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Liu M, Wang L, Yu Q, Song J, Zhu L, Jia KH, Qin X. The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 2024; 161:65-78. [PMID: 38108929 DOI: 10.1007/s11120-023-01062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.
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Affiliation(s)
- Menghua Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Longxin Wang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Qianqian Yu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jialin Song
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
- Shandong University of Arts, Jinan, China
| | - Lixia Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
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Xu L, Liu Y, Feng S, Liu C, Zhong X, Ren Y, Liu Y, Huang Y, Yang M. The relationship between atmospheric particulate matter, leaf surface microstructure, and the phyllosphere microbial diversity of Ulmus L. BMC PLANT BIOLOGY 2024; 24:566. [PMID: 38880875 PMCID: PMC11181616 DOI: 10.1186/s12870-024-05232-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/31/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Plants can retain atmospheric particulate matter (PM) through their unique foliar microstructures, which has a profound impact on the phyllosphere microbial communities. Yet, the underlying mechanisms linking atmospheric particulate matter (PM) retention by foliar microstructures to variations in the phyllosphere microbial communities remain a mystery. In this study, we conducted a field experiment with ten Ulmus lines. A series of analytical techniques, including scanning electron microscopy, atomic force microscopy, and high-throughput amplicon sequencing, were applied to examine the relationship between foliar surface microstructures, PM retention, and phyllosphere microbial diversity of Ulmus L. RESULTS We characterized the leaf microstructures across the ten Ulmus lines. Chun exhibited a highly undulated abaxial surface and dense stomatal distribution. Langya and Xingshan possessed dense abaxial trichomes, while Lieye, Zuiweng, and Daguo had sparsely distributed, short abaxial trichomes. Duomai, Qingyun, and Lang were characterized by sparse stomata and flat abaxial surfaces, whereas Jinye had sparsely distributed but extensive stomata. The mean leaf retention values for total suspended particulate (TSP), PM2.5, PM2.5-10, PM10-100, and PM> 100 were 135.76, 6.60, 20.10, 90.98, and 13.08 µg·cm- 2, respectively. Trichomes substantially contributed to PM2.5 retention, while larger undulations enhanced PM2.5-10 retention, as evidenced by positive correlations between PM2.5 and abaxial trichome density and between PM2.5-10 and the adaxial raw microroughness values. Phyllosphere microbial diversity patterns varied among lines, with bacteria dominated by Sediminibacterium and fungi by Mycosphaerella, Alternaria, and Cladosporium. Redundancy analysis confirmed that dense leaf trichomes facilitated the capture of PM2.5-associated fungi, while bacteria were less impacted by PM and struggled to adhere to leaf microstructures. Long and dense trichomes provided ideal microhabitats for retaining PM-borne microbes, as evidenced by positive feedback loops between PM2.5, trichome characteristics, and the relative abundances of microorganisms like Trichoderma and Aspergillus. CONCLUSIONS Based on our findings, a three-factor network profile was constructed, which provides a foundation for further exploration into how different plants retain PM through foliar microstructures, thereby impacting phyllosphere microbial communities.
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Grants
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
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Affiliation(s)
- Liren Xu
- Hebei Agricultural University, Baoding, 071000, Hebei, China
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yichao Liu
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China
| | - Shuxiang Feng
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China
| | - Chong Liu
- Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Xinyu Zhong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yachao Ren
- Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Yujun Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yinran Huang
- Hebei Agricultural University, Baoding, 071000, Hebei, China.
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China.
| | - Minsheng Yang
- Hebei Agricultural University, Baoding, 071000, Hebei, China.
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Ye H, Wang Y, Liu H, Lei D, Li H, Gao Z, Feng X, Han M, Qie Q, Zhou H. The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1334. [PMID: 38794406 PMCID: PMC11125379 DOI: 10.3390/plants13101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.
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Affiliation(s)
- Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yiling Wang
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Dingfan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Haochen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhimei Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaolong Feng
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Mian Han
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Qiyang Qie
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, China
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Bornhofen E, Fè D, Nagy I, Lenk I, Greve M, Didion T, Jensen CS, Asp T, Janss L. Genetic architecture of inter-specific and -generic grass hybrids by network analysis on multi-omics data. BMC Genomics 2023; 24:213. [PMID: 37095447 PMCID: PMC10127077 DOI: 10.1186/s12864-023-09292-7] [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: 01/10/2023] [Accepted: 04/02/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Understanding the mechanisms underlining forage production and its biomass nutritive quality at the omics level is crucial for boosting the output of high-quality dry matter per unit of land. Despite the advent of multiple omics integration for the study of biological systems in major crops, investigations on forage species are still scarce. RESULTS Our results identified substantial changes in gene co-expression and metabolite-metabolite network topologies as a result of genetic perturbation by hybridizing L. perenne with another species within the genus (L. multiflorum) relative to across genera (F. pratensis). However, conserved hub genes and hub metabolomic features were detected between pedigree classes, some of which were highly heritable and displayed one or more significant edges with agronomic traits in a weighted omics-phenotype network. In spite of tagging relevant biological molecules as, for example, the light-induced rice 1 (LIR1), hub features were not necessarily better explanatory variables for omics-assisted prediction than features stochastically sampled and all available regressors. CONCLUSIONS The utilization of computational techniques for the reconstruction of co-expression networks facilitates the identification of key omic features that serve as central nodes and demonstrate correlation with the manifestation of observed traits. Our results also indicate a robust association between early multi-omic traits measured in a greenhouse setting and phenotypic traits evaluated under field conditions.
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Affiliation(s)
- Elesandro Bornhofen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
| | - Dario Fè
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Ingo Lenk
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Morten Greve
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Thomas Didion
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
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Zhang L, Xie S, Yang C, Cao D, Fan S, Zhang X. Comparative Transcriptome Analysis Reveals Candidate Genes and Pathways for Potential Branch Growth in Elm ( Ulmus pumila) Cultivars. BIOLOGY 2022; 11:711. [PMID: 35625439 PMCID: PMC9139171 DOI: 10.3390/biology11050711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022]
Abstract
Wood plays a vital role in human life. It is important to study the thickening mechanism of tree branches and explore the mechanism of wood formation. Elm (Ulmus pumila) is a strong essential wood, and it is widely used in cabinets, sculptures, and ship making. In the present study, phenotypic and comparative transcriptomic analyses were performed in U. pumila fast- (UGu17 and UZuantian) and slow-growing cultivars (U81-07 and U82-39). Phenotypic observation showed that the thickness of secondary xylem of 2-year-old fast-growing branches was greater compared with slow-growing cultivars. A total of 9367 (up = 4363, down = 5004), 7159 (3413/3746), 7436 (3566/3870), and 5707 (2719/2988) differentially expressed genes (DEGs) were identified between fast- and slow-growing cultivars. Moreover, GO and KEGG enrichment analyses predicted that many pathways were involved in vascular development and transcriptional regulation in elm, such as "plant-type secondary cell wall biogenesis", "cell wall thickening", and "phenylpropanoid biosynthesis". NAC domain transcriptional factors (TFs) and their master regulators (VND1/MYB26), cellulose synthase catalytic subunits (CESAs) (such as IRX5/IRX3/IRX1), xylan synthesis, and secondary wall thickness (such as IRX9/IRX10/IRX8) were supposed to function in the thickening mechanism of elm branches. Our results indicated that the general phenylpropanoid pathway (such as PAL/C4H/4CL) and lignin metabolism (such as HCL/CSE/CCoAOMT/CCR/F5H) had vital functions in the growth of elm branches. Our transcriptome data were consistent with molecular results for branch thickening in elm cultivars.
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Affiliation(s)
| | | | | | | | - Shoujin Fan
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, China; (L.Z.); (S.X.); (C.Y.); (D.C.)
| | - Xuejie Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, China; (L.Z.); (S.X.); (C.Y.); (D.C.)
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Zahra N, Al Hinai MS, Hafeez MB, Rehman A, Wahid A, Siddique KHM, Farooq M. Regulation of photosynthesis under salt stress and associated tolerance mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:55-69. [PMID: 35276596 DOI: 10.1016/j.plaphy.2022.03.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/12/2022] [Accepted: 03/03/2022] [Indexed: 05/24/2023]
Abstract
Photosynthesis is crucial for the survival of all living biota, playing a key role in plant productivity by generating the carbon skeleton that is the primary component of all biomolecules. Salinity stress is a major threat to agricultural productivity and sustainability as it can cause irreversible damage to photosynthetic apparatus at any developmental stage. However, the capacity of plants to become photosynthetically active under adverse saline conditions remains largely untapped. This study addresses this discrepancy by exploring the current knowledge on the impact of salinity on chloroplast operation, metabolism, chloroplast ultrastructure, and leaf anatomy, and highlights the dire consequences for photosynthetic machinery and stomatal conductance. We also discuss enhancing photosynthetic capacity by modifying and redistributing electron transport between photosystems and improving photosystem stability using genetic approaches, beneficial microbial inoculations, and root architecture changes to improve salt stress tolerance under field conditions. Understanding chloroplast operations and molecular engineering of photosynthetic genes under salinity stress will pave the way for developing salt-tolerant germplasm to ensure future sustainability by rehabilitating saline areas.
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Affiliation(s)
- Noreen Zahra
- Department of Botany, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Marwa Sulaiman Al Hinai
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Oman
| | | | - Abdul Rehman
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, 63100, Bahawalpur, Pakistan
| | - Abdul Wahid
- Department of Botany, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Muhammad Farooq
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Oman; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia.
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