylation plays a critical role in the regulation of plant growth and development. Woody bamboos have a unique trait of rapid stem growth resulted from internode elongation at the shooting period. However, it is still unclear whether DNA methylation significantly controls the bamboo rapid stem growth. Here we present whole-genome DNA methylation profiles of the paleotropical woody bamboo Bonia amplexicaulis at five newly defined stages of shoot growth, named ST1-ST5. We found that CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) were significantly lower than in the incubation (ST1) and plateau stages (ST5). The changes in methylation levels mainly occurred in flanking regions of genes and gene body regions, and 23647 differentially methylated regions (DMRs) were identified between ST1 and rapid shoot growth stages (ST2-ST4). Combined with transcriptome analysis, we found that DMR-related genes enriched in the auxin and jasmonic acid (JA) signal transduction, and other pathways closely related to plant growth. Intriguingly, CHH methylation was not involved in the rapid shoot growth, but strongly associated with shoot developmental time by gradually accumulating in transposable elements (TEs) regions. Overall, our results reveal the importance of DNA methylation in regulating the bamboo rapid shoot growth and suggest a role of DNA methylation associated with development time or age in woody bamboos.
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Affiliation(s)
- Liang-Zhong Niu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution. Int J Mol Sci 2022; 23:ijms23158299. [PMID: 35955429 PMCID: PMC9368846 DOI: 10.3390/ijms23158299] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation.
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20
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Zhang Y, Zhang J, Yang D, Jin Y, Liu X, Zhang Z, Gu L, Zhang H. Genome-Wide Identification of NAP1 and Function Analysis in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2022; 23:ijms23126491. [PMID: 35742936 PMCID: PMC9223780 DOI: 10.3390/ijms23126491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/30/2022] Open
Abstract
The nucleosome assembly protein 1 (NAP1) family is the main histone chaperone of histone H2A–H2B. To explore the function of NAP1 family genes in moso bamboo (Phyllostachys edulis), characterized by extremely rapid growth and a long flowering cycle, we originally conducted a genome-wide analysis of the PheNAP1 gene. The phylogenetic relationship, gene expression pattern, DNA methylation, and histone modification were analyzed. Eventually, 12 PheNAP1 genes were recognized from the Phyllostachys edulis genome, divided into two sorts: the NRP subfamily (four members) and the NAP subfamily (eight members). Highly conserved motifs exist in each subfamily, which are distinct between subfamilies. PheNAP1 was distributed homogeneously on 10 out of 24 chromosomes, and gene duplication contributed significantly to the enhancement of the PheNAP1 gene in the genome. Cis-acting element analysis showed that PheNAP1 family genes are involved in light, hormone, and abiotic stress responses and may play an important role in the rapid growth and flowering. PheNAP1 exhibited the highest expression level in fast-growing shoots, indicating it is closely associated with the rapid growth of moso bamboo. Besides, PheNAP1 can rescue the early-flowering phenotype of nrp1-1 nrp2-2, and it affected the expression of genes related to the flowering pathway, like BSU1, suggesting the vital role that PheNAP1 may take in the flowering process of moso bamboo. In addition, histone modification results showed that PheNAP1 could bind to phosphorylation-, acetylation-, and methylation-modified histones to further regulate gene expression. A sketch appears: that PheNAP1 can accompany histones to regulate fast-growth- and flowering-related genes in moso bamboo. The consequences of this study enrich the understanding of the epigenetic regulation mechanism of bamboo plants and lays a foundation for further studies on the role of the NAP1 gene in Phyllostachys edulis and the function of chromatin regulation in forest growth and development.
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Affiliation(s)
- Yaxing Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.J.); (X.L.); (Z.Z.)
| | - Jun Zhang
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yandong Jin
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.J.); (X.L.); (Z.Z.)
| | - Xuqing Liu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.J.); (X.L.); (Z.Z.)
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.J.); (X.L.); (Z.Z.)
| | - Lianfeng Gu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.J.); (X.L.); (Z.Z.)
- Correspondence: (L.G.); (H.Z.)
| | - Hangxiao Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.J.); (X.L.); (Z.Z.)
- Correspondence: (L.G.); (H.Z.)
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21
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Identification and Characterization of circRNAs under Drought Stress in Moso Bamboo (Phyllostachys edulis). FORESTS 2022. [DOI: 10.3390/f13030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Circular RNAs (circRNAs) are a class of endogenous noncoding RNAs formed by 3′-5′ ligation during splicing. They play an important role in the regulation of transcription and miRNA in eukaryotes. Drought is one of the detrimental abiotic stresses that limit plant growth and productivity. How circRNAs influence the response to drought stress in moso bamboo (Phyllostachys edulis) remains elusive. In this study, we investigate the expression pattern of circRNAs in moso bamboo at 6 h, 12 h, 24 h and 48 h after drought treatment by deep sequencing and bioinformatics analysis and identify 4931 circRNAs, 52 of which are differentially expressed (DEcircRNAs) in drought-treated and untreated moso bamboo. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the host genes that generate the DEcircRNAs indcate that these DEcircRNAs are predicted to be involved in biochemical processes in response to drought, such as ubiquitin-mediated proteolysis, calcium-dependent protein kinase phosphorylation, amino acid biosynthesis and plant hormone signal transduction including abscisic acid. In addition, some circRNAs are shown to act as sponges for 291 miRNAs. Taken together, our results characterize the transcriptome profiles of circRNAs in drought responses and provide new insights into resistance breeding of moso bamboo.
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22
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Simon C, Cooley JR, Karban R, Sota T. Advances in the Evolution and Ecology of 13- and 17-Year Periodical Cicadas. ANNUAL REVIEW OF ENTOMOLOGY 2022; 67:457-482. [PMID: 34623904 DOI: 10.1146/annurev-ento-072121-061108] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Apart from model organisms, 13- and 17-year periodical cicadas (Hemiptera: Cicadidae: Magicicada) are among the most studied insects in evolution and ecology. They are attractive subjects because they predictably emerge in large numbers; have a complex biogeography shaped by both spatial and temporal isolation; and include three largely sympatric, parallel species groups that are, in a sense, evolutionary replicates. Magicicada are also relatively easy to capture and manipulate, and their spectacular, synchronized mass emergences facilitate outreach and citizen science opportunities. Since the last major review, studies of Magicicada have revealed insights into reproductive character displacement and the nature of species boundaries, provided additional examples of allochronic speciation, found evidence for repeated and parallel (but noncontemporaneous) evolution of 13- and 17-year life cycles, quantified the amount and direction of gene flow through time, revealed phylogeographic patterning resulting from paleoclimate change, examined the timing of juvenile development, and created hypotheses for the evolution of life-cycle control and the future effects of climate changeon Magicicada life cycles. New ecological studies have supported and questioned the role of prime numbers in Magicicada ecology and evolution, found bidirectional shifts in population size over generations, quantified the contribution of Magicicada to nutrient flow in forest ecosystems, and examined behavioral and biochemical interactions between Magicicada and their fungal parasites and bacterial endosymbionts.
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Affiliation(s)
- Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269, USA;
| | - John R Cooley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Hartford, Connecticut 06103, USA;
| | - Richard Karban
- Department of Entomology and Nematology, University of California, Davis, California 95616, USA;
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan;
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23
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Comprehensive Analysis of Five Phyllostachys edulis SQUA-like Genes and Their Potential Functions in Flower Development. Int J Mol Sci 2021; 22:ijms221910868. [PMID: 34639205 PMCID: PMC8509223 DOI: 10.3390/ijms221910868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
Bamboo is one of the most important non-timber forest resources worldwide. It has considerable economic value and unique flowering characteristics. The long juvenile phase in bamboo and unpredictable flowering time limit breeding and genetic improvement and seriously affect the productivity and application of bamboo forests. Members of SQUA-like subfamily genes play an essential role in controlling flowering time and floral organ identity. A comprehensive study was conducted to explain the functions of five SQUA-like subfamily genes in Phyllostachys edulis. Expression analysis revealed that all PeSQUAs have higher transcript levels in the reproductive period than in the juvenile phase. However, PeSQUAs showed divergent expression patterns during inflorescence development. The protein–protein interaction (PPI) patterns among PeSQUAs and other MADS-box members were analyzed by yeast two-hybrid (Y2H) experiments. Consistent with amino acid sequence similarity and phylogenetic analysis, the PPI patterns clustered into two groups. PeMADS2, 13, and 41 interacted with multiple PeMADS proteins, whereas PeMADS3 and 28 hardly interacted with other proteins. Based on our results, PeSQUA might possess different functions by forming protein complexes with other MADS-box proteins at different flowering stages. Furthermore, we chose PeMADS2 for functional analysis. Ectopic expression of PeMADS2 in Arabidopsis and rice caused early flowering, and abnormal phenotype was observed in transgenic Arabidopsis lines. RNA-seq analysis indicated that PeMADS2 integrated multiple pathways regulating floral transition to trigger early flowering time in rice. This function might be due to the interaction between PeMADS2 and homologous in rice. Therefore, we concluded that the five SQUA-like genes showed functional conservation and divergence based on sequence differences and were involved in floral transitions by forming protein complexes in P. edulis. The MADS-box protein complex model obtained in the current study will provide crucial insights into the molecular mechanisms of bamboo’s unique flowering characteristics.
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