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Wang Y, Li X, Wang C, Gao L, Wu Y, Ni X, Sun J, Jiang J. Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms. BMC Genomics 2021; 22:690. [PMID: 34551715 PMCID: PMC8459517 DOI: 10.1186/s12864-021-07971-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement. Results In this study, through analyzing the transcriptome of mixed samples of leaves and stems using the latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report the first full-length transcriptome dataset of M. sinensis with a total of 58.21 Gb clean data. An average of 15.75 Gb clean reads of each sample were obtained from the PacBio Iso-Seq system, which doubled the data size (6.68 Gb) obtained from the Illumina HiSeq platform. The integrated analyses of PacBio- and Illumina-based transcriptomic data uncovered 408,801 non-redundant transcripts with an average length of 1,685 bp. Of those, 189,406 transcripts were commonly identified by both methods, 169,149 transcripts with an average length of 619 bp were uniquely identified by Illumina HiSeq, and 51,246 transcripts with an average length of 2,535 bp were uniquely identified by PacBio Iso-Seq. Approximately 96 % of the final combined transcripts were mapped back to the Miscanthus genome, reflecting the high quality and coverage of our sequencing results. When comparing our data with genomes of four species of Andropogoneae, M. sinensis showed the closest relationship with sugarcane with up to 93 % mapping ratios, followed by sorghum with up to 80 % mapping ratios, indicating a high conservation of orthologs in these three genomes. Furthermore, 306,228 transcripts were successfully annotated against public databases including cell wall related genes and transcript factor families, thus providing many new insights into gene functions. The PacBio Iso-Seq data also helped identify 3,898 alternative splicing events and 2,963 annotated AS isoforms within 10 function categories. Conclusions Taken together, the present study provides a rich data set of full-length transcripts that greatly enriches our understanding of M. sinensis transcriptomic resources, thus facilitating further genetic improvement and molecular studies of the Miscanthus species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07971-x.
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Affiliation(s)
- Yongli Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Xia Li
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Congsheng Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Lu Gao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Yanfang Wu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Xingnan Ni
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China.
| | - Jianxiong Jiang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China.
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Huang CL, Sarkar R, Hsu TW, Yang CF, Chien CH, Chang WC, Chiang TY. Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients. MICROBIAL ECOLOGY 2020; 80:133-144. [PMID: 31832698 DOI: 10.1007/s00248-019-01467-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.
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Affiliation(s)
- Chao-Li Huang
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Rakesh Sarkar
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, 55244, Taiwan
| | - Chia-Fen Yang
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chia-Hung Chien
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
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3
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Wei L, You W, Gong Y, El Hajjami M, Liang W, Xu J, Poetsch A. Transcriptomic and proteomic choreography in response to light quality variation reveals key adaption mechanisms in marine Nannochloropsis oceanica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137667. [PMID: 32325597 DOI: 10.1016/j.scitotenv.2020.137667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/04/2020] [Accepted: 02/29/2020] [Indexed: 06/11/2023]
Abstract
Photosynthetic organisms need to respond frequently to the fluctuation of light quality and light quantity in their habitat. In response to the fluctuation of different single wavelength lights, these organisms have to adjust and optimize the employment of light energy by redistributing excitation energy and remodeling photosystem stoichiometry or light complex structure. However, the response of whole cellular processes to fluctuations in single wavelength light is mostly unknown. Here, we report the transcriptomic and proteomic dynamics and metabolic adaptation mechanisms of Nannochloropsis oceanica to blue and red light. Preferential exposure to different light spectra induces massive reprogramming of the Nannochloropsis transcriptome and proteome. Combined with physiological and biochemical investigation, the rewiring of many cellular processes was observed, including carbon/nitrogen assimilation, photosynthesis, chlorophyll and cartenoid biosynthesis, reactive oxygen species (ROS) scavenging systems, and chromatin state regulation. A strong and rapid regulation of genes or proteins related to nitrogen metabolism, photosynthesis, chlorophyll synthesis, ROS scavenging system, and carotenoid metabolism were observed during 12 h and 24 h of exposure under red light. Additionally, two light harvesting complex proteins induced by blue light and one by red light were observed. The differential responses of N. oceanica to red and blue irradiation reveal how marine microalgae adapt to change in light quality and can be exploited for biofuel feedstock development.
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Affiliation(s)
- Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wuxin You
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Mohamed El Hajjami
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Wensi Liang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ansgar Poetsch
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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4
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Hager HA, Ryan GD, Newman JA. Effects of elevated CO 2 on competition between native and invasive grasses. Oecologia 2020; 192:1099-1110. [PMID: 32253494 DOI: 10.1007/s00442-020-04636-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/30/2020] [Indexed: 11/24/2022]
Abstract
Elevated atmospheric CO2 concentration increases the performance of invasive plants relative to natives when grown in monoculture, but it is unclear how that will affect the relative competitive abilities per se of invasive and native grasses grown together. We tested competitive outcomes for four native and four invasive perennial C3 and C4 grasses under ambient (390 ppm) and elevated (700 or 1000 ppm) CO2 concentrations in the greenhouse with non-limiting water and nutrients. We predicted that elevated CO2 would increase the competitive suppression of native grasses by invasive grasses. To test this, we determined the relative interaction intensity of biomass allocation for natives grown alone vs. those grown in native-invasive species pairs. We also measured photosynthetic traits that contribute to plant invasiveness and may be affected by elevated CO2 concentrations for species pairs in mixture to determine native-invasive relative performance. We found no effect of CO2 for the aboveground biomass and tiller production measures of interaction intensity or for relative performance for most of the measured photosynthetic traits. In competition, the invaders nearly always outperform natives in biomass and tiller production, regardless of CO2 level. The results suggest that increasing CO2 concentration alone has little effect on grass competitive outcomes under controlled conditions.
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Affiliation(s)
- Heather A Hager
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada. .,Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada.
| | - Geraldine D Ryan
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jonathan A Newman
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
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5
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Hendron RW, Kelly S. Subdivision of Light Signaling Networks Contributes to Partitioning of C 4 Photosynthesis. PLANT PHYSIOLOGY 2020; 182:1297-1309. [PMID: 31862840 PMCID: PMC7054874 DOI: 10.1104/pp.19.01053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/04/2019] [Indexed: 05/29/2023]
Abstract
Plants coordinate the expression of photosynthesis-related genes in response to growth and environmental changes. In species that conduct two-cell C4 photosynthesis, expression of photosynthesis genes is partitioned such that leaf mesophyll and bundle sheath cells accumulate different components of the photosynthetic pathway. The identities of the regulatory networks that facilitate this partitioning are unknown. Here, we show that differences in light perception between mesophyll and bundle sheath cells facilitate differential regulation and accumulation of photosynthesis gene transcripts in the C4 crop maize (Zea mays). Key components of the photosynthesis gene regulatory network differentially accumulated between mesophyll and bundle sheath cells, indicative of differential network activity across cell types. We further show that blue (but not red) light is necessary and sufficient to activate photosystem II assembly in mesophyll cells in etiolated maize. Finally, we demonstrate that 61% of all light-induced mesophyll and bundle sheath genes were induced only by blue light or only by red light, but not both. These findings provide evidence that subdivision of light signaling networks is a component of cellular partitioning of C4 photosynthesis in maize.
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Affiliation(s)
- Ross-W Hendron
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
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6
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Giuliani R, Karki S, Covshoff S, Lin HC, Coe RA, Koteyeva NK, Evans MA, Quick WP, von Caemmerer S, Furbank RT, Hibberd JM, Edwards GE, Cousins AB. Transgenic maize phosphoenolpyruvate carboxylase alters leaf-atmosphere CO 2 and 13CO 2 exchanges in Oryza sativa. PHOTOSYNTHESIS RESEARCH 2019; 142:153-167. [PMID: 31325077 PMCID: PMC6848035 DOI: 10.1007/s11120-019-00655-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 06/11/2019] [Indexed: 05/07/2023]
Abstract
The engineering process of C4 photosynthesis into C3 plants requires an increased activity of phosphoenolpyruvate carboxylase (PEPC) in the cytosol of leaf mesophyll cells. The literature varies on the physiological effect of transgenic maize (Zea mays) PEPC (ZmPEPC) leaf expression in Oryza sativa (rice). Therefore, to address this issue, leaf-atmosphere CO2 and 13CO2 exchanges were measured, both in the light (at atmospheric O2 partial pressure of 1.84 kPa and at different CO2 levels) and in the dark, in transgenic rice expressing ZmPEPC and wild-type (WT) plants. The in vitro PEPC activity was 25 times higher in the PEPC overexpressing (PEPC-OE) plants (~20% of maize) compared to the negligible activity in WT. In the PEPC-OE plants, the estimated fraction of carboxylation by PEPC (β) was ~6% and leaf net biochemical discrimination against 13CO2[Formula: see text] was ~ 2‰ lower than in WT. However, there were no differences in leaf net CO2 assimilation rates (A) between genotypes, while the leaf dark respiration rates (Rd) over three hours after light-dark transition were enhanced (~ 30%) and with a higher 13C composition [Formula: see text] in the PEPC-OE plants compared to WT. These data indicate that ZmPEPC in the PEPC-OE rice plants contributes to leaf carbon metabolism in both the light and in the dark. However, there are some factors, potentially posttranslational regulation and PEP availability, which reduce ZmPEPC activity in vivo.
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Affiliation(s)
- Rita Giuliani
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Shanta Karki
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Hsiang-Chun Lin
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Robert A Coe
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Nuria K Koteyeva
- Laboratory of Anatomy and Morphology, V.L. Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov Street 2, St. Petersburg, Russia, 197376
| | - Marc A Evans
- Department of Mathematics and Statistics, Washington State University, Pullman, WA, 99164-3113, USA
| | - W Paul Quick
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Susanne von Caemmerer
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Robert T Furbank
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Gerald E Edwards
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Asaph B Cousins
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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7
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Bellasio C, Farquhar GD. A leaf-level biochemical model simulating the introduction of C 2 and C 4 photosynthesis in C 3 rice: gains, losses and metabolite fluxes. THE NEW PHYTOLOGIST 2019; 223:150-166. [PMID: 30859576 DOI: 10.1111/nph.15787] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/03/2019] [Indexed: 05/21/2023]
Abstract
This work aims at developing an adequate theoretical basis for comparing assimilation of the ancestral C3 pathway with CO2 concentrating mechanisms (CCM) that have evolved to reduce photorespiratory yield losses. We present a novel model for C3 , C2 , C2 + C4 and C4 photosynthesis simulating assimilatory metabolism, energetics and metabolite traffic at the leaf level. It integrates a mechanistic description of light reactions to simulate ATP and NADPH production, and a variable engagement of cyclic electron flow. The analytical solutions are compact and thus suitable for larger scale simulations. Inputs were derived with a comprehensive gas-exchange experiment. We show trade-offs in the operation of C4 that are in line with ecophysiological data. C4 has the potential to increase assimilation over C3 at high temperatures and light intensities, but this benefit is reversed under low temperatures and light. We apply the model to simulate the introduction of progressively complex levels of CCM into C3 rice, which feeds > 3.5 billion people. Increasing assimilation will require considerable modifications such as expressing the NAD(P)H Dehydrogenase-like complex and upregulating cyclic electron flow, enlarging the bundle sheath, and expressing suitable transporters to allow adequate metabolite traffic. The simpler C2 rice may be a desirable alternative.
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Affiliation(s)
- Chandra Bellasio
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
- University of the Balearic Islands, Palma, Illes Balears, 07122, Spain
- Trees and Timber Institute, National Research Council of Italy, Sesto Fiorentino, Florence, 50019, Italy
| | - Graham D Farquhar
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
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8
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Giuliani R, Karki S, Covshoff S, Lin HC, Coe RA, Koteyeva NK, Quick WP, Von Caemmerer S, Furbank RT, Hibberd JM, Edwards GE, Cousins AB. Knockdown of glycine decarboxylase complex alters photorespiratory carbon isotope fractionation in Oryza sativa leaves. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2773-2786. [PMID: 30840760 PMCID: PMC6506765 DOI: 10.1093/jxb/erz083] [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: 10/23/2018] [Accepted: 02/12/2019] [Indexed: 05/07/2023]
Abstract
The influence of reduced glycine decarboxylase complex (GDC) activity on leaf atmosphere CO2 and 13CO2 exchange was tested in transgenic Oryza sativa with the GDC H-subunit knocked down in leaf mesophyll cells. Leaf measurements on transgenic gdch knockdown and wild-type plants were carried out in the light under photorespiratory and low photorespiratory conditions (i.e. 18.4 kPa and 1.84 kPa atmospheric O2 partial pressure, respectively), and in the dark. Under approximately current ambient O2 partial pressure (18.4 kPa pO2), the gdch knockdown plants showed an expected photorespiratory-deficient phenotype, with lower leaf net CO2 assimilation rates (A) than the wild-type. Additionally, under these conditions, the gdch knockdown plants had greater leaf net discrimination against 13CO2 (Δo) than the wild-type. This difference in Δo was in part due to lower 13C photorespiratory fractionation (f) ascribed to alternative decarboxylation of photorespiratory intermediates. Furthermore, the leaf dark respiration rate (Rd) was enhanced and the 13CO2 composition of respired CO2 (δ13CRd) showed a tendency to be more depleted in the gdch knockdown plants. These changes in Rd and δ13CRd were due to the amount and carbon isotopic composition of substrates available for dark respiration. These results demonstrate that impairment of the photorespiratory pathway affects leaf 13CO2 exchange, particularly the 13C decarboxylation fractionation associated with photorespiration.
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Affiliation(s)
- Rita Giuliani
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Shanta Karki
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hsiang-Chun Lin
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Robert A Coe
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Nuria K Koteyeva
- Laboratory of Anatomy and Morphology, V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - W Paul Quick
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Susanne Von Caemmerer
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Robert T Furbank
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Gerald E Edwards
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Asaph B Cousins
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
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9
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Ellsworth PV, Ellsworth PZ, Koteyeva NK, Cousins AB. Cell wall properties in Oryza sativa influence mesophyll CO 2 conductance. THE NEW PHYTOLOGIST 2018; 219:66-76. [PMID: 29676468 DOI: 10.1111/nph.15173] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/18/2018] [Indexed: 06/08/2023]
Abstract
Diffusion of CO2 from the leaf intercellular air space to the site of carboxylation (gm ) is a potential trait for increasing net rates of CO2 assimilation (Anet ), photosynthetic efficiency, and crop productivity. Leaf anatomy plays a key role in this process; however, there are few investigations into how cell wall properties impact gm and Anet . Online carbon isotope discrimination was used to determine gm and Anet in Oryza sativa wild-type (WT) plants and mutants with disruptions in cell wall mixed-linkage glucan (MLG) production (CslF6 knockouts) under high- and low-light growth conditions. Cell wall thickness (Tcw ), surface area of chloroplast exposed to intercellular air spaces (Sc ), leaf dry mass per area (LMA), effective porosity, and other leaf anatomical traits were also analyzed. The gm of CslF6 mutants decreased by 83% relative to the WT, with c. 28% of the reduction in gm explained by Sc . Although Anet /LMA and Anet /Chl partially explained differences in Anet between genotypes, the change in cell wall properties influenced the diffusivity and availability of CO2 . The data presented here indicate that the loss of MLG in CslF6 plants had an impact on gm and demonstrate the importance of cell wall effective porosity and liquid path length on gm .
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Affiliation(s)
- Patrícia V Ellsworth
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Patrick Z Ellsworth
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Nuria K Koteyeva
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
- Laboratory of Anatomy and Morphology, V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St Petersburg, 197376, Russia
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
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10
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Transcriptomics and proteomics reveal genetic and biological basis of superior biomass crop Miscanthus. Sci Rep 2017; 7:13777. [PMID: 29062090 PMCID: PMC5653860 DOI: 10.1038/s41598-017-14151-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/05/2017] [Indexed: 12/18/2022] Open
Abstract
Miscanthus is a rhizomatous C4 grass which is considered as potential high-yielding energy crop with the low-nutrient requirements, high water-use efficiency, and capability of C mitigation. To better understand the genetic basis, an integrative analysis of the transcriptome and proteome was performed to identify important genes and pathways involved in Miscanthus leaves. At the transcript level, 64,663 transcripts in M. lutarioriparius, 97,043 in M. sacchariflorus, 97,043 in M. sinensis, 67,323 in M. floridulus and 70,021 in M. × giganteus were detected by an RNA sequencing approach. At the protein level, 1964 peptide-represented proteins were identified and 1933 proteins differed by 1.5-fold or more in their relative abundance, as indicated by iTRAQ (isobaric tags for relative and absolute quantitation) analysis. Phylogenies were constructed from the nearly taxa of Miscanthus. A large number of genes closely related to biomass production were found. And SSR markers and their corresponding primers were derived from Miscanthus transcripts and 90% of them were successfully detected by PCR amplification among Miacanthus species. These similarities and variations on the transcriptional and proteomic level between Miscanthus species will serve as a resource for research in Miscanthus and other lignocellulose crops.
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11
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Ma JY, Sun W, Koteyeva NK, Voznesenskaya E, Stutz SS, Gandin A, Smith-Moritz AM, Heazlewood JL, Cousins AB. Influence of light and nitrogen on the photosynthetic efficiency in the C 4 plant Miscanthus × giganteus. PHOTOSYNTHESIS RESEARCH 2017; 131:1-13. [PMID: 27531584 DOI: 10.1007/s11120-016-0281-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 05/26/2016] [Indexed: 06/06/2023]
Abstract
There are numerous studies describing how growth conditions influence the efficiency of C4 photosynthesis. However, it remains unclear how changes in the biochemical capacity versus leaf anatomy drives this acclimation. Therefore, the aim of this study was to determine how growth light and nitrogen availability influence leaf anatomy, biochemistry and the efficiency of the CO2 concentrating mechanism in Miscanthus × giganteus. There was an increase in the mesophyll cell wall surface area but not cell well thickness in the high-light (HL) compared to the low-light (LL) grown plants suggesting a higher mesophyll conductance in the HL plants, which also had greater photosynthetic capacity. Additionally, the HL plants had greater surface area and thickness of bundle-sheath cell walls compared to LL plants, suggesting limited differences in bundle-sheath CO2 conductance because the increased area was offset by thicker cell walls. The gas exchange estimates of phosphoenolpyruvate carboxylase (PEPc) activity were significantly less than the in vitro PEPc activity, suggesting limited substrate availability in the leaf due to low mesophyll CO2 conductance. Finally, leakiness was similar across all growth conditions and generally did not change under the different measurement light conditions. However, differences in the stable isotope composition of leaf material did not correlate with leakiness indicating that dry matter isotope measurements are not a good proxy for leakiness. Taken together, these data suggest that the CO2 concentrating mechanism in Miscanthus is robust under low-light and limited nitrogen growth conditions, and that the observed changes in leaf anatomy and biochemistry likely help to maintain this efficiency.
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Affiliation(s)
- Jian-Ying Ma
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- School of Biological Science, Washington State University, Pullman, WA, 99163, USA
| | - Wei Sun
- School of Biological Science, Washington State University, Pullman, WA, 99163, USA
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Nuria K Koteyeva
- Laboratory of Anatomy and Morphology, V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Elena Voznesenskaya
- Laboratory of Anatomy and Morphology, V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Samantha S Stutz
- School of Biological Science, Washington State University, Pullman, WA, 99163, USA
| | - Anthony Gandin
- School of Biological Science, Washington State University, Pullman, WA, 99163, USA
| | - Andreia M Smith-Moritz
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Asaph B Cousins
- School of Biological Science, Washington State University, Pullman, WA, 99163, USA.
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12
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Ellsworth PZ, Cousins AB. Carbon isotopes and water use efficiency in C4 plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:155-61. [PMID: 27155062 DOI: 10.1016/j.pbi.2016.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/07/2016] [Accepted: 04/14/2016] [Indexed: 05/13/2023]
Abstract
Drought is a major agricultural problem worldwide. Therefore, selection for increased water use efficiency (WUE) in food and biofuel crop species will be an important trait in plant breeding programs. The leaf carbon isotopic composition (δ(13)Cleaf) has been suggested to serve as a rapid and effective high throughput phenotyping method for WUE in both C3 and C4 species. This is because WUE, leaf carbon discrimination (Δ(13)Cleaf), and δ(13)Cleaf are correlated through their relationships with intercellular to ambient CO2 partial pressures (Ci/Ca). However, in C4 plants, changing environmental conditions may influence photosynthetic efficiency (bundle-sheath leakiness) and post-photosynthetic fractionation that will potentially alter the relationship between δ(13)Cleaf and Ci/Ca. Here we discuss how these factors influence the relationship between δ(13)Cleaf and WUE, and the potential of using δ(13)Cleaf as a meaningful proxy for WUE.
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Affiliation(s)
| | - Asaph B Cousins
- Washington State University, Pullman, WA 99163, United States.
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13
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Xing S, Kang L, Xu Q, Fan Y, Liu W, Zhu C, Song Z, Wang Q, Yan J, Li J, Sang T. The Coordination of Gene Expression within Photosynthesis Pathway for Acclimation of C4 Energy Crop Miscanthus lutarioriparius. FRONTIERS IN PLANT SCIENCE 2016; 7:109. [PMID: 26904072 PMCID: PMC4746358 DOI: 10.3389/fpls.2016.00109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/21/2016] [Indexed: 05/27/2023]
Abstract
As a promising candidate for the second-generation C4 energy crop, Miscanthus lutarioriparius has well acclimated to the water-limited and high-light Loess Plateau in China by improving photosynthesis rate and water use efficiency (WUE) compared to its native habitat along Yangtze River. Photosynthetic genes were demonstrated as one major category of the candidate genes underlying the physiological superiority. To further study how photosynthetic genes interact to improve the acclimation potential of M. lutarioriparius, population expression patterns within photosynthesis pathway were explored between one mild environment and one harsh environment. We found that 108 transcripts in assembled transcriptome of M. lutarioriparius were highly similar to genes in three Kyoto Encyclopedia of Genes and Genomes (KEGG) photosynthesis pathways of sorghum and maize. Phylogenetic analyses using sorghum, maize, rice, and Arabidopsis genes of dark reaction identified 23 orthologs and 30 paralogs of M. lutarioriparius photosynthetic genes. These genes were also clustered into two kinds of expression pattern. 87% of transcripts in dark reaction were up-regulated and all 14 chloroplast-encoded transcripts in light reaction increased degradation in the harsh environment compared to the mild environment. Moreover, 80.8% of photosynthetic transcripts were coordinated at transcription level under the two environments. Interestingly, LHCI and PSI were significantly correlated with F-ATPase and C4 cycle. Overall, this study indicates the coordinated expression between cyclic electron transport (consisting of LHCI, PSI, and ATPase) and CO2-concentrating mechanism (C4 cycle) could account for photosynthesis plasticity on M. lutarioriparius acclimation potential.
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Affiliation(s)
- Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Lifang Kang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Qin Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Yangyang Fan
- University of Chinese Academy of SciencesBeijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Wei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Caiyun Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Zhihong Song
- University of Chinese Academy of SciencesBeijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Qian Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Jianqiang Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Tao Sang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
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Kromdijk J, Ubierna N, Cousins AB, Griffiths H. Bundle-sheath leakiness in C4 photosynthesis: a careful balancing act between CO2 concentration and assimilation. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3443-57. [PMID: 24755278 DOI: 10.1093/jxb/eru157] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Crop species with the C4 photosynthetic pathway are generally characterized by high productivity, especially in environmental conditions favouring photorespiration. In comparison with the ancestral C3 pathway, the biochemical and anatomical modifications of the C4 pathway allow spatial separation of primary carbon acquisition in mesophyll cells and subsequent assimilation in bundle-sheath cells. The CO2-concentrating C4 cycle has to operate in close coordination with CO2 reduction via the Calvin-Benson-Bassham (CBB) cycle in order to keep the C4 pathway energetically efficient. The gradient in CO2 concentration between bundle-sheath and mesophyll cells facilitates diffusive leakage of CO2. This rate of bundle-sheath CO2 leakage relative to the rate of phosphoenolpyruvate carboxylation (termed leakiness) has been used to probe the balance between C4 carbon acquisition and subsequent reduction as a result of environmental perturbations. When doing so, the correct choice of equations to derive leakiness from stable carbon isotope discrimination (Δ(13)C) during gas exchange is critical to avoid biased results. Leakiness responses to photon flux density, either short-term (during measurements) or long-term (during growth and development), can have important implications for C4 performance in understorey light conditions. However, recent reports show leakiness to be subject to considerable acclimation. Additionally, the recent discovery of two decarboxylating C4 cycles operating in parallel in Zea mays suggests that flexibility in the transported C4 acid and associated decarboxylase could also aid in maintaining C4/CBB balance in a changing environment. In this paper, we review improvements in methodology to estimate leakiness, synthesize reports on bundle-sheath leakiness, discuss different interpretations, and highlight areas where future research is necessary.
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Affiliation(s)
- Johannes Kromdijk
- Institute for Genomic Biology, University of Illinois, 1206W Gregory drive, Urbana, IL 61801, USA
| | - Nerea Ubierna
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA99164-4236, USA
| | - Howard Griffiths
- Physiological Ecology Group, Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB23EA, UK
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