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Gao S, Zhao W, Li X, You Q, Shen X, Guo W, Wang S, Shi G, Liu Z, Jiao Y. Identification and characterization of miRNAs in two closely related C 4 and C 3 species of Cleome by high-throughput sequencing. Sci Rep 2017; 7:46552. [PMID: 28422166 PMCID: PMC5396198 DOI: 10.1038/srep46552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/17/2017] [Indexed: 01/14/2023] Open
Abstract
Cleome gynandra and Cleome hassleriana, which are C4 and C3 plants, respectively, are two species of Cleome. The close genetic relationship between C. gynandra and C. hassleriana provides advantages for discovering the differences in leaf development and physiological processes between C3 and C4 plants. MicroRNAs (miRNAs) are a class of important regulators of various biological processes. In this study, we investigate the differences in the characteristics of miRNAs between C. gynandra and C. hassleriana using high-throughput sequencing technology. In total, 94 and 102 known miRNAs were identified in C. gynandra and C. hassleriana, respectively, of which 3 were specific for C. gynandra and 10 were specific for C. hassleriana. Ninety-one common miRNAs were identified in both species. In addition, 4 novel miRNAs were detected, including three in C. gynandra and three in C. hassleriana. Of these miRNAs, 67 were significantly differentially expressed between these two species and were involved in extensive biological processes, such as glycol-metabolism and photosynthesis. Our study not only provided resources for C. gynandra and C. hassleriana research but also provided useful clues for the understanding of the roles of miRNAs in the alterations of biological processes in leaf tissues during the evolution of the C4 pathway.
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Affiliation(s)
- Shuangcheng Gao
- College of Agriculture, Henan University of Science and Technology, Luoyang, Henan Province, 471003, P. R. China
| | - Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P. R. China
| | - Xiang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P. R. China
| | - Qingbo You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P. R. China
| | - Xinjie Shen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P. R. China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P. R. China
| | - Shihua Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang, Henan Province, 471003, P. R. China
| | - Guoan Shi
- College of Agriculture, Henan University of Science and Technology, Luoyang, Henan Province, 471003, P. R. China
| | - Zheng Liu
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, P. R. China
| | - Yongqing Jiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, P. R. China
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Kagale S, Robinson SJ, Nixon J, Xiao R, Huebert T, Condie J, Kessler D, Clarke WE, Edger PP, Links MG, Sharpe AG, Parkin IAP. Polyploid evolution of the Brassicaceae during the Cenozoic era. Plant Cell 2014; 26:2777-91. [PMID: 25035408 PMCID: PMC4145113 DOI: 10.1105/tpc.114.126391] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/07/2014] [Accepted: 06/19/2014] [Indexed: 05/18/2023]
Abstract
The Brassicaceae (Cruciferae) family, owing to its remarkable species, genetic, and physiological diversity as well as its significant economic potential, has become a model for polyploidy and evolutionary studies. Utilizing extensive transcriptome pyrosequencing of diverse taxa, we established a resolved phylogeny of a subset of crucifer species. We elucidated the frequency, age, and phylogenetic position of polyploidy and lineage separation events that have marked the evolutionary history of the Brassicaceae. Besides the well-known ancient α (47 million years ago [Mya]) and β (124 Mya) paleopolyploidy events, several species were shown to have undergone a further more recent (∼7 to 12 Mya) round of genome multiplication. We identified eight whole-genome duplications corresponding to at least five independent neo/mesopolyploidy events. Although the Brassicaceae family evolved from other eudicots at the beginning of the Cenozoic era of the Earth (60 Mya), major diversification occurred only during the Neogene period (0 to 23 Mya). Remarkably, the widespread species divergence, major polyploidy, and lineage separation events during Brassicaceae evolution are clustered in time around epoch transitions characterized by prolonged unstable climatic conditions. The synchronized diversification of Brassicaceae species suggests that polyploid events may have conferred higher adaptability and increased tolerance toward the drastically changing global environment, thus facilitating species radiation.
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Affiliation(s)
- Sateesh Kagale
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | | | - John Nixon
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Rong Xiao
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Terry Huebert
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | - Dallas Kessler
- Plant Gene Resources of Canada, Saskatoon SK S7N 0X2, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Matthew G Links
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
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Koteyeva NK, Voznesenskaya EV, Roalson EH, Edwards GE. Diversity in forms of C4 in the genus Cleome (Cleomaceae). Ann Bot 2011; 107:269-83. [PMID: 21147832 PMCID: PMC3025737 DOI: 10.1093/aob/mcq239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/31/2010] [Accepted: 11/11/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Cleomaceae is one of 19 angiosperm families in which C(4) photosynthesis has been reported. The aim of the study was to determine the type, and diversity, of structural and functional forms of C(4) in genus Cleome. Methods Plants of Cleome species were grown from seeds, and leaves were subjected to carbon isotope analysis, light and scanning electron microscopy, western blot analysis of proteins, and in situ immunolocalization for ribulose bisphosphate carboxylase oxygenase (Rubisco) and phosphoenolpyruvate carboxylase (PEPC). KEY RESULTS Three species with C(4)-type carbon isotope values occurring in separate lineages in the genus (Cleome angustifolia, C. gynandra and C. oxalidea) were shown to have features of C(4) photosynthesis in leaves and cotyledons. Immunolocalization studies show that PEPC is localized in mesophyll (M) cells and Rubisco is selectively localized in bundle sheath (BS) cells in leaves and cotyledons, characteristic of species with Kranz anatomy. Analyses of leaves for key photosynthetic enzymes show they have high expression of markers for the C(4) cycle (compared with the C(3)-C(4) intermediate C. paradoxa and the C(3) species C. africana). All three are biochemically NAD-malic enzyme sub-type, with higher granal development in BS than in M chloroplasts, characteristic of this biochemical sub-type. Cleome gynandra and C. oxalidea have atriplicoid-type Kranz anatomy with multiple simple Kranz units around individual veins. However, C. angustifolia anatomy is represented by a double layer of concentric chlorenchyma forming a single compound Kranz unit by surrounding all the vascular bundles and water storage cells. CONCLUSIONS NAD-malic enzyme-type C(4) photosynthesis evolved multiple times in the family Cleomaceae, twice with atriplicoid-type anatomy in compound leaves having flat, broad leaflets in the pantropical species C. gynandra and the Australian species C. oxalidea, and once by forming a single Kranz unit in compound leaves with semi-terete leaflets in the African species C. angustifolia. The leaf morphology of C. angustifolia, which is similar to that of the sister, C(3)-C(4) intermediate African species C. paradoxa, suggests adaptation of this lineage to arid environments, which is supported by biogeographical information.
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Affiliation(s)
- Nuria K. Koteyeva
- Laboratory of Anatomy and Morphology, V. L. Komarov Botanical Institute of Russian Academy of Sciences, Prof. Popov Street 2, 197376, St. Petersburg, Russia
| | - Elena V. Voznesenskaya
- Laboratory of Anatomy and Morphology, V. L. Komarov Botanical Institute of Russian Academy of Sciences, Prof. Popov Street 2, 197376, St. Petersburg, Russia
| | - Eric H. Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Gerald E. Edwards
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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Abstract
Recent studies have elucidated the ancient polyploid history of the Arabidopsis thaliana (Brassicaceae) genome. The studies concur that there was at least one polyploidy event occurring some 14.5 to 86 million years ago (Mya), possibly near the divergence of the Brassicaceae from its sister family, Cleomaceae. Using a comparative genomics approach, we asked whether this polyploidy event was unique to members of the Brassicaceae, shared with the Cleomaceae, or an independent polyploidy event in each lineage. We isolated and sequenced three genomic regions from diploid Cleome spinosa (Cleomaceae) that are each homoeologous to a duplicated region shared between At3 and At5, centered on the paralogs of SEPALLATA (SEP) and CONSTANS (CO). Phylogenetic reconstructions and analysis of synonymous substitution rates support the hypothesis that a genomic triplication in Cleome occurred independently of and more recently than the duplication event in the Brassicaceae. There is a strong correlation in the copy number (single versus duplicate) of individual genes, suggesting functionally consistent influences operating on gene copy number in these two independently evolving lineages. However, the amount of gene loss in Cleome is greater than in Arabidopsis. The genome of C. spinosa is only 1.9 times the size of A. thaliana, enabling comparative genome analysis of separate but related polyploidy events.
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Affiliation(s)
- M Eric Schranz
- Department of Genetics and Evolution, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany.
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Schranz ME, Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell 2006; 18:1152-1165. [PMID: 16617098 DOI: 10.1105/tpc.106.041111.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent studies have elucidated the ancient polyploid history of the Arabidopsis thaliana (Brassicaceae) genome. The studies concur that there was at least one polyploidy event occurring some 14.5 to 86 million years ago (Mya), possibly near the divergence of the Brassicaceae from its sister family, Cleomaceae. Using a comparative genomics approach, we asked whether this polyploidy event was unique to members of the Brassicaceae, shared with the Cleomaceae, or an independent polyploidy event in each lineage. We isolated and sequenced three genomic regions from diploid Cleome spinosa (Cleomaceae) that are each homoeologous to a duplicated region shared between At3 and At5, centered on the paralogs of SEPALLATA (SEP) and CONSTANS (CO). Phylogenetic reconstructions and analysis of synonymous substitution rates support the hypothesis that a genomic triplication in Cleome occurred independently of and more recently than the duplication event in the Brassicaceae. There is a strong correlation in the copy number (single versus duplicate) of individual genes, suggesting functionally consistent influences operating on gene copy number in these two independently evolving lineages. However, the amount of gene loss in Cleome is greater than in Arabidopsis. The genome of C. spinosa is only 1.9 times the size of A. thaliana, enabling comparative genome analysis of separate but related polyploidy events.
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Affiliation(s)
- M Eric Schranz
- Department of Genetics and Evolution, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany.
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Abstract
C4 photosynthesis has evolved multiple times among the angiosperms: the spatial rearrangement of the photosynthetic apparatus, combined with alterations to the leaf structure, allows CO2 to be concentrated around Rubisco. Higher CO2 concentrations at Rubisco decrease the rate of oxygenation and therefore reduce the amount of energy lost through photorespiration. C4 plants are particularly prevalent in tropical and subtropical regions because they can sustain higher rates of net photosynthesis; they also represent some of our most productive crops. To date, most progress in identifying genes crucial for C4 photosynthesis has been made using maize and Flaveria. We propose that Cleome, the most closely related genus containing C4 species to the C3 model Arabidopsis, be used together with Arabidopsis resources to accelerate our progress in elucidating the genetic basis of C4 photosynthesis.
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Affiliation(s)
- Naomi J Brown
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK CB2 3EA
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