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Wickell D, Kuo LY, Yang HP, Dhabalia Ashok A, Irisarri I, Dadras A, de Vries S, de Vries J, Huang YM, Li Z, Barker MS, Hartwick NT, Michael TP, Li FW. Underwater CAM photosynthesis elucidated by Isoetes genome. Nat Commun 2021; 12:6348. [PMID: 34732722 PMCID: PMC8566536 DOI: 10.1038/s41467-021-26644-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.
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Affiliation(s)
- David Wickell
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Amra Dhabalia Ashok
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences, University of Goettingen, Goettingen, Germany
| | | | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Nolan T Hartwick
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Todd P Michael
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Fay-Wei Li
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
- Boyce Thompson Institute, Ithaca, NY, USA.
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152
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Zhao Y, Zhou W, Chen Y, Li Z, Song X, Wang J, Tian D, Niu J. Metabolite analysis in Nymphaea 'Blue Bird' petals reveal the roles of flavonoids in color formation, stress amelioration, and bee orientation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111025. [PMID: 34620430 DOI: 10.1016/j.plantsci.2021.111025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/04/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
In this study, metabolome of open petals (OP) and closed petals (CP) from Nymphaea 'Blue Bird' was firstly investigated. A total of 455 metabolites was identified in Nymphaea 'Blue Bird' petals, which was mainly composed of 100 flavonoids, 83 phenolic acids, 64 amino acids and derivatives, 60 lipids, 32 alkaloids, 32 organic acids, 24 nucleotides and derivatives, and 12 lignans and coumarins. By differential analysis, 192 metabolites were identified with variable importance in project ≥ 1, among which 83 and 109 metabolites were up- and down-regulated in OP group, respectively. Further analysis (Log2 fold change ≥ 1) identified 26 and 7 metabolites exhibited significantly lower and higher contents in CP group, relative to OP group. Importantly, KEGG analysis indicated that flavonoid biosynthesis exhibited the most significant enrichment. qRT-PCR analysis indicated that the PAL, CHS, and HCDBR genes showed a significantly higher expression in OP group than in CP group. These data explain the increase of naringenin chalcone and phloretin in OP. However, there was no significant difference of total flavonoids between OP and CP groups. Considering the increase of H2O2 content and ultraviolet (UV) absorption peak in OP, our results implied that diurnal stressful conditions induced the degradation of flavonoids, which contributed to environmental stress amelioration. Moreover, a higher absorption peak of 360-380 nm UV was observed in the extract liquor of OP. The sensitivity maximum of the UV-photoreceptor of bees is situated around 340-380 nm UV. This suggested, as noted for the maximum absorption of dihydrokaempferol in 340-370 nm, rhythmic accumulation and loss of these differential flavonoids in Nymphaea 'Blue Bird' petals might enhance UV pattern to some degree, influencing pollinator attraction.
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Affiliation(s)
- Ying Zhao
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Weijuan Zhou
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Yan Chen
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Zhaoji Li
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Xiqiang Song
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Jian Wang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Daike Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jun Niu
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China.
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153
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Jiang Y, Liu G, Zhang W, Zhang C, Chen X, Chen Y, Yu C, Yu D, Fu J, Chen F. Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoriacruziana. PHYTOCHEMISTRY 2021; 191:112899. [PMID: 34481346 DOI: 10.1016/j.phytochem.2021.112899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/27/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Among the factors that have made flowering plants the most species-rich lineage of land plants is the interaction between flower and insect pollinators, for which floral scent plays a pivotal role. Water lilies belong to the ANA (Amborellales, Nymphaeales, and Austrobaileyales) grade of basal flowering plants. In this study, Victoria cruziana was investigated as a model night-blooming water lily for floral scent biosynthesis. Four volatile compounds, including three benzenoids and one fatty acid methyl ester methyl hexanoate, were detected from the flowers of V. cruziana during their first bloom, with methyl hexanoate accounting for 45 % of total floral volatile emission. Emission rates were largely constant before significant drop starting at the end of second bloom. To understand the molecular basis of floral scent biosynthesis in V. cruziana, particularly methyl hexanoate, a transcriptome from the whole flowers at the full-bloom stage was created and analyzed. Methyl hexanoate was hypothesized to be biosynthesized by SABATH methyltransferases. From the transcriptome, three full-length SABATH genes designated VcSABATH1-3 were identified. A full-length cDNA for each of the three VcSABATH genes was expressed in Escherichia coli to produce recombinant proteins. When tested in in vitro methyltransferase enzyme assays with different fatty acids, both VcSABATH1 and VcSABATH3 exhibited highest levels of activity with hexanoic acid to produce methyl hexanoate, with the specific activity of VcSABATH1 being about 15 % of that for VcSABATH3. VcSABATH1 and VcSABATH3 showed the highest levels of expression in stamen and pistil, respectively. In phylogenetic analysis, three VcSABATH genes clustered with other water lily SABATH methyltransferase genes including the one known for making other fatty acid methyl esters, implying both a common evolutionary origin and functional divergence. Fatty acid methyl esters are not frequent constituents of floral scents of mesangiosperms, pointing to the importance for the evolution of novel fatty acid methyltransferase for making fatty acid methyl esters in the pollination biology of water lilies.
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Affiliation(s)
- Yifan Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guanhua Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanbo Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chi Zhang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Yuchu Chen
- Hangzhou Tianjing Aquatic Botanical Garden, Zhejiang Humanities Landscape Co., Ltd., Hangzhou 310000, China
| | - Cuiwei Yu
- Hangzhou Tianjing Aquatic Botanical Garden, Zhejiang Humanities Landscape Co., Ltd., Hangzhou 310000, China
| | - Dongbei Yu
- Hangzhou Tianjing Aquatic Botanical Garden, Zhejiang Humanities Landscape Co., Ltd., Hangzhou 310000, China
| | - Jianyu Fu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, PR China
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA.
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154
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Li HT, Luo Y, Gan L, Ma PF, Gao LM, Yang JB, Cai J, Gitzendanner MA, Fritsch PW, Zhang T, Jin JJ, Zeng CX, Wang H, Yu WB, Zhang R, van der Bank M, Olmstead RG, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Yi TS, Li DZ. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol 2021; 19:232. [PMID: 34711223 PMCID: PMC8555322 DOI: 10.1186/s12915-021-01166-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. RESULTS Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. CONCLUSIONS We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lu Gan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10025, USA
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hong Wang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195-5325, USA
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, England, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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155
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Hao Y, Zhou YZ, Chen B, Chen GZ, Wen ZY, Zhang D, Sun WH, Liu DK, Huang J, Chen JL, Zhou XQ, Fan WL, Zhang WC, Luo L, Han WC, Zheng Y, Li L, Lu PC, Xing Y, Liu SY, Sun JT, Cao YH, Zhang YP, Shi XL, Wu SS, Ai Y, Zhai JW, Lan SR, Liu ZJ, Peng DH. The Melastoma dodecandrum genome and the evolution of Myrtales. J Genet Genomics 2021; 49:120-131. [PMID: 34757038 DOI: 10.1016/j.jgg.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 12/16/2022]
Abstract
Melastomataceae have abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the first chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size was 299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum, Eucalyptus grandis and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. We found that the SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.
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Affiliation(s)
- Yang Hao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Yu-Zhen Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Bin Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Zhen-Ying Wen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Jin-Liao Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Xiao-Qin Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Wan-Lin Fan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Wen-Chun Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Lin Luo
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Wen-Chao Han
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Yan Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Long Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Peng-Cheng Lu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Yue Xing
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Shu-Ya Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Jia-Ting Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Ying-Hui Cao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Yan-Ping Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Xiao-Ling Shi
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Sha-Sha Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Ye Ai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Jun-Wen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Art & Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, Fuzhou 350002, China.
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156
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Li X, St Laurent R, Earl C, Doorenweerd C, van Nieukerken EJ, Davis DR, Johns CA, Kawakita A, Kobayashi S, Zwick A, Lopez-Vaamonde C, Ohshima I, Kawahara AY. Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data. Cladistics 2021; 38:277-300. [PMID: 34710244 DOI: 10.1111/cla.12490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/27/2022] Open
Abstract
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.
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Affiliation(s)
- Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Camiel Doorenweerd
- Department of Plant and Environmental Protection Services, University of Hawaii, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | | | - Donald R Davis
- Department of Entomology, NHB 105, Smithsonian Institution, Washington, DC, USA
| | - Chris A Johns
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Kawakita
- The Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, 112-0001, Japan
| | - Shigeki Kobayashi
- Entomological Laboratory, Graduate School of life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Andreas Zwick
- Australian National Insect Collection, National Research Collections Australia, CSIRO, Canberra, ACT, 2601, Australia
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orléans, France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France
| | - Issei Ohshima
- Department of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan.,Center for Frontier Natural History, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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157
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Gong P, Song C, Liu H, Li P, Zhang M, Zhang J, Zhang S, He C. Physalis floridana CRABS CLAW mediates neofunctionalization of GLOBOSA genes in carpel development. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6882-6903. [PMID: 34181715 PMCID: PMC8547157 DOI: 10.1093/jxb/erab309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/23/2021] [Indexed: 05/20/2023]
Abstract
Floral B-function MADS-box genes, such as GLOBOSA (GLO), function in corolla and stamen organ identity specification. The functions of these genes outside these floral whorls are rarely reported. DOLL1 is a GLO gene controlling corolla and androecium organ identity. In this study we found that, in Physalis floridana double-layered-lantern 1 (doll1) mutant pollinated with wild-type pollen, fruit set was extremely low, indicating that doll1 females are dysfunctional. Stigma and style structure, stigma receptivity, pollen tube guidance, and embryo sac development were also impaired in doll1. P. floridana CRABS CLAW (PFCRC), predominantly expressed in carpels, was repressed in doll1 native carpels. Loss-of-function of PFCRC altered carpel meristem determinacy, carpel closure, and ovule number, and the resultant 'pistil' consisted of multiple spirally-arranged dorsiventral carpels occasionally with 1-2 naked ovules on the margin and trichomes at each mutated carpel tip, implying an alteration of carpel organ identity. Regulatory and genetic interactions between B-class MADS-box genes and PFCRC were revealed in a context-dependent manner in floral development. Our work reveals a new role for the B-function genes in carpel and ovule development via regulating PFCRC, providing a new understanding of genetic regulatory networks between MADS-domain and CRC transcription factors in mediating carpel organ specification, functionality, and origin.
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Affiliation(s)
- Pichang Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
| | - Chunjing Song
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peigang Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingshu Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jisi Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaohua Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Correspondence:
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158
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Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production. Commun Biol 2021; 4:1203. [PMID: 34671091 PMCID: PMC8528922 DOI: 10.1038/s42003-021-02697-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/18/2021] [Indexed: 11/08/2022] Open
Abstract
Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4-213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.
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159
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Li Z, Zhou W, Wang P, Chen Y, Huo S, Wang J, Tian D, Niu J, Zhao Y, Song X. Transcriptome Analysis Reveals the Senescence Process Controlling the Flower Opening and Closure Rhythm in the Waterlilies ( Nymphaea L.). FRONTIERS IN PLANT SCIENCE 2021; 12:701633. [PMID: 34671367 PMCID: PMC8521120 DOI: 10.3389/fpls.2021.701633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Most waterlily flowers open at dawn and close after noon usually for three to four days, and thereafter wilt. The short lifespan of flowers restricts the development of the flower postharvest industry. The termination of flower movements is a key event during flower aging process. However, it is still unclear when the senescence process initiates and how it terminates the movement rhythm. In this study, we observed that the opening diameter of flowers was the smallest on the fourth (last) flowering day. Subsequent transcriptome profiles generated from petals at different flowering stages showed that the multiple signaling pathways were activated at the last closure stage (Time 3, T3) of the flowers, including Ca2+, reactive oxygen species and far red light signaling pathways, as well as auxin, ethylene and jasmonic acid signaling pathways. Moreover, In terms of cell metabolism regulation, the genes related to hydrolase (protease, phospholipase, nuclease) were upregulated at T3 stage, indicating that petals entered the senescence stage at that time; and the genes related to water transport and cell wall modification were also differentially regulated at T3 stage, which would affect the ability of cell expand and contract, and eventually lead to petal not open after the fourth day. Collectively, our data provided a new insight into the termination of flower opening in the waterlilies, and a global understanding of the senescence process of those opening-closure rhythm flowers.
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Affiliation(s)
- Zhaoji Li
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Weijuan Zhou
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yanfu Chen
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Shaojie Huo
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Jian Wang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Daike Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jun Niu
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Ying Zhao
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Xiqiang Song
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
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160
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Moschin S, Nigris S, Ezquer I, Masiero S, Cagnin S, Cortese E, Colombo L, Casadoro G, Baldan B. Expression and Functional Analyses of Nymphaea caerulea MADS-Box Genes Contribute to Clarify the Complex Flower Patterning of Water Lilies. FRONTIERS IN PLANT SCIENCE 2021; 12:730270. [PMID: 34630477 PMCID: PMC8492926 DOI: 10.3389/fpls.2021.730270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Nymphaeaceae are early diverging angiosperms with large flowers characterized by showy petals and stamens not clearly whorled but presenting a gradual morphological transition from the outer elements to the inner stamens. Such flower structure makes these plant species relevant for studying flower evolution. MADS-domain transcription factors are crucial components of the molecular network that controls flower development. We therefore isolated and characterized MADS-box genes from the water lily Nymphaea caerulea. RNA-seq experiments on floral buds have been performed to obtain the transcript sequences of floral organ identity MADS-box genes. Maximum Likelihood phylogenetic analyses confirmed their belonging to specific MADS-box gene subfamilies. Their expression was quantified by RT-qPCR in all floral organs at two stages of development. Protein interactions among these transcription factors were investigated by yeast-two-hybrid assays. We found especially interesting the involvement of two different AGAMOUS-like genes (NycAG1 and NycAG2) in the water lily floral components. They were therefore functionally characterized by complementing Arabidopsis ag and shp1 shp2 mutants. The expression analysis of MADS-box genes across flower development in N. caerulea described a complex scenario made of numerous genes in numerous floral components. Their expression profiles in some cases were in line with what was expected from the ABC model of flower development and its extensions, while in other cases presented new and interesting gene expression patterns, as for instance the involvement of NycAGL6 and NycFL. Although sharing a high level of sequence similarity, the two AGAMOUS-like genes NycAG1 and NycAG2 could have undergone subfunctionalization or neofunctionalization, as only one of them could partially restore the euAG function in Arabidopsis ag-3 mutants. The hereby illustrated N. caerulea MADS-box gene expression pattern might mirror the morphological transition from the outer to the inner floral organs, and the presence of transition organs such as the petaloid stamens. This study is intended to broaden knowledge on the role and evolution of floral organ identity genes and the genetic mechanisms causing biodiversity in angiosperm flowers.
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Affiliation(s)
- Silvia Moschin
- Botanical Garden, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Sebastiano Nigris
- Botanical Garden, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Ignacio Ezquer
- Department of Biosciences, University of Milan, Milan, Italy
| | - Simona Masiero
- Department of Biosciences, University of Milan, Milan, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padua, Padua, Italy
- CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - Enrico Cortese
- Department of Biology, University of Padua, Padua, Italy
| | - Lucia Colombo
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Barbara Baldan
- Botanical Garden, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
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161
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He ZS, Zhu A, Yang JB, Fan W, Li DZ. Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing. Int J Mol Sci 2021; 22:ijms22189842. [PMID: 34576004 PMCID: PMC8466565 DOI: 10.3390/ijms22189842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based on the Illumina short reads which were unable to capture the full spectrum of transcript intermediates within an organelle. To fully investigate the intermediates during intron splicing and the underlying relationships with RNA editing, we used PacBio DNA-seq and Iso-seq, together with Illumina short reads genome and transcriptome sequencing data to assemble the chloroplast and mitochondrial genomes of Nymphaea 'Joey Tomocik' and analyze their posttranscriptional features. With the direct evidence from Iso-seq, multiple intermediates partially or fully intron-spliced were observed, and we also found that both cis- and trans-splicing introns were spliced randomly. Moreover, by using rRNA-depleted and non-Oligo(dT)-enrichment strand-specific RNA-seq data and combining direct SNP-calling and transcript-mapping methods, we identified 98 and 865 RNA-editing sites in the plastome and mitogenome of N. 'Joey Tomocik', respectively. The target codon preference, the tendency of increasing protein hydrophobicity, and the bias distribution of editing sites are similar in both organelles, suggesting their common evolutionary origin and shared editing machinery. The distribution of RNA editing sites also implies that the RNA editing sites in the intron and exon regions may splice synchronously, except those exonic sites adjacent to intron which could only be edited after being intron-spliced. Our study provides solid evidence for the multiple intermediates co-existing during intron-splicing and their interplay with RNA editing in organelle genomes of a basal angiosperm.
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Affiliation(s)
- Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
- Correspondence: (W.F.); (D.-Z.L.); Tel.: +86-871-6523-8370 (W.F.); +86-871-6522-3503 (D.-Z.L.)
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-S.H.); (A.Z.); (J.-B.Y.)
- Correspondence: (W.F.); (D.-Z.L.); Tel.: +86-871-6523-8370 (W.F.); +86-871-6522-3503 (D.-Z.L.)
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162
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Affiliation(s)
- Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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163
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Qin L, Hu Y, Wang J, Wang X, Zhao R, Shan H, Li K, Xu P, Wu H, Yan X, Liu L, Yi X, Wanke S, Bowers JE, Leebens-Mack JH, dePamphilis CW, Soltis PS, Soltis DE, Kong H, Jiao Y. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. NATURE PLANTS 2021; 7:1239-1253. [PMID: 34475528 PMCID: PMC8445822 DOI: 10.1038/s41477-021-00990-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/22/2021] [Indexed: 05/04/2023]
Abstract
Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.
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Affiliation(s)
- Liuyu Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoliang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanying Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lumei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Stefan Wanke
- Institute of Botany, Dresden University of Technology, Dresden, Germany
| | - John E Bowers
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | | | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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164
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Liu Z, Zhang D, Zhang W, Xiong L, Liu Q, Liu F, Li H, An X, Cui L, Tian D. Molecular Cloning and Expression Profile of Class E Genes Related to Sepal Development in Nelumbo nucifera. PLANTS 2021; 10:plants10081629. [PMID: 34451674 PMCID: PMC8398900 DOI: 10.3390/plants10081629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
The lotus (Nelumbo Adans.) is an important aquatic plant with ornamental, medicinal and edible values and cultural connotations. It has single-, semi-double-, double- and thousand-petalled types of flower shape and is an ideal material for developmental research of flower doubling. The lotus is a basal eudicot species without a morphological difference between the sepals and petals and occupies a critical phylogenetic position in flowering plants. In order to investigate the genetic relationship between the sepals and petals in the lotus, the class E genes which affect sepal formation were focused on and analyzed. Here, SEPALLATA 1(NnSEP1) and its homologous genes AGAMOUS-LIKE MADS-BOXAGL9 (NnAGL9) and MADS-BOX TRANSCRIPTION FACTOR 6-like (NnMADS6-like) of the class E gene family were isolated from the flower buds of the Asian lotus (Nelumbo nucifera Gaertn.). The protein structure, subcellular localization and expression patterns of these three genes were investigated. All three genes were verified to locate in the nucleus and had typical MADS-box characteristics. NnSEP1 and NnMADS6-like were specifically expressed in the sepals, while NnAGL9 was highly expressed in the petals, suggesting that different developmental mechanisms exist in the formation of the sepals and petals in the lotus. The significant functional differences between NnSEP1, NnMADS6-like and NnAGL9 were also confirmed by a yeast two-hybrid assay. These results expand our knowledge on the class E gene family in sepal formation and will benefit fundamental research on the development of floral organs in Nelumbo.
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Affiliation(s)
- Zhuoxing Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
| | - Dasheng Zhang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Weiwei Zhang
- Department of Plant Science and Technology, Shanghai Vocational College of Agriculture and Forestry, Shanghai 201699, China;
| | - Lei Xiong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
| | - Qingqing Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Fengluan Liu
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
| | - Hanchun Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Xiangjie An
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Lijie Cui
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
- Correspondence: (L.C.); (D.T.); Tel.: +86-21-37792288-932; Fax: +86-21-57762652
| | - Daike Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
- Correspondence: (L.C.); (D.T.); Tel.: +86-21-37792288-932; Fax: +86-21-57762652
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165
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Genome of the world's smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology. Commun Biol 2021; 4:900. [PMID: 34294872 PMCID: PMC8298427 DOI: 10.1038/s42003-021-02422-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/17/2021] [Indexed: 11/17/2022] Open
Abstract
Watermeal, Wolffia australiana, is the smallest known flowering monocot and is rich in protein. Despite its great potential as a biotech crop, basic research on Wolffia is in its infancy. Here, we generated the reference genome of a species of watermeal, W. australiana, and identified the genome-wide features that may contribute to its atypical anatomy and physiology, including the absence of roots, adaxial stomata development, and anaerobic life as a turion. In addition, we found evidence of extensive genome rearrangements that may underpin the specialized aquatic lifestyle of watermeal. Analysis of the gene inventory of this intriguing species helps explain the distinct characteristics of W. australiana and its unique evolutionary trajectory. Halim Park and Jin Hwa Park et al. report the nuclear genome sequence of the duckweed Wolffia australiana, the smallest known flowering plant. The genome assembly represents an improvement over a recently published genome and highlights genome rearrangements that may be linked to its specialized aquatic adaptations.
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166
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Pu X, Dong X, Li Q, Chen Z, Liu L. An update on the function and regulation of methylerythritol phosphate and mevalonate pathways and their evolutionary dynamics. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1211-1226. [PMID: 33538411 DOI: 10.1111/jipb.13076] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/02/2021] [Indexed: 05/29/2023]
Abstract
Isoprenoids are among the largest and most chemically diverse classes of organic compounds in nature and are involved in the processes of photosynthesis, respiration, growth, development, and plant responses to stress. The basic building block units for isoprenoid synthesis-isopentenyl diphosphate and its isomer dimethylallyl diphosphate-are generated by the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways. Here, we summarize recent advances on the roles of the MEP and MVA pathways in plant growth, development and stress responses, and attempt to define the underlying gene networks that orchestrate the MEP and MVA pathways in response to developmental or environmental cues. Through phylogenomic analysis, we also provide a new perspective on the evolution of the plant isoprenoid pathway. We conclude that the presence of the MVA pathway in plants may be associated with the transition from aquatic to subaerial and terrestrial environments, as lineages for its core components are absent in green algae. The emergence of the MVA pathway has acted as a key evolutionary event in plants that facilitated land colonization and subsequent embryo development, as well as adaptation to new and varied environments.
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Affiliation(s)
- Xiaojun Pu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 434200, China
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
| | - Xiumei Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 434200, China
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
| | - Qing Li
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zexi Chen
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 434200, China
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
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167
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Chen F, Su L, Hu S, Xue JY, Liu H, Liu G, Jiang Y, Du J, Qiao Y, Fan Y, Liu H, Yang Q, Lu W, Shao ZQ, Zhang J, Zhang L, Chen F, Cheng ZMM. A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics. HORTICULTURE RESEARCH 2021; 8:141. [PMID: 34145222 PMCID: PMC8213826 DOI: 10.1038/s41438-021-00594-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 05/09/2023]
Abstract
Rosa rugosa, commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for R. rugosa to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of R. rugosa, and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of R. rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred ~100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of R. rugosa and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose R. chinensis and a retroposition in strawberry caused by post-WGT events. We also found that floral development- and stress response signaling-related gene modules were retained after the WGT. Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 (DRIP2) and PEPTIDE TRANSPORTER 3 (PTR3) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of R. rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.
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Affiliation(s)
- Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liyao Su
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuaiya Hu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jia-Yu Xue
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanhua Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yifan Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianke Du
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yushan Qiao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yannan Fan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huan Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Qi Yang
- Grandomics Biosciences Co., Ltd, Wuhan, China
| | - Wenjie Lu
- Grandomics Biosciences Co., Ltd, Wuhan, China
| | - Zhu-Qing Shao
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Jian Zhang
- College of life science, Nantong University, Nantong, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feng Chen
- Department of plant sciences, University of Tennessee, Knoxville, TN, USA
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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168
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Liu Y, Wang B, Shu S, Li Z, Song C, Liu D, Niu Y, Liu J, Zhang J, Liu H, Hu Z, Huang B, Liu X, Liu W, Jiang L, Alami MM, Zhou Y, Ma Y, He X, Yang Y, Zhang T, Hu H, Barker MS, Chen S, Wang X, Nie J. Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids. Nat Commun 2021; 12:3276. [PMID: 34078898 PMCID: PMC8172641 DOI: 10.1038/s41467-021-23611-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.
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Affiliation(s)
- Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China.
| | - Bo Wang
- Hubei Institute for Drug Control, Wuhan, China
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Chi Song
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Di Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Jinxin Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Heping Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Bisheng Huang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiuyu Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Liping Jiang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | | | - Yuxin Zhou
- Hubei Institute for Drug Control, Wuhan, China
| | - Yutao Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiangxiang He
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Yicheng Yang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Tianyuan Zhang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Hui Hu
- Jing Brand Chizhengtang Pharmaceutical Company Limited, Huangshi, China
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Xuekui Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Jing Nie
- Hubei Institute for Drug Control, Wuhan, China.
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169
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Ke CJ, Lin XJ, Zhang BY, Chen LY. Turgor regulation defect 1 proteins play a conserved role in pollen tube reproductive innovation of the angiosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1356-1365. [PMID: 33735469 DOI: 10.1111/tpj.15241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Sexual reproduction in angiosperms is siphonogamous, and the interaction between pollen tube and pistil is critical for successful fertilization. Our previous study demonstrated that mutation of the Arabidopsis turgor regulation defect 1 (TOD1) gene leads to reduced male fertility, a result of retarded pollen tube growth in the pistil. TOD1 encodes a Golgi-localized alkaline ceramidase, a key enzyme for the production of sphingosine-1-phosphate (S1P), which is involved in the regulation of turgor pressure in plant cells. However, whether TOD1s play a conserved role in the innovation of siphonogamy is largely unknown. In this study, we provide evidence that OsTOD1, which is similar to AtTOD1, is also preferentially expressed in rice pollen grains and pollen tubes. OsTOD1 knockout results in reduced pollen tube growth potential in rice pistil. Both the OsTOD1 genomic sequence with its own promoter and the coding sequence under the AtTOD1 promoter can partially rescue the attod1 mutant phenotype. Furthermore, TOD1s from other angiosperm species can partially rescue the attod1 mutant phenotype, while TOD1s from gymnosperm species are not able to complement the attod1 mutant phenotype. Our data suggest that TOD1 acts conservatively in angiosperms, and this opens up an opportunity to dissect the role of sphingolipids in pollen tube growth in angiosperms.
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Affiliation(s)
- Chang-Jiao Ke
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xian-Ju Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bao-Yu Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li-Yu Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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170
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Zhao Y, Zhang R, Jiang KW, Qi J, Hu Y, Guo J, Zhu R, Zhang T, Egan AN, Yi TS, Huang CH, Ma H. Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae. MOLECULAR PLANT 2021; 14:748-773. [PMID: 33631421 DOI: 10.1016/j.molp.2021.02.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/31/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Fabaceae are the third largest angiosperm family, with 765 genera and ∼19 500 species. They are important both economically and ecologically, and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability. However, resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive, precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae. Here, we report a highly resolved phylogeny using >1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species, along with other datasets, for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera. The subfamilies are maximally supported as monophyletic. The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes, and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae. Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary, marked by mass extinction, and subsequent divergence of most tribe-level clades within ∼15 million years. Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae, including those at the ancestors of Fabaceae and five of the subfamilies, and further analyses supported the Fabaceae ancestral polyploidy. The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switch(es) to rhizobial nodulation followed by multiple losses. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.
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Affiliation(s)
- Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, PR China; Ningbo Botanical Garden Herbarium, Ningbo 315201, PR China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Renbin Zhu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, PR China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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171
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Nishiyama E, Nonogaki M, Yamazaki S, Nonogaki H, Ohshima K. Ancient and recent gene duplications as evolutionary drivers of the seed maturation regulators DELAY OF GERMINATION1 family genes. THE NEW PHYTOLOGIST 2021; 230:889-901. [PMID: 33454982 DOI: 10.1111/nph.17201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
The DELAY OF GERMINATION1 (DOG1) family genes (DFGs) in Arabidopsis thaliana are involved in seed dormancy, reserve accumulation, and desiccation tolerance. Decoding the molecular evolution of DFGs is key to understanding how these seed programs evolved. This article demonstrates that DFGs have diverged in the four lineages DOG1, DOG1-LIKE4 (DOGL4), DOGL5 and DOGL6, whereas DOGL1, DOGL2 and DOGL3 arose separately within the DOG1 lineage. The systematic DFG nomenclature proposed in this article addresses the current issues of inconsistent DFG annotation and highlights DFG genomic synteny in angiosperms. DFG pseudogenes, or collapsed coding sequences, hidden in the genomes of early-diverging angiosperms are documented here. They suggest ancient birth and loss of DFGs over the course of angiosperm evolution. The proposed models suggest that the origin of DFG diversification dates back to the most recent common ancestor of living angiosperms. The presence of a single form of DFG in nonflowering plants is discussed. Phylogenetic analysis of gymnosperm, lycophyte, and liverwort DFGs and similar genes found in mosses and algae suggests that DFGs diverged from the TGACG motif-binding transcription factor genes before the divergence of the bryophyte lineage.
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Affiliation(s)
- Eri Nishiyama
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Mariko Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Satoru Yamazaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Hiroyuki Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Kazuhiko Ohshima
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
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Kitazawa MS. Developmental stochasticity and variation in floral phyllotaxis. JOURNAL OF PLANT RESEARCH 2021; 134:403-416. [PMID: 33821352 PMCID: PMC8106590 DOI: 10.1007/s10265-021-01283-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Floral phyllotaxis is a relatively robust phenotype; trimerous and pentamerous arrangements are widely observed in monocots and core eudicots. Conversely, it also shows variability in some angiosperm clades such as 'ANA' grade (Amborellales, Nymphaeales, and Austrobaileyales), magnoliids, and Ranunculales. Regardless of the phylogenetic relationship, however, phyllotactic pattern formation appears to be a common process. What are the causes of the variability in floral phyllotaxis and how has the variation of floral phyllotaxis contributed to floral diversity? In this review, I summarize recent progress in studies on two related fields to develop answers to these questions. First, it is known that molecular and cellular stochasticity are inevitably found in biological systems, including plant development. Organisms deal with molecular stochasticity in several ways, such as dampening noise through gene networks or maintaining function through cellular redundancy. Recent studies on molecular and cellular stochasticity suggest that stochasticity is not always detrimental to plants and that it is also essential in development. Second, studies on vegetative and inflorescence phyllotaxis have shown that plants often exhibit variability and flexibility in phenotypes. Three types of phyllotaxis variations are observed, namely, fluctuation around the mean, transition between regular patterns, and a transient irregular organ arrangement called permutation. Computer models have demonstrated that stochasticity in the phyllotactic pattern formation plays a role in pattern transitions and irregularities. Variations are also found in the number and positioning of floral organs, although it is not known whether such variations provide any functional advantages. Two ways of diversification may be involved in angiosperm floral evolution: precise regulation of organ position and identity that leads to further specialization of organs and organ redundancy that leads to flexibility in floral phyllotaxis.
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Affiliation(s)
- Miho S Kitazawa
- Center for Education in Liberal Arts and Sciences, Osaka University, 1-16 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan.
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173
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Zhao X, Yang J, Li G, Sun Z, Hu S, Chen Y, Guo W, Hou H. Genome-wide identification and comparative analysis of the WRKY gene family in aquatic plants and their response to abiotic stresses in giant duckweed (Spirodela polyrhiza). Genomics 2021; 113:1761-1777. [PMID: 33862182 DOI: 10.1016/j.ygeno.2021.03.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/02/2021] [Accepted: 03/06/2021] [Indexed: 12/11/2022]
Abstract
WRKY is one of the largest transcription factor families across higher plant species and is involved in important biological processes and plant responses to various biotic/abiotic stresses. However, only a few investigations on WRKYs have been conducted in aquatic plants. This study first systematically analyzed the gene structure, protein properties, and phylogenetic relationship of 693 WRKYs in nine aquatic and two wetland plants at the genome-wide level. The pattern of WRKY groups in two aquatic ferns provided new evidence for the origin and evolution of WRKY genes. ARE cis-regulatory elements show an unusual high frequency in the promoter region of WRKY genes, indicating the adaptation to the aquatic habitat in aquatic plants. The WRKY gene family experienced a series of gene loss events in aquatic plants, especially group III. Further studies were conducted on the interaction network of SpWRKYs, their target genes, and non-coding RNAs. The expression profile of SpWRKYs under phosphate starvation, cold, and submergence conditions revealed that most SpWRKYs are involved in the response to abiotic stresses. Our investigations lay the foundation for further study on the mechanism of WRKYs responding to abiotic stresses in aquatic plants.
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Affiliation(s)
- Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Environment and Chemical Engineering, Pingdingshan University, Pingdingshan 467000, Henan, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiqi Hu
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Guo
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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174
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Muñoz-Gómez S, Suárez-Baron H, Alzate JF, González F, Pabón-Mora N. Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales. FRONTIERS IN PLANT SCIENCE 2021; 12:633227. [PMID: 33897722 PMCID: PMC8063865 DOI: 10.3389/fpls.2021.633227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/08/2021] [Indexed: 05/27/2023]
Abstract
Flavonoids, carotenoids, betalains, and chlorophylls are the plant pigments responsible for floral color. Anthocyanins, a class of flavonoids, are largely responsible for the red, purple, pink, and blue colors. R2R3-MYB genes belonging to subgroup 6 (SG6) are the upstream regulatory factors of the anthocyanin biosynthetic pathway. The canonical members of these genes in Arabidopsis include AtMYB75, AtMYB90, AtMYB113, and AtMYB114. The Aristolochiaceae is an angiosperm lineage with diverse floral groundplans and perianth colors. Saruma henryi exhibits a biseriate perianth with green sepals and yellow petals. All other genera have sepals only, with colors ranging from green (in Lactoris) to a plethora of yellow to red and purple mixtures. Here, we isolated and reconstructed the SG6 R2R3-MYB gene lineage evolution in angiosperms with sampling emphasis in Aristolochiaceae. We found numerous species-specific duplications of this gene lineage in core eudicots and local duplications in Aristolochiaceae for Saruma and Asarum. Expression of SG6 R2R3-MYB genes examined in different developmental stages and plant organs of four Aristolochiaceae species, largely overlaps with red and purple pigments, suggesting a role in anthocyanin and flavonoid synthesis and accumulation. A directed RNA-seq analysis corroborated our RT-PCR analyses, by showing that these structural enzymes activate during perianth development in Aristolochia fimbriata and that the regulatory genes are expressed in correlation with color phenotype. Finally, the reconstruction of the flavonoid and anthocyanin metabolic pathways using predicted peptides from transcriptomic data show that all pivotal enzymes are present in the analyzed species. We conclude that the regulatory genes as well as the biosynthetic pathway are largely conserved across angiosperms. In addition, the Aristolochiaceae emerges as a remarkable group to study the genetic regulatory network for floral color, as their members exhibit an outstanding floral diversity with elaborate color patterns and the genetic complement for SG6 R2R3-MYB genes is simpler than in core eudicot model species.
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Affiliation(s)
- Sarita Muñoz-Gómez
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Harold Suárez-Baron
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica – CNSG, Sede de Investigación Universitaria, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, Bogotá, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
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175
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. TRENDS IN PLANT SCIENCE 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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176
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Zheng T, Li P, Li L, Zhang Q. Research advances in and prospects of ornamental plant genomics. HORTICULTURE RESEARCH 2021; 8:65. [PMID: 33790259 PMCID: PMC8012582 DOI: 10.1038/s41438-021-00499-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
The term 'ornamental plant' refers to all plants with ornamental value, which generally have beautiful flowers or special plant architectures. China is rich in ornamental plant resources and known as the "mother of gardens". Genomics is the science of studying genomes and is useful for carrying out research on genome evolution, genomic variations, gene regulation, and important biological mechanisms based on detailed genome sequence information. Due to the diversity of ornamental plants and high sequencing costs, the progress of genome research on ornamental plants has been slow for a long time. With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant (Prunus mume) was completed in 2012, whole-genome sequencing of more than 69 ornamental plants has been completed in <10 years. In this review, whole-genome sequencing and resequencing of ornamental plants will be discussed. We provide analysis with regard to basic data from whole-genome studies of important ornamental plants, the regulation of important ornamental traits, and application prospects.
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Affiliation(s)
- Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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177
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Silvestro D, Bacon CD, Ding W, Zhang Q, Donoghue PCJ, Antonelli A, Xing Y. Fossil data support a pre-Cretaceous origin of flowering plants. Nat Ecol Evol 2021; 5:449-457. [PMID: 33510432 DOI: 10.1038/s41559-020-01387-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023]
Abstract
Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin's hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling.
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Affiliation(s)
- Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, Fribourg, Switzerland.
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Wenna Ding
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Qiuyue Zhang
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yaowu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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178
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Tihelka E, Li L, Fu Y, Su Y, Huang D, Cai C. Angiosperm pollinivory in a Cretaceous beetle. NATURE PLANTS 2021; 7:445-451. [PMID: 33846595 DOI: 10.1038/s41477-021-00893-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Despite the crucial importance of flower-visiting insects in modern ecosystems, there is little fossil evidence on the origins of angiosperm pollination. Most reports of pollination in the Mesozoic fossil record have been based on the co-occurrence of the purported pollinators with pollen grains and assumed morphological adaptations for vectoring pollen. Here, we describe an exceptionally preserved short-winged flower beetle (Cucujoidea: Kateretidae) from mid-Cretaceous amber, Pelretes vivificus gen. et sp. nov., associated with pollen aggregations and coprolites consisting mainly of pollen, providing direct evidence of pollen-feeding in a Cretaceous beetle and confirming that diverse beetle lineages visited early angiosperms in the Cretaceous. The exquisite preservation of our fossil permits the identification of the pollen grains as Tricolpopollenites (Asteridae or Rosidae), representing a record of flower beetle pollination of a group of derived angiosperms in the Mesozoic and suggesting that potentially diverse beetle lineages visited early angiosperms by the mid-Cretaceous.
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Affiliation(s)
- Erik Tihelka
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Liqin Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Yanzhe Fu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Yitong Su
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
- School of Earth Sciences, University of Bristol, Bristol, UK.
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179
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Wyżewski Z, Gradowski M, Krysińska M, Dudkiewicz M, Pawłowski K. A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PeerJ 2021; 9:e11051. [PMID: 33854844 PMCID: PMC7955679 DOI: 10.7717/peerj.11051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/11/2021] [Indexed: 01/12/2023] Open
Abstract
The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers full understanding of the functioning of the living cells. ADP-ribosylation is a common post-translational modification of proteins; also nucleic acids and small molecules can be modified by the covalent attachment of ADP-ribose. This modification, important in cellular signalling and infection processes, is usually executed by enzymes from the large superfamily of ADP-ribosyltransferases (ARTs). Here, using bioinformatics approaches, we identify a novel putative ADP-ribosyltransferase family, conserved in eukaryotic evolution, with a divergent active site. The hallmark of these proteins is the ART domain nestled between flanking leucine-rich repeat (LRR) domains. LRRs are typically involved in innate immune surveillance. The novel family appears as putative novel ADP-ribosylation-related actors, most likely pseudoenzymes. Sequence divergence and lack of clearly detectable “classical” ART active site suggests the novel domains are pseudoARTs, yet atypical ART activity, or alternative enzymatic activity cannot be excluded. We propose that this family, including its human member LRRC9, may be involved in an ancient defense mechanism, with analogies to the innate immune system, and coupling pathogen detection to ADP-ribosyltransfer or other signalling mechanisms.
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Affiliation(s)
- Zbigniew Wyżewski
- Institute of Biological Sciences, Cardinal Stefan Wyszynski University in Warsaw, Warszawa, Poland
| | - Marcin Gradowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Marianna Krysińska
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Translational Medicine, Lund University, Lund, Sweden
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180
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Chen X, Tong C, Zhang X, Song A, Hu M, Dong W, Chen F, Wang Y, Tu J, Liu S, Tang H, Zhang L. A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:615-630. [PMID: 33073445 PMCID: PMC7955885 DOI: 10.1111/pbi.13493] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 05/03/2023]
Abstract
Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high-quality genome assembly of a typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most of the high-confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR-RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide-binding leucine-rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head-to-head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi-winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.
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Affiliation(s)
- Xuequn Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aixia Song
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Wei Dong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Fei Chen
- College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic ImprovementNational Center of Rapeseed ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Genomics and Genetic Engineering Laboratory of Ornamental PlantsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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181
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Wang P, Meng F, Moore BM, Shiu SH. Impact of short-read sequencing on the misassembly of a plant genome. BMC Genomics 2021; 22:99. [PMID: 33530937 PMCID: PMC7852129 DOI: 10.1186/s12864-021-07397-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/19/2021] [Indexed: 12/16/2022] Open
Abstract
Background Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively. Results To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads and the generality of these causes and factors should be tested further in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07397-5.
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Affiliation(s)
- Peipei Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,DOE Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Fanrui Meng
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,DOE Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Bethany M Moore
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,The Ecology, Evolution, and Behavioral Biology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. .,DOE Great Lake Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA. .,The Ecology, Evolution, and Behavioral Biology Program, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
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182
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Wang Y, Zhao Y, Wang S, Liu J, Wang X, Han Y, Liu F. Up-regulated 2-alkenal reductase expression improves low-nitrogen tolerance in maize by alleviating oxidative stress. PLANT, CELL & ENVIRONMENT 2021; 43:2957-2968. [PMID: 33215716 DOI: 10.1111/pce.13907] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 05/13/2023]
Abstract
In plants, cellular lipid peroxidation is enhanced under low nitrogen (LN) stress; this increases the lipid-derived reactive carbonyl species (RCS) levels. The cellular toxicity of RCS can be reduced by various RCS-scavenging enzymes. However, the roles of these enzymes in alleviating oxidative stress and improving nutrient use efficiency (NUE) under nutrient stress remain unknown. Here, we overexpressed maize endogenous NADPH-dependent 2-alkenal reductase (ZmAER) in maize; it significantly increased the tolerance of transgenic plants (OX-AER) to LN stress. Under LN condition, the biomass, nitrogen accumulation, NUE, and leaf photosynthesis of the OX-AER plants were significantly higher than those of the wild-type (WT) plants. The leaf and root malondialdehyde and H2 O2 levels in the transgenic plants were significantly lower than those in WT. The expression of antioxidant enzyme-related genes ZmCAT3, ZmPOD5 and ZmPOD13 was significantly higher in the transgenic lines than in WT. Under LN stress, the nitrate reductase activity in the OX-AER leaves was significantly increased compared with that in the WT leaves. Furthermore, under LN stress, ZmNRT1.1 and ZmNRT2.5 expression was upregulated in the OX-AER plants compared with that in WT. Overall, up-regulated ZmAER expression could enhance maize's tolerance to LN stress by alleviating oxidative stress and improve NUE.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yanxiang Zhao
- College of Plant Protection, China Agricultural University, Beijing, China
- Key Lab of Integrated Crop Disease and Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shanshan Wang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Junfeng Liu
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiqing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Yanlai Han
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, China
| | - Fang Liu
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
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183
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Hu J, Chang X, Zhang Y, Yu X, Qin Y, Sun Y, Zhang L. The pineapple MADS-box gene family and the evolution of early monocot flower. Sci Rep 2021; 11:849. [PMID: 33441609 PMCID: PMC7806820 DOI: 10.1038/s41598-020-79163-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/27/2020] [Indexed: 11/23/2022] Open
Abstract
Unlike the flower of the model monocot rice, which has diverged greatly from the ancestral monocot flower, the pineapple (Ananas comosus) flower is more typical of monocot flowers. Here, we identified 43 pineapple genes containing MADS-box domains, including 11 type I and 32 type II genes. RNA-seq expression data generated from five pineapple floral organs (sepals, petals, stamens, pistils, and ovules) and quantitative real-time PCR revealed tissue-specific expression patterns for some genes. We found that AcAGL6 and AcFUL1 were mainly expressed in sepals and petals, suggesting their involvement in the regulation of these floral organs. A pineapple ‘ABCDE’ model was proposed based on the phylogenetic analysis and expression patterns of MADS-box genes. Unlike rice and orchid with frequent species-specific gene duplication and subsequent expression divergence, the composition and expression of the ABCDE genes were conserved in pineapple. We also found that AcSEP1/3, AcAG, AcAGL11a/b/c, and AcFUL1 were highly expressed at different stages of fruit development and have similar expression profiles, implicating these genes’ role in fruit development and ripening processes. We propose that the pineapple flower can be used as a model for studying the ancestral form of monocot flowers to investigate their development and evolutionary history.
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Affiliation(s)
- Juan Hu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaojun Chang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xianxian Yu
- School of Urban-Rural Planning and Landscape Architecture, Xuchang University, Xuchang, 461000, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yun Sun
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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184
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Schnabel A, Cotinguiba F, Athmer B, Vogt T. Piper nigrum CYP719A37 Catalyzes the Decisive Methylenedioxy Bridge Formation in Piperine Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2021; 10:128. [PMID: 33435446 PMCID: PMC7826766 DOI: 10.3390/plants10010128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/16/2022]
Abstract
Black pepper (Piper nigrum) is among the world's most popular spices. Its pungent principle, piperine, has already been identified 200 years ago, yet the biosynthesis of piperine in black pepper remains largely enigmatic. In this report we analyzed the characteristic methylenedioxy bridge formation of the aromatic part of piperine by a combination of RNA-sequencing, functional expression in yeast, and LC-MS based analysis of substrate and product profiles. We identified a single cytochrome P450 transcript, specifically expressed in black pepper immature fruits. The corresponding gene was functionally expressed in yeast (Saccharomyces cerevisiae) and characterized for substrate specificity with a series of putative aromatic precursors with an aromatic vanilloid structure. Methylenedioxy bridge formation was only detected when feruperic acid (5-(4-hydroxy-3-methoxyphenyl)-2,4-pentadienoic acid) was used as a substrate, and the corresponding product was identified as piperic acid. Two alternative precursors, ferulic acid and feruperine, were not accepted. Our data provide experimental evidence that formation of the piperine methylenedioxy bridge takes place in young black pepper fruits after a currently hypothetical chain elongation of ferulic acid and before the formation of the amide bond. The partially characterized enzyme was classified as CYP719A37 and is discussed in terms of specificity, storage, and phylogenetic origin of CYP719 catalyzed reactions in magnoliids and eudicots.
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Affiliation(s)
- Arianne Schnabel
- Leibniz Institute of Plant Biochemistry, Department Cell and Metabolic Biology, Weinberg 3, D-06120 Halle (Saale), Germany; (A.S.); (B.A.)
| | - Fernando Cotinguiba
- Instituto de Pesquisas de Produtos Naturais (IPPN), Universidade Federal do Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro/RJ, Brazil;
| | - Benedikt Athmer
- Leibniz Institute of Plant Biochemistry, Department Cell and Metabolic Biology, Weinberg 3, D-06120 Halle (Saale), Germany; (A.S.); (B.A.)
| | - Thomas Vogt
- Leibniz Institute of Plant Biochemistry, Department Cell and Metabolic Biology, Weinberg 3, D-06120 Halle (Saale), Germany; (A.S.); (B.A.)
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185
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Zhang H, Yu Z, Yao X, Chen J, Chen X, Zhou H, Lou Y, Ming F, Jin Y. Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response. BMC PLANT BIOLOGY 2021; 21:4. [PMID: 33407147 PMCID: PMC7789510 DOI: 10.1186/s12870-020-02781-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/02/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Auxin is critical to plant growth and development, as well as stress responses. Small auxin-up RNA (SAUR) is the largest family of early auxin responsive genes in higher plants. However, the function of few SAUR genes is known owing to functional redundancy among the many family members. RESULTS In this study, we conducted a phylogenetic analysis using protein sequences of 795 SAURs from Anthoceros angustus, Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Ginkgo biloba, Gnetum montanum, Amborella trichopoda, Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Medicago truncatula and Setaria italica. The phylogenetic trees showed that the SAUR proteins could be divided into 10 clades and three subfamilies, and that SAUR proteins of three bryophyte species were only located in subfamily III, which suggested that they may be ancestral. From bryophyta to anthophyta, SAUR family have appeared very large expansion. The number of SAUR gene in Fabaceae species was considerably higher than that in other plants, which may be associated with independent whole genome duplication event in the Fabaceae lineages. The phylogenetic trees also showed that SAUR genes had expanded independently monocotyledons and dicotyledons in angiosperms. Conserved motif and protein structure prediction revealed that SAUR proteins were highly conserved among higher plants, and two leucine residues in motif I were observed in almost all SAUR proteins, which suggests the residues plays a critical role in the stability and function of SAUR proteins. Expression analysis of SAUR genes using publicly available RNA-seq data from rice and soybean indicated functional similarity of members in the same clade, which was also further confirmed by qRT-PCR. Summarization of SAUR functions also showed that SAUR functions were usually consistent within a subclade. CONCLUSIONS This study provides insights into the evolution and function of the SAUR gene family from bryophyta to anthophyta, particularly in Fabaceae plants. Future investigation to understand the functions of SAUR family members should employ a clade as the study unit.
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Affiliation(s)
- Hao Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Zhenjia Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Xiaodie Yao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Jingli Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Xing Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Huiwen Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Yuxia Lou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China
| | - Feng Ming
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China.
| | - Yue Jin
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China.
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186
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Furumizu C, Sawa S. The RGF/GLV/CLEL Family of Short Peptides Evolved Through Lineage-Specific Losses and Diversification and Yet Conserves Its Signaling Role Between Vascular Plants and Bryophytes. FRONTIERS IN PLANT SCIENCE 2021; 12:703012. [PMID: 34354727 PMCID: PMC8329595 DOI: 10.3389/fpls.2021.703012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/28/2021] [Indexed: 05/12/2023]
Abstract
Short secreted plant peptides act as key signaling molecules and control a plethora of developmental and physiological processes. The ROOT GROWTH FACTOR (RGF)/GOLVEN (GLV)/CLE-Like (CLEL) family of peptides was discovered to be involved in root development in Arabidopsis thaliana. In contrast to active research efforts, which have been revealing receptors and downstream signaling components, little attention has been paid to evolutionary processes that shaped the RGF signaling system as we know it in angiosperms today. As a first step toward understanding how RGF signaling emerged and evolved, this study aimed to elucidate the phylogenetic distribution and functional conservation of RGF-like sequences. Using publicly available, genome and transcriptome data, RGF-like sequences were searched in 27 liverworts, 22 mosses, 8 hornworts, 23 lycophytes, 23 ferns, 38 gymnosperms, and 8 angiosperms. This led to the identification of more than four hundreds of RGF-like sequences in all major extant land plant lineages except for hornworts. Sequence comparisons within and between taxonomic groups identified lineage-specific characters. Notably, one of the two major RGF subgroups, represented by A. thaliana RGF6/GLV1/CLEL6, was found only in vascular plants. This subgroup, therefore, likely emerged in a common ancestor of vascular plants after its divergence from bryophytes. In bryophytes, our results infer independent losses of RGF-like sequences in mosses and hornworts. On the other hand, a single, highly similar RGF-like sequence is conserved in liverworts, including Marchantia polymorpha, a genetically tractable model species. When constitutively expressed, the M. polymorpha RGF-like sequence (MpRGF) affected plant development and growth both in A. thaliana and M. polymorpha. This suggests that MpRGF can exert known RGF-like effects and that MpRGF is under transcriptional control so that its potent activities are precisely controlled. These data suggest that RGFs are conserved as signaling molecules in both vascular plants and bryophytes and that lineage-specific diversification has increased sequence variations of RGFs. All together, our findings form a basis for further studies into RGF peptides and their receptors, which will contribute to our understandings of how peptide signaling pathways evolve.
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187
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Wang X, An Y, Xu P, Xiao J. Functioning of PPR Proteins in Organelle RNA Metabolism and Chloroplast Biogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:627501. [PMID: 33633768 PMCID: PMC7900629 DOI: 10.3389/fpls.2021.627501] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/04/2021] [Indexed: 05/05/2023]
Abstract
The pentatricopeptide repeat (PPR) proteins constitute one of the largest nuclear-encoded protein families in higher plants, with over 400 members in most sequenced plant species. The molecular functions of these proteins and their physiological roles during plant growth and development have been widely studied. Generally, there is mounting evidence that PPR proteins are involved in the post-transcriptional regulation of chloroplast and/or mitochondrial genes, including RNA maturation, editing, intron splicing, transcripts' stabilization, and translation initiation. The cooperative action of RNA metabolism has profound effects on the biogenesis and functioning of both chloroplasts and mitochondria and, consequently, on the photosynthesis, respiration, and development of plants and their environmental responses. In this review, we summarize the latest research on PPR proteins, specifically how they might function in the chloroplast, by documenting their mechanism of molecular function, their corresponding RNA targets, and their specific effects upon chloroplast biogenesis and host organisms.
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Affiliation(s)
- Xinwei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yaqi An
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Pan Xu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jianwei Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Jianwei Xiao,
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188
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Shi T, Chen J. A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication. Genome Biol 2020; 21:295. [PMID: 33292440 PMCID: PMC7722308 DOI: 10.1186/s13059-020-02212-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/23/2020] [Indexed: 11/25/2022] Open
Abstract
The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots.
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Affiliation(s)
- Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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189
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The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. Genome Biol 2020; 21:291. [PMID: 33267872 PMCID: PMC7709256 DOI: 10.1186/s13059-020-02198-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 11/06/2020] [Indexed: 12/25/2022] Open
Abstract
Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation. Supplementary information The online version contains supplementary material available at 10.1186/s13059-020-02198-7.
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190
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Chen ZH, Soltis DE. Evolution of environmental stress responses in plants. PLANT, CELL & ENVIRONMENT 2020; 43:2827-2831. [PMID: 33103798 DOI: 10.1111/pce.13922] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
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191
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Zhang L, Wu S, Chang X, Wang X, Zhao Y, Xia Y, Trigiano RN, Jiao Y, Chen F. The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress. PLANT, CELL & ENVIRONMENT 2020; 43:2847-2856. [PMID: 33001478 DOI: 10.1111/pce.13898] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/22/2020] [Accepted: 09/26/2020] [Indexed: 05/24/2023]
Abstract
Flowering plants, or angiosperms, consist of more than 300,000 species, far more than any other land plant lineages. The accumulated evidence indicates that multiple ancient polyploidy events occurred around 100 to 120 million years ago during the Cretaceous and drove the early diversification of four major clades of angiosperms: gamma whole-genome triplication in the common ancestor of core eudicots, tau whole-genome duplication during the early diversification of monocots, lambda whole-genome duplication during the early diversification of magnoliids, and pi whole-genome duplication in the Nymphaeales lineage. These four polyploidy events have played essential roles in the adaptive evolution and diversification of major clades of flowering plants. Here, we specifically review the current understanding of this wave of ancient whole-genome duplications and their evolutionary significance. Notably, although these ancient whole-genome duplications occurred independently, they have contributed to the expansion of many stress-related genes (e.g., heat shock transcription factors and Arabidopsis response regulators),and these genes could have been selected for by global environmental changes in the Cretaceous. Therefore, this ancient wave of paleopolyploidy events could have significantly contributed to the adaptation of angiosperms to environmental changes, and potentially promoted the wide diversification of flowering plants.
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Affiliation(s)
- Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shengdan Wu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Xiaojun Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiuyun Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunpeng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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192
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Yu J, Li L, Wang S, Dong S, Chen Z, Patel N, Goffinet B, Chen H, Liu H, Liu Y. Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta). GIGABYTE 2020; 2020:gigabyte8. [PMID: 36824590 PMCID: PMC9631980 DOI: 10.46471/gigabyte.8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/13/2020] [Indexed: 11/09/2022] Open
Abstract
Mosses comprise one of three lineages forming a sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to, and colonization of, land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss that is widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo-assembled its genome using the 10X Genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO Viridiplantae odb10 dataset. The newly generated F. antipyretica genome is the third moss genome, and the second seedless aquatic plant genome, to be sequenced and assembled to date.
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Affiliation(s)
- Jin Yu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Shanshan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
| | - Ziqiang Chen
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130012, China
| | - Nikisha Patel
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Hongfeng Chen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
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193
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Zheng X, He L, Liu Y, Mao Y, Wang C, Zhao B, Li Y, He H, Guo S, Zhang L, Schneider H, Tadege M, Chang F, Chen J. A study of male fertility control in Medicago truncatula uncovers an evolutionarily conserved recruitment of two tapetal bHLH subfamilies in plant sexual reproduction. THE NEW PHYTOLOGIST 2020; 228:1115-1133. [PMID: 32594537 DOI: 10.1111/nph.16770] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
Male sterility is an important tool for plant breeding and hybrid seed production. Male-sterile mutants are largely due to an abnormal development of either the sporophytic or gametophytic anther tissues. Tapetum, a key sporophytic tissue, provides nutrients for pollen development, and its delayed degeneration induces pollen abortion. Numerous bHLH proteins have been documented to participate in the degeneration of the tapetum in angiosperms, but relatively little attention has been given to the evolution of the involved developmental pathways across the phylogeny of land plants. A combination of cellular, molecular, biochemical and evolutionary analyses was used to investigate the male fertility control in Medicago truncatula. We characterized the male-sterile mutant empty anther1 (ean1) and identified EAN1 as a tapetum-specific bHLH transcription factor necessary for tapetum degeneration. Our study uncovered an evolutionarily conserved recruitment of bHLH subfamily II and III(a + c)1 in the regulation of tapetum degeneration. EAN1 belongs to the subfamily II and specifically forms heterodimers with the subfamily III(a + c)1 members, which suggests a heterodimerization mechanism conserved in angiosperms. Our work suggested that the pathway of two tapetal-bHLH subfamilies is conserved in all land plants, and likely was established before the divergence of the spore-producing land plants.
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Affiliation(s)
- Xiaoling Zheng
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoqun Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Youhan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hua He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shiqi Guo
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Fang Chang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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194
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Kirie S, Iwasaki H, Noshita K, Iwata H. A theoretical morphological model for quantitative description of the three-dimensional floral morphology in water lily (Nymphaea). PLoS One 2020; 15:e0239781. [PMID: 33045021 PMCID: PMC7549838 DOI: 10.1371/journal.pone.0239781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/13/2020] [Indexed: 12/01/2022] Open
Abstract
Water lilies (Nymphaea spp.) have diverse floral morphologies. Water lilies are not only commonly used as ornamental plants, but they are also important for understanding the diversification of basal angiosperms. Although the diversity in floral morphology of water lily provides useful information for evolutionary biology, horticulture, and horticultural science, it is difficult to describe and analyze the three-dimensional morphology of flowers. In this study, we propose a method to describe the floral morphology of water lily using a three-dimensional theoretical morphological model. The theoretical model was constructed based on three components, i.e., (1) the gradual change in size of floral organs, (2) spiral phyllotaxis, and (3) the interpolation of elevation angles, which were integrated into the model. We generated three-dimensional representation of water lily flowers and visualized theoretical morphospaces by varying each morphological parameter. The theoretical morphospace is a mathematical space of morphological spectrum generated by a theoretical morphological model. These morphospaces seems to display the large part of morphological variations of water lily. We measured morphological parameters of real flowers based on our theoretical model and display the occupation pattern of morphological parameters. We also surveyed the relation between morphological parameters and flower shape descriptions found in a catalog. In some parameters, we found breeders’ description can link to our morphological model. In addition, the relationship between the global features of floral morphology and the parameters of the theoretical model was calculated with flower silhouettes simulated with a range of parameter values and the global features of the silhouette. We used two simple indices to assess the global morphological features, which were calculated with the convex hull. The results indicated that our method can effectively provide an objective and quantitative overview of the diversity in the floral morphology of water lily.
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Affiliation(s)
- Shiryu Kirie
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hideo Iwasaki
- metaPhorest, Department of Electrical Engineering and Bioscience, Waseda University, TWIns, Shinjuku, Tokyo, Japan
| | - Koji Noshita
- Department of Biology, Faculty of Science of Science, Kyushu University, Fukuoka, Fukuoka, Japan
- Plant Frontier Research Center, Kyushu University, Fukuoka, Fukuoka, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail:
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195
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Guo Y, Qiao D, Yang C, Chen J, Li Y, Liang S, Lin K, Chen Z. Genome-wide identification and expression analysis of SABATH methyltransferases in tea plant ( Camellia sinensis): insights into their roles in plant defense responses. PLANT SIGNALING & BEHAVIOR 2020; 15:1804684. [PMID: 32787495 PMCID: PMC8550540 DOI: 10.1080/15592324.2020.1804684] [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: 07/05/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 06/02/2023]
Abstract
SABATH methyltransferases convent plant small-molecule metabolites into volatile methyl esters, which play important roles in many biological processes and defense reactions in plants. In this study, a total of 32 SABATH genes were identified in the Camellia sinensis var. sinensis (CSS) genome, which were renamed CsSABATH1 to CsSABATH32. Genome location annotation suggested that tandem duplication was responsible for the expansion of SABATH genes in tea plant. Multiple sequence alignment and phylogenetic analysis showed that the CsSABATHs could be classified into three groups (I, II and III), which were also supported by gene structures and conserved motifs analysis. Group II contained only two CsSABATH proteins, which were closely related to PtIAMT, AtIAMT and OsIAMT. The group III SABATH genes of tea plant exhibited expansion on the CSS genome compared with Camellia sinensis var. assamica (CSA) genome. Based on RNA-seq data, the CsSABATHs exhibited tissue-specific expression patterns, and the members with high expression in buds and young leaves were also obviously upregulated after MeJA treatment. The expression of many transcription factors was significantly correlated with that of different members of the CsSABATH gene family, suggesting a potential regulatory relationship between them. Quantitative real-time PCR (qPCR) expression analysis showed that CsSABATHs could respond to exogenous JA, SA and MeSA treatments in tea plants. RNA-seq data analysis and qPCR validation suggested that CsSABATH8, 11, 16, 25, 29 and 32 might play a special role in plant defense against insect herbivory. These results provide references for evolutionary studies of the plant SABATH family and the exploration of the potential roles of CsSABATHs in tea plant defense responses.
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Affiliation(s)
- Yan Guo
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Dahe Qiao
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Chun Yang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Juan Chen
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yan Li
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Sihui Liang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Kaiqin Lin
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Zhengwu Chen
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
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196
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Spencer V, Nemec Venza Z, Harrison CJ. What can lycophytes teach us about plant evolution and development? Modern perspectives on an ancient lineage. Evol Dev 2020; 23:174-196. [PMID: 32906211 DOI: 10.1111/ede.12350] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
All Evo-Devo studies rely on representative sampling across the tree of interest to elucidate evolutionary trajectories through time. In land plants, genetic resources are well established in model species representing lineages including bryophytes (mosses, liverworts, and hornworts), monilophytes (ferns and allies), and seed plants (gymnosperms and flowering plants), but few resources are available for lycophytes (club mosses, spike mosses, and quillworts). Living lycophytes are a sister group to the euphyllophytes (the fern and seed plant clade), and have retained several ancestral morphological traits despite divergence from a common ancestor of vascular plants around 420 million years ago. This sister relationship offers a unique opportunity to study the conservation of traits such as sporophyte branching, vasculature, and indeterminacy, as well as the convergent evolution of traits such as leaves and roots which have evolved independently in each vascular plant lineage. To elucidate the evolution of vascular development and leaf formation, molecular studies using RNA Seq, quantitative reverse transcription polymerase chain reaction, in situ hybridisation and phylogenetics have revealed the diversification and expression patterns of KNOX, ARP, HD-ZIP, KANADI, and WOX gene families in lycophytes. However, the molecular basis of further trait evolution is not known. Here we describe morphological traits of living lycophytes and their extinct relatives, consider the molecular underpinnings of trait evolution and discuss future research required in lycophytes to understand the key evolutionary innovations enabling the growth and development of all vascular plants.
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Affiliation(s)
- Victoria Spencer
- School of Biological Sciences, The University of Bristol, Bristol, UK
| | - Zoe Nemec Venza
- School of Biological Sciences, The University of Bristol, Bristol, UK
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197
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Shi T, Rahmani RS, Gugger PF, Wang M, Li H, Zhang Y, Li Z, Wang Q, Van de Peer Y, Marchal K, Chen J. Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants. Mol Biol Evol 2020; 37:2394-2413. [PMID: 32343808 PMCID: PMC7403625 DOI: 10.1093/molbev/msaa105] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K-pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein-protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein-protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.
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Affiliation(s)
- Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD
| | - Muhua Wang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hui Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhizhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingfeng Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDLab, IMEC, Ghent University, Ghent, Belgium
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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198
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LI XW, CHEN SL. Herbgenomics facilitates biological study of TCM. Chin J Nat Med 2020; 18:561-562. [DOI: 10.1016/s1875-5364(20)30067-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Indexed: 11/28/2022]
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199
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Lv Q, Qiu J, Liu J, Li Z, Zhang W, Wang Q, Fang J, Pan J, Chen Z, Cheng W, Barker MS, Huang X, Wei X, Cheng K. The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1910-1923. [PMID: 32524692 DOI: 10.1111/tpj.14874] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 05/11/2023]
Abstract
Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome-level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated protein-coding genes. Phylogenetic analyses revealed that magnoliids were sister to the eudicots. Two rounds of ancient whole-genome duplication were inferred in the C. salicifolious genome. One is shared by Calycanthaceae after its divergence with Lauraceae, and the other is in the ancestry of Magnoliales and Laurales. Notably, long genes with > 20 kb in length were much more prevalent in the magnoliid genomes compared with other angiosperms, which could be caused by the length expansion of introns inserted by transposon elements. Homologous genes within the flavonoid pathway for C. salicifolius were identified, and correlation of the gene expression and the contents of flavonoid metabolites revealed potential critical genes involved in flavonoids biosynthesis. This study not only provides an additional whole-genome sequence from the magnoliids, but also opens the door to functional genomic research and molecular breeding of C. salicifolius.
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Affiliation(s)
- Qundan Lv
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | - Wenting Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Fang
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Junjie Pan
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Zhengdao Chen
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Wenliang Cheng
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Kejun Cheng
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
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200
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Nymphaea colorata (Blue-Petal Water Lily). Trends Genet 2020; 36:718-719. [PMID: 32631632 DOI: 10.1016/j.tig.2020.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 11/22/2022]
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