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Cao J, Wang H, Cao Y, Kan S, Li J, Liu Y. Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats. Int J Mol Sci 2024; 25:2278. [PMID: 38396955 PMCID: PMC10888665 DOI: 10.3390/ijms25042278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of Eomecon chionantha, while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.
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Affiliation(s)
- Jialiang Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Hongwei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Yanan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Shenglong Kan
- Marine College, Shandong University, Weihai 264209, China;
| | - Jiamei Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanyan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
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Zhao S, Gao X, Yu X, Yuan T, Zhang G, Liu C, Li X, Wei P, Li X, Liu X. Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation. Int J Mol Sci 2024; 25:2193. [PMID: 38396871 PMCID: PMC10888623 DOI: 10.3390/ijms25042193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.
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Affiliation(s)
- Shuqi Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoman Gao
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Xiaolei Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tao Yuan
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Guiyu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xinzhong Li
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan 430072, China;
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
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Lei W, Zhu H, Cao M, Zhang F, Lai Q, Lu S, Dong W, Sun J, Ru D. From genomics to metabolomics: Deciphering sanguinarine biosynthesis in Dicranostigma leptopodum. Int J Biol Macromol 2024; 257:128727. [PMID: 38092109 DOI: 10.1016/j.ijbiomac.2023.128727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023]
Abstract
Dicranostigma leptopodum (Maxim) Fedde (DLF) is a renowned medicinal plant in China, known to be rich in alkaloids. However, the unavailability of a reference genome has impeded investigation into its plant metabolism and genetic breeding potential. Here we present a high-quality chromosomal-level genome assembly for DLF, derived using a combination of Nanopore long-read sequencing, Illumina short-read sequencing and Hi-C technologies. Our assembly genome spans a size of 621.81 Mb with an impressive contig N50 of 93.04 Mb. We show that the species-specific whole-genome duplication (WGD) of DLF and Papaver somniferum corresponded to two rounds of WGDs of Papaver setigerum. Furthermore, we integrated comprehensive homology searching, gene family analyses and construction of a gene-to-metabolite network. These efforts led to the discovery of co-expressed transcription factors, including NAC and bZIP, alongside sanguinarine (SAN) pathway genes CYP719 (CFS and SPS). Notably, we identified P6H as a promising gene for enhancing SAN production. By providing the first reference genome for Dicranostigma, our study confirms the genomic underpinning of SAN biosynthesis and establishes a foundation for advancing functional genomic research on Papaveraceae species. Our findings underscore the pivotal role of high-quality genome assemblies in elucidating genetic variations underlying the evolutionary origin of secondary metabolites.
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Affiliation(s)
- Weixiao Lei
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Man Cao
- Gansu Pharmacovigilance Center, Lanzhou 730070, China
| | - Feng Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qing Lai
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shengming Lu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Jiahui Sun
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China.
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Wu D, Qin Q, Wang X, Niu Y, Zhang S, Mu Z. Sequence Analysis of the Plastomes of Two Tibetan Medicinal Plants of the Family Papaveraceae. FRONT BIOSCI-LANDMRK 2023; 28:352. [PMID: 38179751 DOI: 10.31083/j.fbl2812352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/12/2023] [Accepted: 09/05/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND With the rapid development of next-generation sequencing technology, more plants plastomes have been sequenced, further advancing species identification and phylogenetic studies. However, there are a few studies on the genetic and phylogenetic analysis of the plastomes of Dicranostigma lactucoides Hook. f. et Thoms. and Hypecoum leptocarpum Hook. f. et Thoms. METHODS In this study, we sequenced and analyzed the plastomes of Dicranostigma lactucoides Hook. f. et Thoms. and Hypecoum leptocarpum Hook. f. et Thoms., and conducted a phylogenetic analysis using 13 related species. RESULTS The results showed that the plastomes of both D. lactucoides and H. leptocarpum had a typical tetrad structure, with sizes of 166,819 bp and 163,282 bp, respectively. We annotated 133 genes for D. lactucoides and 120 genes for H. leptocarpum. A total of 72 and 43 simple repetitive sequences were detected in D. lactucoides and H. leptocarpum, respectively. Codon preference analysis showed that the relative usage frequency of codons and the relative abundance of synonymous codons used were the same for both plastomes. Nucleotide polymorphism analysis identified seven variant loci with high nucleotide diversity (Pi) values, all located in the large single copy (LSC) region. Inverted repeat (IR) boundary analysis revealed differences in gene types and locations on both sides of the boundary, except for the small single copy/inverted repeat a (SSC/IRa) boundary. The phylogenetic analysis showed the species clustered into two major groups, one with five genera (Hypecoum, Corydalis, Papaver, Meconopsis, and Dicranostigma) and the other with two genera (Coreanomecon; and Hylomecon). CONCLUSIONS Comparative analysis of the plastome genomic characteristics and phylogeny of D. lactucoides and H. leptocarpum laid the foundation for identifying the above two species and the phylogenetic study and comprehensive exploitation of the Papaveraceae.
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Affiliation(s)
- Danyang Wu
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Qian Qin
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Xiaoyun Wang
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Yiming Niu
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Shouwen Zhang
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Zejing Mu
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
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Kim SC, Ha YH, Park BK, Jang JE, Kang ES, Kim YS, Kimspe TH, Kim HJ. Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. PLoS One 2023; 18:e0289625. [PMID: 37733832 PMCID: PMC10513226 DOI: 10.1371/journal.pone.0289625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/24/2023] [Indexed: 09/23/2023] Open
Abstract
Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.
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Affiliation(s)
- Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Beom Kyun Park
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Ju Eun Jang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Eun Su Kang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Soo Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Tae-Hee Kimspe
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyuk-Jin Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
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Xu Z, Li Z, Ren F, Gao R, Wang Z, Zhang J, Zhao T, Ma X, Pu X, Xin T, Rombauts S, Sun W, Van de Peer Y, Chen S, Song J. The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales. Plant J 2022; 111:217-230. [PMID: 35476217 PMCID: PMC7614287 DOI: 10.1111/tpj.15788] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/05/2022] [Accepted: 04/24/2022] [Indexed: 05/05/2023]
Abstract
Species belonging to the order Ranunculales have attracted much attention because of their phylogenetic position as a sister group to all other eudicot lineages and their ability to produce unique yet diverse benzylisoquinoline alkaloids (BIAs). The Papaveraceae family in Ranunculales is often used as a model system for studying BIA biosynthesis. Here, we report the chromosome-level genome assembly of Corydalis tomentella, a species of Fumarioideae, one of the two subfamilies of Papaveraceae. Based on comparisons of sequenced Ranunculalean species, we present clear evidence of a shared whole-genome duplication (WGD) event that has occurred before the divergence of Ranunculales but after its divergence from other eudicot lineages. The C. tomentella genome enabled us to integrate isotopic labeling and comparative genomics to reconstruct the BIA biosynthetic pathway for both sanguinarine biosynthesis shared by papaveraceous species and the cavidine biosynthesis that is specific to Corydalis. Also, our comparative analysis revealed that gene duplications, especially tandem gene duplications, underlie the diversification of BIA biosynthetic pathways in Ranunculales. In particular, tandemly duplicated berberine bridge enzyme-like genes appear to be involved in cavidine biosynthesis. In conclusion, our study of the C. tomentella genome provides important insights into the occurrence of WGDs during the early evolution of eudicots, as well as into the evolution of BIA biosynthesis in Ranunculales.
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Affiliation(s)
- Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Fengming Ren
- Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, China
| | - Ranran Gao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Zhe Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinlan Zhang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- Academy for Advanced Interdisciplinary Studies and College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Corresponding Authors: Jingyuan Song (), Shilin Chen (), and Yves Van de Peer ()
| | - Shilin Chen
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
- Corresponding Authors: Jingyuan Song (), Shilin Chen (), and Yves Van de Peer ()
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong 666100, China
- Corresponding Authors: Jingyuan Song (), Shilin Chen (), and Yves Van de Peer ()
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Dudek B, Warskulat AC, Vogel H, Wielsch N, Menezes RC, Hupfer Y, Paetz C, Gebauer-Jung S, Svatoš A, Schneider B. An Integrated-Omics/Chemistry Approach Unravels Enzymatic and Spontaneous Steps to Form Flavoalkaloidal Nudicaulin Pigments in Flowers of Papaver nudicaule L. Int J Mol Sci 2021; 22:ijms22084129. [PMID: 33923591 PMCID: PMC8073789 DOI: 10.3390/ijms22084129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022] Open
Abstract
Flower colour is an important trait for plants to attract pollinators and ensure their reproductive success. Among yellow flower pigments, the nudicaulins in Papaver nudicaule L. (Iceland poppy) are unique due to their rarity and unparalleled flavoalkaloid structure. Nudicaulins are derived from pelargonidin glycoside and indole, products of the flavonoid and indole/tryptophan biosynthetic pathway, respectively. To gain insight into the molecular and chemical basis of nudicaulin biosynthesis, we combined transcriptome, differential gel electrophoresis (DIGE)-based proteome, and ultra-performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS)-based metabolome data of P. nudicaule petals with chemical investigations. We identified candidate genes and proteins for all biosynthetic steps as well as some key metabolites across five stages of petal development. Candidate genes of amino acid biosynthesis showed a relatively stable expression throughout petal development, whereas most candidate genes of flavonoid biosynthesis showed increasing expression during development followed by downregulation in the final stage. Notably, gene candidates of indole-3-glycerol-phosphate lyase (IGL), sharing characteristic sequence motifs with known plant IGL genes, were co-expressed with flavonoid biosynthesis genes, and are probably providing free indole. The fusion of indole with pelargonidin glycosides was retraced synthetically and promoted by high precursor concentrations, an excess of indole, and a specific glycosylation pattern of pelargonidin. Thus, nudicaulin biosynthesis combines the enzymatic steps of two different pathways with a spontaneous fusion of indole and pelargonidin glycoside under precisely tuned reaction conditions.
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Li Y, Winzer T, He Z, Graham IA. Over 100 Million Years of Enzyme Evolution Underpinning the Production of Morphine in the Papaveraceae Family of Flowering Plants. Plant Commun 2020; 1:100029. [PMID: 32685922 PMCID: PMC7357826 DOI: 10.1016/j.xplc.2020.100029] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/06/2019] [Accepted: 02/03/2020] [Indexed: 05/06/2023]
Abstract
Phylogenomic analysis of whole genome sequences of five benzylisoquinoline alkaloid (BIA)-producing species from the Ranunculales and Proteales orders of flowering plants revealed the sequence and timing of evolutionary events leading to the diversification of these compounds. (S)-Reticuline is a pivotal intermediate in the synthesis of many BIAs and our analyses revealed parallel evolution between the two orders, which diverged ∼122 million years ago (MYA). Berberine is present in species across the entire Ranunculales, and we found co-evolution of genes essential for production of the protoberberine class. The benzophenanthridine class, which includes the antimicrobial compound sanguinarine, is specific to the Papaveraceae family of Ranunculales, and biosynthetic genes emerged after the split with the Ranunculaceae family ∼110 MYA but before the split of the three Papaveraceae species used in this study at ∼77 MYA. The phthalideisoquinoline noscapine and morphinan class of BIAs are exclusive to the opium poppy lineage. Ks estimation of paralogous pairs indicates that morphine biosynthesis evolved more recently than 18 MYA in the Papaver genus. In the preceding 100 million years gene duplication, neofunctionalization and recruitment of additional enzyme classes, combined with gene clustering, gene fusion, and gene amplification, resulted in emergence of medicinally valuable BIAs including morphine and noscapine.
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Affiliation(s)
- Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
| | - Thilo Winzer
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
| | - Zhesi He
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
| | - Ian A. Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
- Corresponding author
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Zhao Y, Pfannebecker K, Dommes AB, Hidalgo O, Becker A, Elomaa P. Evolutionary diversification of CYC/TB1-like TCP homologs and their recruitment for the control of branching and floral morphology in Papaveraceae (basal eudicots). New Phytol 2018; 220:317-331. [PMID: 29949661 DOI: 10.1111/nph.15289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
Angiosperms possess enormous morphological variation in plant architectures and floral forms. Previous studies in Pentapetalae and monocots have demonstrated the involvement of TCP domain CYCLOIDEA/TEOSINTE BRANCHED1-like (CYC/TB1) genes in the control of floral symmetry and shoot branching. However, how TCP/CYC-like (CYL) genes originated, evolved and functionally diversified remain unclear. We conducted a comparative functional study in Ranunculales, the sister lineage to all other eudicots, between Eschscholzia californica and Cysticapnos vesicaria, two species of Papaveraceae with actinomorphic and zygomorphic flowers, respectively. Phylogenetic analysis indicates that CYL genes in Papaveraceae form two paralogous lineages, PapaCYL1 and PapaCYL2. Papaveraceae CYL genes show highly diversified expression patterns as well as functions. Enhanced branching by silencing of EscaCYL1 suggests that the role of CYC/TB1-like genes in branching control is conserved in Papaveraceae. In contrast to the arrest of stamen development in Pentapetalae, PapaCYL genes promote stamen initiation and growth. In addition, we demonstrate that CyveCYLs are involved in perianth development, specifying sepal and petal identity in Cysticapnos by regulating the B-class floral organ identity genes. Our data also suggest the involvement of CyveCYL genes in the regulation of flower symmetry in Cysticapnos. Our work provides evidence of the importance of TCP/CYC-like genes in the promotion of morphological diversity across angiosperms.
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Affiliation(s)
- Yafei Zhao
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Kai Pfannebecker
- Institute of Botany, University of Giessen, Giessen, 35392, Germany
| | | | - Oriane Hidalgo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
| | - Annette Becker
- Institute of Botany, University of Giessen, Giessen, 35392, Germany
| | - Paula Elomaa
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
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10
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Park S, An B, Park S. Reconfiguration of the plastid genome in Lamprocapnos spectabilis: IR boundary shifting, inversion, and intraspecific variation. Sci Rep 2018; 8:13568. [PMID: 30206286 PMCID: PMC6134119 DOI: 10.1038/s41598-018-31938-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/09/2018] [Indexed: 12/23/2022] Open
Abstract
We generated a complete plastid genome (plastome) sequence for Lamprocapnos spectabilis, providing the first complete plastome from the subfamily Fumarioideae (Papaveraceae). The Lamprocapnos plastome shows large differences in size, structure, gene content, and substitution rates compared with two sequenced Papaveraceae plastomes. We propose a model that explains the major rearrangements observed, involving at least six inverted repeat (IR) boundary shifts and five inversions, generating a number of gene duplications and relocations, as well as a two-fold expansion of the IR and miniaturized small single-copy region. A reduction in the substitution rates for genes transferred from the single-copy regions to the IR was observed. Accelerated substitution rates of plastid accD and clpP were detected in the Lamprocapnos plastome. The accelerated substitution rate for the accD gene was correlated with a large insertion of amino acid repeat (AAR) motifs in the middle region, but the forces driving the higher substitution rate of the clpP gene are unclear. We found a variable number of AARs in Lamprocapnos accD and ycf1 genes within individuals, and the repeats were associated with coiled-coil regions. In addition, comparative analysis of three Papaveraceae plastomes revealed loss of rps15 in Papaver, and functional replacement to the nucleus was identified.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - Boram An
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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11
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Huang P, Xia L, Liu W, Jiang R, Liu X, Tang Q, Xu M, Yu L, Tang Z, Zeng J. Hairy root induction and benzylisoquinoline alkaloid production in Macleaya cordata. Sci Rep 2018; 8:11986. [PMID: 30097605 PMCID: PMC6086913 DOI: 10.1038/s41598-018-30560-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/02/2018] [Indexed: 01/29/2023] Open
Abstract
Sanguinarine is currently widely used to replace antibiotic growth promoters in animal feeding and has demonstrated useful anticancer activity. Currently, the main source of sanguinarine is from an important medicinal plant, Macleaya cordata. To obtain a new source of sanguinarine production, we established hairy root cultures of M. cordata by co-cultivating leaf and stem explants with Agrobacterium rhizogenes. Except the co-cultivation medium, all growth media contained 200 mg/L timentin to eliminate A. rhizogenes. Through comparing the metabolic profiles and gene expression of hairy roots and wild-type roots sampled at five time points, we found that the sanguinarine and dihydrosanguinarine contents of hairy roots were far higher than those of wild-type roots, and we revealed the molecular mechanism that causes these metabolites to increase. Consequently, this study demonstrated that the hairy root system has further potential for bioengineering and sustainable production of sanguinarine on a commercial scale. To the best of our knowledge, this is the first efficient protocol reported for the establishment of hairy root cultures in M. cordata using A. rhizogenes.
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Affiliation(s)
- Peng Huang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Liqiong Xia
- School of pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Wei Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
- Center of Analytic Service, Hunan Agriculture University, 410208, Changsha, China
| | - Ruolan Jiang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Xiubin Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
- Center of Analytic Service, Hunan Agriculture University, 410208, Changsha, China
| | - Qi Tang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Min Xu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Linlan Yu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | | | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China.
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China.
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha, Hunan, 410128, China.
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12
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Huang P, Xia L, Liu W, Jiang R, Liu X, Tang Q, Xu M, Yu L, Tang Z, Zeng J. Hairy root induction and benzylisoquinoline alkaloid production in Macleaya cordata. Sci Rep 2018. [PMID: 30097605 DOI: 10.1038/s41598-018-30560-30560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Sanguinarine is currently widely used to replace antibiotic growth promoters in animal feeding and has demonstrated useful anticancer activity. Currently, the main source of sanguinarine is from an important medicinal plant, Macleaya cordata. To obtain a new source of sanguinarine production, we established hairy root cultures of M. cordata by co-cultivating leaf and stem explants with Agrobacterium rhizogenes. Except the co-cultivation medium, all growth media contained 200 mg/L timentin to eliminate A. rhizogenes. Through comparing the metabolic profiles and gene expression of hairy roots and wild-type roots sampled at five time points, we found that the sanguinarine and dihydrosanguinarine contents of hairy roots were far higher than those of wild-type roots, and we revealed the molecular mechanism that causes these metabolites to increase. Consequently, this study demonstrated that the hairy root system has further potential for bioengineering and sustainable production of sanguinarine on a commercial scale. To the best of our knowledge, this is the first efficient protocol reported for the establishment of hairy root cultures in M. cordata using A. rhizogenes.
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Affiliation(s)
- Peng Huang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Liqiong Xia
- School of pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Wei Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
- Center of Analytic Service, Hunan Agriculture University, 410208, Changsha, China
| | - Ruolan Jiang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Xiubin Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
- Center of Analytic Service, Hunan Agriculture University, 410208, Changsha, China
| | - Qi Tang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Min Xu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Linlan Yu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | | | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China.
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, Hunan, 410128, China.
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha, Hunan, 410128, China.
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13
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Liu X, Liu Y, Huang P, Ma Y, Qing Z, Tang Q, Cao H, Cheng P, Zheng Y, Yuan Z, Zhou Y, Liu J, Tang Z, Zhuo Y, Zhang Y, Yu L, Huang J, Yang P, Peng Q, Zhang J, Jiang W, Zhang Z, Lin K, Ro DK, Chen X, Xiong X, Shang Y, Huang S, Zeng J. The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism. Mol Plant 2017; 10:975-989. [PMID: 28552780 DOI: 10.1016/j.molp.2017.05.007] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 05/19/2023]
Abstract
The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids (BIAs) such as sanguinarine (SAN) and chelerythrine (CHE), but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding 13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.
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Affiliation(s)
- Xiubin Liu
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yisong Liu
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Veterinary Medicine College, Hunan Agricultural University, Changsha 410128, China
| | - Peng Huang
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yongshuo Ma
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhixing Qing
- Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Qi Tang
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Huifen Cao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Pi Cheng
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yajie Zheng
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Zejun Yuan
- Micolta Bioresource Inc., Changsha 410016, China
| | - Yuan Zhou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Jinfeng Liu
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Zhaoshan Tang
- Herbal Extract Engineering Research Center, Changsha 410331, China
| | - Yixiu Zhuo
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Yancong Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Linlan Yu
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China
| | - Jialu Huang
- Veterinary Medicine College, Hunan Agricultural University, Changsha 410128, China
| | - Peng Yang
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Qiong Peng
- Biotechnology Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jinbo Zhang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary T2N1N4, Canada
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Xingyao Xiong
- Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China.
| | - Yi Shang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Jianguo Zeng
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Hunan Agricultural University, Changsha 410128, China; Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China.
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14
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Chang L, Hagel JM, Facchini PJ. Isolation and Characterization of O-methyltransferases Involved in the Biosynthesis of Glaucine in Glaucium flavum. Plant Physiol 2015; 169:1127-40. [PMID: 26297140 PMCID: PMC4587479 DOI: 10.1104/pp.15.01240] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 08/20/2015] [Indexed: 05/25/2023]
Abstract
Transcriptome resources for the medicinal plant Glaucium flavum were searched for orthologs showing identity with characterized O-methyltransferases (OMTs) involved in benzylisoquinoline alkaloid biosynthesis. Seven recombinant proteins were functionally tested using the signature alkaloid substrates for six OMTs: norlaudanosoline 6-OMT, 6-O-methyllaudanosoline 4'-OMT, reticuline 7-OMT, norreticuline 7-OMT, scoulerine 9-OMT, and tetrahydrocolumbamine OMT. A notable alkaloid in yellow horned poppy (G. flavum [GFL]) is the aporphine alkaloid glaucine, which displays C8-C6' coupling and four O-methyl groups at C6, C7, C3', and C4' as numbered on the 1-benzylisoquinoline scaffold. Three recombinant enzymes accepted 1-benzylisoquinolines with differential substrate and regiospecificity. GFLOMT2 displayed the highest amino acid sequence identity with norlaudanosoline 6-OMT, showed a preference for the 6-O-methylation of norlaudanosoline, and O-methylated the 3' and 4' hydroxyl groups of certain alkaloids. GFLOMT1 showed the highest sequence identity with 6-O-methyllaudanosoline 4'OMT and catalyzed the 6-O-methylation of norlaudanosoline, but more efficiently 4'-O-methylated the GFLOMT2 reaction product 6-O-methylnorlaudanosoline and its N-methylated derivative 6-O-methyllaudanosoline. GFLOMT1 also effectively 3'-O-methylated both reticuline and norreticuline. GFLOMT6 was most similar to scoulerine 9-OMT and efficiently catalyzed both 3'- and 7'-O-methylations of several 1-benzylisoquinolines, with a preference for N-methylated substrates. All active enzymes accepted scoulerine and tetrahydrocolumbamine. Exogenous norlaudanosoline was converted to tetra-O-methylated laudanosine using combinations of Escherichia coli producing (1) GFLOMT1, (2) either GFLOMT2 or GFLOMT6, and (3) coclaurine N-methyltransferase from Coptis japonica. Expression profiles of GFLOMT1, GFLOMT2, and GFLOMT6 in different plant organs were in agreement with the O-methylation patterns of alkaloids in G. flavum determined by high-resolution, Fourier-transform mass spectrometry.
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Affiliation(s)
- Limei Chang
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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15
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Hagel JM, Morris JS, Lee EJ, Desgagné-Penix I, Bross CD, Chang L, Chen X, Farrow SC, Zhang Y, Soh J, Sensen CW, Facchini PJ. Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants. BMC Plant Biol 2015; 15:227. [PMID: 26384972 PMCID: PMC4575454 DOI: 10.1186/s12870-015-0596-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/15/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Benzylisoquinoline alkaloids (BIAs) represent a diverse class of plant specialized metabolites sharing a common biosynthetic origin beginning with tyrosine. Many BIAs have potent pharmacological activities, and plants accumulating them boast long histories of use in traditional medicine and cultural practices. The decades-long focus on a select number of plant species as model systems has allowed near or full elucidation of major BIA pathways, including those of morphine, sanguinarine and berberine. However, this focus has created a dearth of knowledge surrounding non-model species, which also are known to accumulate a wide-range of BIAs but whose biosynthesis is thus far entirely unexplored. Further, these non-model species represent a rich source of catalyst diversity valuable to plant biochemists and emerging synthetic biology efforts. RESULTS In order to access the genetic diversity of non-model plants accumulating BIAs, we selected 20 species representing 4 families within the Ranunculales. RNA extracted from each species was processed for analysis by both 1) Roche GS-FLX Titanium and 2) Illumina GA/HiSeq platforms, generating a total of 40 deep-sequencing transcriptome libraries. De novo assembly, annotation and subsequent full-length coding sequence (CDS) predictions indicated greater success for most species using the Illumina-based platform. Assembled data for each transcriptome were deposited into an established web-based BLAST portal ( www.phytometasyn.ca) to allow public access. Homology-based mining of libraries using BIA-biosynthetic enzymes as queries yielded ~850 gene candidates potentially involved in alkaloid biosynthesis. Expression analysis of these candidates was performed using inter-library FPKM normalization methods. These expression data provide a basis for the rational selection of gene candidates, and suggest possible metabolic bottlenecks within BIA metabolism. Phylogenetic analysis was performed for each of 15 different enzyme/protein groupings, highlighting many novel genes with potential involvement in the formation of one or more alkaloid types, including morphinan, aporphine, and phthalideisoquinoline alkaloids. Transcriptome resources were used to design and execute a case study of candidate N-methyltransferases (NMTs) from Glaucium flavum, which revealed predicted and novel enzyme activities. CONCLUSIONS This study establishes an essential resource for the isolation and discovery of 1) functional homologues and 2) entirely novel catalysts within BIA metabolism. Functional analysis of G. flavum NMTs demonstrated the utility of this resource and underscored the importance of empirical determination of proposed enzymatic function. Publically accessible, fully annotated, BLAST-accessible transcriptomes were not previously available for most species included in this report, despite the rich repertoire of bioactive alkaloids found in these plants and their importance to traditional medicine. The results presented herein provide essential sequence information and inform experimental design for the continued elucidation of BIA metabolism.
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Affiliation(s)
- Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Jeremy S Morris
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Eun-Jeong Lee
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Isabel Desgagné-Penix
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
- Current address: Département de Chimie, Biochimie et Physique, Université du Québec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada.
| | - Crystal D Bross
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Limei Chang
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Xue Chen
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Scott C Farrow
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Ye Zhang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Jung Soh
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Christoph W Sensen
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- Current address: Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria.
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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Hagel JM, Mandal R, Han B, Han J, Dinsmore DR, Borchers CH, Wishart DS, Facchini PJ. Metabolome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants. BMC Plant Biol 2015; 15:220. [PMID: 26369413 PMCID: PMC4570626 DOI: 10.1186/s12870-015-0594-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/14/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Recent progress toward the elucidation of benzylisoquinoline alkaloid (BIA) metabolism has focused on a small number of model plant species. Current understanding of BIA metabolism in plants such as opium poppy, which accumulates important pharmacological agents such as codeine and morphine, has relied on a combination of genomics and metabolomics to facilitate gene discovery. Metabolomics studies provide important insight into the primary biochemical networks underpinning specialized metabolism, and serve as a key resource for metabolic engineering, gene discovery, and elucidation of governing regulatory mechanisms. Beyond model plants, few broad-scope metabolomics reports are available for the vast number of plant species known to produce an estimated 2500 structurally diverse BIAs, many of which exhibit promising medicinal properties. RESULTS We applied a multi-platform approach incorporating four different analytical methods to examine 20 non-model, BIA-accumulating plant species. Plants representing four families in the Ranunculales were chosen based on reported BIA content, taxonomic distribution and importance in modern/traditional medicine. One-dimensional (1)H NMR-based profiling quantified 91 metabolites and revealed significant species- and tissue-specific variation in sugar, amino acid and organic acid content. Mono- and disaccharide sugars were generally lower in roots and rhizomes compared with stems, and a variety of metabolites distinguished callus tissue from intact plant organs. Direct flow infusion tandem mass spectrometry provided a broad survey of 110 lipid derivatives including phosphatidylcholines and acylcarnitines, and high-performance liquid chromatography coupled with UV detection quantified 15 phenolic compounds including flavonoids, benzoic acid derivatives and hydroxycinnamic acids. Ultra-performance liquid chromatography coupled with high-resolution Fourier transform mass spectrometry generated extensive mass lists for all species, which were mined for metabolites putatively corresponding to BIAs. Different alkaloids profiles, including both ubiquitous and potentially rare compounds, were observed. CONCLUSIONS Extensive metabolite profiling combining multiple analytical platforms enabled a more complete picture of overall metabolism occurring in selected plant species. This study represents the first time a metabolomics approach has been applied to most of these species, despite their importance in modern and traditional medicine. Coupled with genomics data, these metabolomics resources serve as a key resource for the investigation of BIA biosynthesis in non-model plant species.
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Affiliation(s)
- Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1 N4, Canada.
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Beomsoo Han
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Jun Han
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada.
| | - Donald R Dinsmore
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1 N4, Canada.
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada.
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1 N4, Canada.
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Dou RK, Bi ZF, Bai RX, Ren YY, Tan R, Song LK, Li DQ, Mao CQ. [Identification and analysis of Corydalis boweri, Meconopsis horridula and their close related species of the same genus by using ITS2 DNA barcode]. Zhongguo Zhong Yao Za Zhi 2015; 40:1453-1458. [PMID: 26281578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The study is aimed to ensure the quality and safety of medicinal plants by using ITS2 DNA barcode technology to identify Corydalis boweri, Meconopsis horridula and their close related species. The DNA of 13 herb samples including C. boweri and M. horridula from Lhasa of Tibet was extracted, ITS PCR were amplified and sequenced. Both assembled and web downloaded 71 ITS2 sequences were removed of 5. 8S and 28S. Multiple sequence alignment was completed and the intraspecific and interspecific genetic distances were calculated by MEGA 5.0, while the neighbor-joining phylogenetic trees were constructed. We also predicted the ITS2 secondary structure of C. boweri, M. horridula and their close related species. The results showed that ITS2 as DNA barcode was able to identify C. boweri, M. horridula as well as well as their close related species effectively. The established based on ITS2 barcode method provides the regular and safe detection technology for identification of C. boweri, M. horridula and their close related species, adulterants and counterfeits, in order to ensure their quality control, safe medication, reasonable development and utilization.
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Liu YC, Liu YN, Yang FS, Wang XQ. Molecular phylogeny of Asian Meconopsis based on nuclear ribosomal and chloroplast DNA sequence data. PLoS One 2014; 9:e104823. [PMID: 25118100 PMCID: PMC4130606 DOI: 10.1371/journal.pone.0104823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/09/2014] [Indexed: 11/19/2022] Open
Abstract
The taxonomy and phylogeny of Asian Meconopsis (Himalayan blue poppy) remain largely unresolved. We used the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and the chloroplast DNA (cpDNA) trnL-F region for phylogenetic reconstruction of Meconopsis and its close relatives Papaver, Roemeria, and Stylomecon. We identified five main clades, which were well-supported in the gene trees reconstructed with the nrDNA ITS and cpDNA trnL-F sequences. We found that 41 species of Asian Meconopsis did not constitute a monophyletic clade, but formed two solid clades (I and V) separated in the phylogenetic tree by three clades (II, III and IV) of Papaver and its allies. Clade V includes only four Asian Meconopsis species, with the remaining 90 percent of Asian species included in clade I. In this core Asian Meconopsis clade, five subclades (Ia-Ie) were recognized in the nrDNA ITS tree. Three species (Meconopsis discigera, M. pinnatifolia, and M. torquata) of subgenus Discogyne were imbedded in subclade Ia, indicating that the present definition of subgenera in Meconopsis should be rejected. These subclades are inconsistent with any series or sections of the present classifications, suggesting that classifications of the genus should be completely revised. Finally, proposals for further revision of the genus Meconopsis were put forward based on molecular, morphological, and biogeographical evidences.
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Affiliation(s)
- Yu-Cheng Liu
- 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
| | - Ya-Nan Liu
- 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
| | - Fu-Sheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- 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
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Damerval C, Citerne H, Le Guilloux M, Domenichini S, Dutheil J, Ronse de Craene L, Nadot S. Asymmetric morphogenetic cues along the transverse plane: shift from disymmetry to zygomorphy in the flower of Fumarioideae. Am J Bot 2013; 100:391-402. [PMID: 23378492 DOI: 10.3732/ajb.1200376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Zygomorphy has evolved multiple times in angiosperms. Near-actinomorphy is the ancestral state in the early diverging eudicot family Papaveraceae. Zygomorphy evolved once in the subfamily Fumarioideae from a disymmetric state. Unusual within angiosperms, zygomorphy takes place along the transverse plane of the flower. METHODS We investigated floral development to understand the developmental bases of the evolution of floral symmetry in Papaveraceae. We then assessed the expression of candidate genes for the key developmental events responsible for the shift from disymmetry to transverse zygomorphy, namely CrabsClaw for nectary formation (PapCRC), ShootMeristemless (PapSTL) for spur formation, and Cycloidea (PapCYL) for growth control. KEY RESULTS We found that an early disymmetric groundplan is common to all species studied, and that actinomorphy was acquired after sepal initiation in Papaveroideae. The shift from disymmetry to zygomorphy in Fumarioideae was associated with early asymmetric growth of stamen filaments, followed by asymmetric development of nectary outgrowth and spur along the transverse plane. Patterns of PapSTL expression could not be clearly related to spur formation. PapCRC and PapCYL genes were expressed in the nectary outgrowths, with a pattern of expression correlated with asymmetric nectary development in the zygomorphic species. Additionally, PapCYL genes were found asymmetrically expressed along the transverse plane in the basal region of outer petals in the zygomorphic species. CONCLUSION Genes of PapCRC and PapCYL families could be direct or indirect targets of the initial transversally asymmetric cue responsible for the shift from disymmetry to zygomorphy in Fumarioideae.
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Affiliation(s)
- Catherine Damerval
- UMR de Génétique Végétale, CNRS/Université Paris-Sud/INRA, Ferme du Moulon 91190 Gif-sur-Yvette, France.
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Zeng J, Liu Y, Liu W, Liu X, Liu F, Huang P, Zhu P, Chen J, Shi M, Guo F, Cheng P, Zeng J, Liao Y, Gong J, Zhang HM, Wang D, Guo AY, Xiong X. Integration of transcriptome, proteome and metabolism data reveals the alkaloids biosynthesis in Macleaya cordata and Macleaya microcarpa. PLoS One 2013; 8:e53409. [PMID: 23326424 PMCID: PMC3541140 DOI: 10.1371/journal.pone.0053409] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/29/2012] [Indexed: 12/22/2022] Open
Abstract
Background The Macleaya spp., including Macleaya cordata and Macleaya microcarpa, are traditional anti-virus, inflammation eliminating, and insecticide herb medicines for their isoquinoline alkaloids. They are also known as the basis of the popular natural animal food addictive in Europe. However, few studies especially at genomics level were conducted on them. Hence, we performed the Macleaya spp. transcriptome and integrated it with iTRAQ proteome analysis in order to identify potential genes involved in alkaloids biosynthesis. Methodology and Principal Findings We elaborately designed the transcriptome, proteome and metabolism profiling for 10 samples of both species to explore their alkaloids biosynthesis. From the transcriptome data, we obtained 69367 and 78255 unigenes for M. cordata and M. microcarpa, in which about two thirds of them were similar to sequences in public databases. By metabolism profiling, reverse patterns for alkaloids sanguinarine, chelerythrine, protopine, and allocryptopine were observed in different organs of two species. We characterized the expressions of enzymes in alkaloid biosynthesis pathways. We also identified more than 1000 proteins from iTRAQ proteome data. Our results strongly suggest that the root maybe the organ for major alkaloids biosynthesis of Macleaya spp. Except for biosynthesis, the alkaloids storage and transport were also important for their accumulation. The ultrastructure of laticifers by SEM helps us to prove the alkaloids maybe accumulated in the mature roots. Conclusions/Significance To our knowledge this is the first study to elucidate the genetic makeup of Macleaya spp. This work provides clues to the identification of the potential modulate genes involved in alkaloids biosynthesis in Macleaya spp., and sheds light on researches for non-model medicinal plants by integrating different high-throughput technologies.
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Affiliation(s)
- Jianguo Zeng
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
- * E-mail: (JZ); (AG); (XX)
| | - Yisong Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | - Wei Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Xiubing Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | | | - Peng Huang
- Herbal Extract Engineering Research Center (HerbEx), Hunan, China
- Micolta BioResource Inc., Hunan, China
| | - Pengcheng Zhu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | - Jinjun Chen
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
| | | | | | - Pi Cheng
- Herbal Extract Engineering Research Center (HerbEx), Hunan, China
| | - Jing Zeng
- Herbal Extract Engineering Research Center (HerbEx), Hunan, China
| | - Yifang Liao
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Jing Gong
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Hong-Mei Zhang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - Depeng Wang
- Nextomics Biosciences Co., Ltd. Wuhan, China
| | - An-Yuan Guo
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (JZ); (AG); (XX)
| | - Xingyao Xiong
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, China
- * E-mail: (JZ); (AG); (XX)
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Voss N, Eckstein RL, Durka W. Range expansion of a selfing polyploid plant despite widespread genetic uniformity. Ann Bot 2012; 110:585-593. [PMID: 22730022 PMCID: PMC3400446 DOI: 10.1093/aob/mcs117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/04/2012] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Ongoing and previous range expansions have a strong influence on population genetic structure of plants. In turn, genetic variation in the new range may affect the population dynamics and the expansion process. The annual Ceratocapnos claviculata (Papaveraceae) has expanded its Atlantic European range in recent decades towards the north and east. Patterns of genetic diversity were investigated across the native range to assess current population structure and phylogeographical patterns. A test was then made as to whether genetic diversity is reduced in the neophytic range and an attempt was made to identify source regions of the expansion. METHODS Samples were taken from 55 populations in the native and 34 populations in the neophytic range (Sweden, north-east Germany). Using amplified fragment length polymorphism markers an analysis was made of genetic variation and population structure (Bayesian statistical modelling) and population differentiation was quantified. Pollen/ovule ratio was analysed as a proxy for the breeding system. KEY RESULTS Genetic diversity at population level was very low (mean H(e) = 0·004) and two multilocus genotypes dominated large parts of the new range. Population differentiation was strong (F(ST) = 0·812). These results and a low pollen/ovule ratio are consistent with an autogamous breeding system. Genetic variation decreased from the native to the neophytic range. Within the native range, H(e) decreased towards the north-east, whereas population size increased. According to the Bayesian cluster analysis, the putative source regions of the neophytic range are situated in north-west Germany and adjacent regions. CONCLUSIONS Ceratocapnos claviculata shows a cline of genetic variation due to postglacial recolonization from putative Pleistocene refugia in south-west Europe. Nevertheless, the species has expanded successfully during the past 40 years to southern Sweden and north-east Germany where it occurs as an opportunistic neophyte. Recent expansion was mainly human-mediated by single long-distance diaspore transport and was facilitated by habitat modification.
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Affiliation(s)
- Nicole Voss
- Institute of Landscape Ecology and Resource Management, Research Centre for BioSystems, Land Use and Nutrition (IFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.
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Yang FS, Qin AL, Li YF, Wang XQ. Great genetic differentiation among populations of Meconopsis integrifolia and its implication for plant speciation in the Qinghai-Tibetan Plateau. PLoS One 2012; 7:e37196. [PMID: 22590654 PMCID: PMC3349641 DOI: 10.1371/journal.pone.0037196] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/18/2012] [Indexed: 11/26/2022] Open
Abstract
The complex tectonic events and climatic oscillations in the Qinghai-Tibetan Plateau (QTP), the largest and highest plateau in the world, are thought to have had great effects on the evolutionary history of the native plants. Of great interest is to investigate plant population genetic divergence in the QTP and its correlation with the geologic and climatic changes. We conducted a range-wide phylogeographical analysis of M. integrifolia based on the chloroplast DNA (cpDNA) trnL-trnF and trnfM-trnS regions, and defined 26 haplotypes that were phylogenetically divided into six clades dated to the late Tertiary. The six clades correspond, respectively, to highly differentiated population groups that do not overlap in geographic distribution, implying that the mountain ranges acting as corridors or barriers greatly affected the evolutionary history of the QTP plants. The older clade of M. integrifolia only occurs in the southwest of the species' range, whereas the distributions of younger clades extend northeastward in the eastern QTP, suggesting that climatic divergence resulting from the uplift of the QTP triggered the initial divergence of M. integrifolia native to the plateau. Also, the nrDNA ITS region was used to clarify the unexpected phylogenetic relationships of cpDNA haplotypes between M. integrifolia and M. betonicifolia. The topological incongruence between the two phylogenies suggests an ancestral hybridization between the two species. Our study indicates that geographic isolation and hybridization are two important mechanisms responsible for the population differentiation and speciation of Meconopsis, a species-rich genus with complex polyploids.
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Affiliation(s)
- Fu-Sheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Ai-Li Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Yu-Fei Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
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Hidalgo O, Bartholmes C, Gleissberg S. Virus-induced gene silencing (VIGS) in Cysticapnos vesicaria, a zygomorphic-flowered Papaveraceae (Ranunculales, basal eudicots). Ann Bot 2012; 109:911-20. [PMID: 22307568 PMCID: PMC3310490 DOI: 10.1093/aob/mcs008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Studies of evolutionary diversification in the basal eudicot family Papaveraceae, such as the transition from actinomorphy to zygomorphy, are hampered by the lack of comparative functional studies. So far, gene silencing methods are only available in the actinomorphic species Eschscholzia californica and Papaver somniferum. This study addresses the amenability of Cysticapnos vesicaria, a derived fumitory with zygomorphic flowers, to virus-induced gene silencing (VIGS), and describes vegetative and reproductive traits in this species. METHODS VIGS-mediated downregulation of the C. vesicaria PHYTOENE DESATURASE gene (CvPDS) and of the FLORICAULA gene CvFLO was carried out using Agrobacterium tumefaciens transfer of Tobacco rattle virus (TRV)-based vectors. Wild-type and vector-treated plants were characterized using reverse transcription-PCR (RT-PCR), in situ hybridization, and macroscopic and scanning electron microscopic imaging. KEY RESULTS Cysticapnos vesicaria germinates rapidly, can be grown at high density, has a short life cycle and is self-compatible. Inoculation of C. vesicaria with a CvPDS-VIGS vector resulted in strong photobleaching of green parts and reduction of endogenous CvPDS transcript levels. Gene silencing persisted during inflorescence development until fruit set. Inoculation of plants with CvFLO-VIGS affected floral phyllotaxis, symmetry and floral organ identities. CONCLUSIONS The high penetrance, severity and stability of pTRV-mediated silencing, including the induction of meristem-related phenotypes, make C. vesicaria a very promising new focus species for evolutionary-developmental (evo-devo) studies in the Papaveraceae. This now enables comparative studies of flower symmetry, inflorescence determinacy and other traits that diversified in the Papaveraceae.
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Pérez-Gutiérrez MA, Romero-García AT, Salinas MJ, Blanca G, Fernández MC, Suárez-Santiago VN. Phylogeny of the tribe Fumarieae (Papaveraceae s.l.) based on chloroplast and nuclear DNA sequences: evolutionary and biogeographic implications. Am J Bot 2012; 99:517-528. [PMID: 22334448 DOI: 10.3732/ajb.1100374] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Little research has been done at the molecular level on the tribe Fumarieae (Papaveraceae). Papaveraceae is a model plant group for studying evolutionary patterns despite the lack of a reference phylogeny for this tribe. We investigated the phylogenetic relationships within the tribe to complete the molecular data for this family in order to help understand its character evolution and biogeographic pattern. METHODS We used maximum-parsimony and Bayesian approaches to analyze five DNA regions for 25 species representing 10 of the 11 Fumarieae genera and five outgroups. Evolutionary pathways of four characters (habit, life span, type of fruit, and number of seeds per fruit) were inferred on the phylogeny using parsimony. The ancestral distribution areas were reconstructed using dispersal-vicariance analysis. KEY RESULTS Fumarieae is monophyletic and includes three groups that agree with the morphology-based subtribes: Discocapninae, Fumariinae, and Sarcocapninae. Within subtribes, the relationships among genera were different from those obtained with morphological data. Annual life span, nonchasmophytic habit, and a several-seeded capsule were the basal character states for the tribe. The ancestor occupied a continuous area between West Eurasia and Africa. Vicariances explain the divergence between lineages Discocapninae (South Africa) and Fumariinae-Sarcocapninae (Mediterranean), and the disjunction of Fumariinae (Mediterranean-Central Asia). CONCLUSIONS Molecular phylogeny confirms the subtribal classification of Fumarieae based on morphology. However it provides different results regarding the relationships among genera within each subtribe, which affects the inference of the evolutionary pathway followed by the four selected characters. The disjunct distribution of the tribe is explained by different vicariance scenarios.
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Affiliation(s)
- Miguel A Pérez-Gutiérrez
- Departamento de Botánica, Facultad de Ciencias, Universidad de Granada, c/ Severo Ochoa, s/n 18071 Granada, Spain
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Pérez-Gutiérrez MA, Suárez-Santiago VN, López-Flores I, Romero AT, Garrido-Ramos MA. Concerted evolution of satellite DNA in Sarcocapnos: a matter of time. Plant Mol Biol 2012; 78:19-29. [PMID: 22081315 DOI: 10.1007/s11103-011-9848-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/18/2011] [Indexed: 05/31/2023]
Abstract
SarkOne is a genus-specific satellite-DNA family, isolated from the genomes of the species of the genus Sarcocapnos. This satellite DNA is composed of repeats with a consensus length of 855 bp and a mean G+C content of 52.5%. We have sequenced a total of 189 SarkOne monomeric repeats belonging to a total of seven species of the genus Sarcocapnos. The comparative analysis of these sequences both at the intraspecific and the interspecific levels have revealed divergence patterns between species are proportional to between-species divergence according to the phylogeny of the genus. Our study demonstrates that the molecular drive leading to the concerted-evolution pattern of this satellite DNA is a time-dependent process by which new mutations are spreading through genomes and populations at a gradual pace. However, time is a limiting factor in the observation of concerted evolution in some pairwise comparisons. Thus, pairwise comparisons of species sharing a recent common ancestor did not reveal nucleotide sites in transitional stages higher than stage III according to the Strachan's model. By contrast, there was a gradation in the percentage of upper transition stages (IV, V, VI) the more phylogenetically distant the species were. In addition, closely related species shared a high number of polymorphic sites, but these types of sites were not common when comparing more distant species. All these data are discussed in the light of current life-cycle models of satellite-DNA evolution.
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Samatadze TE, Zelenin AV, Suslina SN, Amosova AV, Popov KV, Zagumennikova TN, Tsitsilin AN, Bykov VA, Muravenko OV. [Comparative cytogenetic study of the forms of Macleaya cordata (Willd.) R. Br. from different localities]. Genetika 2012; 48:72-79. [PMID: 22567856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A comparative cytogenetic study of two introduced forms of Makleaya cordata (Willd.) R. Br. = syn. Bocconia cordata Willd. grown in different ecological and geographical regions (Moscow and Donetsk areas) was carried out. In the study, a complex of methods utilizing various chromosomal markers, i.e., C- and DAPI-banding technique, fluorescence in situ hybridization (FISH) with probes of26S and 5S rDNA, as well as estimation of the total area of C-positive regions (C-HCH) in prophase nucleoli and meiosis analysis, was used. In the karyotypes (2n = 20), each chromosome was identified on the basis of C-banding and FISH patterns and the chromosome ideograms were built. Pericentrometric and telomeric C-positive bands in chromosomes of the Moscow form karyotype were found to be smaller and intercalary bands, larger than the corresponding bands in the M. cordata form grown in Donetsk. It was found that the content of C-HCH in prophase nucleoli in the form of M. cordata grown in Donetsk was higher than in the form grown in Moscow. In both forms sites of 26S rDNA and 5s rDNA were localized on satellite chromosome 1 and on chromosome 4 respectively but the signals were more intensive in the plant form grown in Donetsk. The results of this study enable selecting M. cordata forms for use in pharmacology and recommending them for cultivation in various ecological and geographical regions.
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Paape T, Miyake T, Takebayashi N, Wolf D, Kohn JR. Evolutionary genetics of an S-like polymorphism in Papaveraceae with putative function in self-incompatibility. PLoS One 2011; 6:e23635. [PMID: 21912602 PMCID: PMC3166141 DOI: 10.1371/journal.pone.0023635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 07/21/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Papaver rhoeas possesses a gametophytic self-incompatibility (SI) system not homologous to any other SI mechanism characterized at the molecular level. Four previously published full length stigmatic S-alleles from the genus Papaver exhibited remarkable sequence divergence, but these studies failed to amplify additional S-alleles despite crossing evidence for more than 60 S-alleles in Papaver rhoeas alone. METHODOLOGY/PRINCIPAL FINDINGS Using RT-PCR we identified 87 unique putative stigmatic S-allele sequences from the Papaveraceae Argemone munita, Papaver mcconnellii, P. nudicuale, Platystemon californicus and Romneya coulteri. Hand pollinations among two full-sib families of both A. munita and P. californicus indicate a strong correlation between the putative S-genotype and observed incompatibility phenotype. However, we also found more than two S-like sequences in some individuals of A. munita and P. californicus, with two products co-segregating in both full-sib families of P. californicus. Pairwise sequence divergence estimates within and among taxa show Papaver stigmatic S-alleles to be the most variable with lower divergence among putative S-alleles from other Papaveraceae. Genealogical analysis indicates little shared ancestral polymorphism among S-like sequences from different genera. Lack of shared ancestral polymorphism could be due to long divergence times among genera studied, reduced levels of balancing selection if some or all S-like sequences do not function in incompatibility, population bottlenecks, or different levels of recombination among taxa. Preliminary estimates of positive selection find many sites under selective constraint with a few undergoing positive selection, suggesting that self-recognition may depend on amino acid substitutions at only a few sites. CONCLUSIONS/SIGNIFICANCE Because of the strong correlation between genotype and SI phenotype, sequences reported here represent either functional stylar S-alleles, tightly linked paralogs of the S-locus or a combination of both. The considerable complexity revealed in this study shows we have much to learn about the evolutionary dynamics of self-incompatibility systems.
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Affiliation(s)
- Timothy Paape
- College of Biological Sciences, University of Minnesota, St. Paul, Minnesota, United States of America.
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Kaloumenos NS, Adamouli VN, Dordas CA, Eleftherohorinos IG. Corn poppy (Papaver rhoeas) cross-resistance to ALS-inhibiting herbicides. Pest Manag Sci 2011; 67:574-585. [PMID: 21308964 DOI: 10.1002/ps.2104] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Revised: 10/08/2010] [Accepted: 11/06/2010] [Indexed: 05/27/2023]
Abstract
BACKGROUND Papaver rhoeas (L.) has evolved resistance to tribenuron in winter wheat fields in northern Greece owing to multiple Pro(197) substitutions. Therefore, the cross-resistance pattern to other sulfonylurea and non-sulfonylurea ALS-inhibiting herbicides of the tribenuron resistant (R) and susceptible (S) corn poppy populations was studied by using whole-plant trials and in vitro ALS catalytic activity assays. RESULTS The whole-plant trials revealed that tribenuron R populations were also cross-resistant to sulfonylureas mesosulfuron + iodosulfuron, chlorsulfuron and triasulfuron. The whole-plant resistance factors (RFs) calculated for pyrithiobac, imazamox and florasulam ranged from 12.4 to > 88, from 1.5 to 28.3 and from 5.6 to 25.4, respectively, and were lower than the respective tribenuron RF values (137 to > 2400). The ALS activity assay showed higher resistance of the ALS enzyme to sulfonylurea herbicides (tribenuron > chlorsulfuron) and lower resistance to non-sulfonylurea ALS-inhibiting herbicides (pyrithiobac > florasulam ≈ imazamox). CONCLUSION These findings indicate that Pro(197) substitution by Ala, Ser, Arg or Thr in corn poppy results in a less sensitive ALS enzyme to sulfonylurea herbicides than to other ALS-inhibiting herbicides. The continued use of sulfonylurea herbicides led to cross-resistance to all ALS-inhibiting herbicides, making their use impossible in corn poppy resistance management programmes.
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Affiliation(s)
- Nikolaos S Kaloumenos
- Laboratory of Agronomy, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Damerval C, Le Guilloux M, Jager M, Charon C. Diversity and evolution of CYCLOIDEA-like TCP genes in relation to flower development in Papaveraceae. Plant Physiol 2007; 143:759-72. [PMID: 17189327 PMCID: PMC1803737 DOI: 10.1104/pp.106.090324] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Monosymmetry evolved several times independently during flower evolution. In snapdragon (Antirrhinum majus), a key gene for monosymmetry is CYCLOIDEA (CYC), which belongs to the class II TCP gene family encoding transcriptional activators. We address the questions of the evolutionary history of this gene family and of possible recruitment of genes homologous to CYC in floral development and symmetry in the Papaveraceae. Two to three members of the class II TCP family were found in each species analyzed, two of which were CYC-like genes, on the basis of the presence of both the TCP and R conserved domains. The duplication that gave rise to these two paralogous lineages (named PAPACYL1 and PAPACYL2) probably predates the divergence of the two main clades within the Papaveraceae. Phylogenetic relationships among angiosperm class II TCP genes indicated that (1) PAPACYL genes were closest to Arabidopsis (Arabidopsis thaliana) AtTCP18, and a duplication at the base of the core eudicot would have given rise to two supplementary CYC-like lineages; and (2) at least three class II TCP genes were present in the ancestor of monocots and eudicots. Semiquantitative reverse transcription-polymerase chain reaction and in situ hybridization approaches in three species with different floral symmetry indicated that both PAPACYL paralogs were expressed during floral development. A pattern common to all three species was observed at organ junctions in inflorescences and flowers. Expression in the outer petals was specifically observed in the two species with nonactinomorphic flowers. Hypotheses concerning the ancestral pattern of expression and function of CYC-like genes and their possible role in floral development of Papaveraceae species leading to bisymmetric buds are discussed.
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Affiliation(s)
- Catherine Damerval
- Unité Mixte de Recherche Génétique Végétale, Institut National Agronomique Paris-Grignon, Ferme du Moulon, Gif-sur-Yvette 91190, France.
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Carlson JE, Leebens-Mack JH, Wall PK, Zahn LM, Mueller LA, Landherr LL, Hu Y, Ilut DC, Arrington JM, Choirean S, Becker A, Field D, Tanksley SD, Ma H, dePamphilis CW. EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot. Plant Mol Biol 2006; 62:351-69. [PMID: 16915518 DOI: 10.1007/s11103-006-9025-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Accepted: 05/24/2006] [Indexed: 05/08/2023]
Abstract
The Floral Genome Project (FGP) selected California poppy (Eschscholzia californica Cham. ssp. Californica) to help identify new florally-expressed genes related to floral diversity in basal eudicots. A large, non-normalized cDNA library was constructed from premeiotic and meiotic floral buds and sequenced to generate a database of 9,079 high quality Expressed Sequence Tags (ESTs). These sequences clustered into 5,713 unigenes, including 1,414 contigs and 4,299 singletons. Homologs of genes regulating many aspects of flower development were identified, including those for organ identity and development, cell and tissue differentiation, cell cycle control, and secondary metabolism. Over 5% of the transcriptome consisted of homologs to known floral gene families. Most are the first representatives of their respective gene families in basal eudicots and their conservation suggests they are important for floral development and/or function. App. 10% of the transcripts encoded transcription factors and other regulatory genes, including nine genes from the seven major lineages of the important MADS-box family of developmental regulators. Homologs of alkaloid pathway genes were also recovered, providing opportunities to explore adaptive evolution in secondary products. Furthermore, comparison of the poppy ESTs with the Arabidopsis genome provided support for putative Arabidopsis genes that previously lacked annotation. Finally, over 1,800 unique sequences had no observable homology in the public databases. The California poppy EST database and library will help bridge our understanding of flower initiation and development among higher eudicot and monocot model plants and provide new opportunities for comparative analysis of gene families across angiosperm species.
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Affiliation(s)
- John E Carlson
- The School of Forest Resources and Huck Institutes for Life Sciences, Pennsylvania State University, 323 Forest Resources Building, University Park, 16802, USA.
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Kölsch A, Gleissberg S. Diversification of CYCLOIDEA-like TCP genes in the basal eudicot families Fumariaceae and Papaveraceae s.str. Plant Biol (Stuttg) 2006; 8:680-7. [PMID: 16883484 DOI: 10.1055/s-2006-924286] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
CYCLOIDEA-like genes belong to the TCP family of transcriptional regulators and have been shown to control different aspects of shoot development in various angiosperm lineages, including flower monosymmetry in asterids and axillary meristem growth in monocots. Genes related to the CYC gene from ANTIRRHINUM show independent duplications in both asterids and rosids. However, it remains unclear to what extent this affected the evolution of flower symmetry and shoot branching in these and other eudicot lineages. Here, we show that CYC-like genes have also undergone duplications in two related Ranunculales families, Fumariaceae and Papaveraceae s.str. These families exhibit morphological diversity in flower symmetry and inflorescence architecture that is potentially related to functions of CYC-like genes. We present sequences of 14 CYC-related genes covering 9 genera. Phylogenetic analyses indicate the presence of three clades of CYC-like genes. Shared motifs in the region between the TCP and R domains of CYC-like genes between Fumariaceae, Papaveraceae s.str., and AQUILEGIA (Ranunculaceae) indicate that the observed duplications originated from a single CYC gene present in all Ranunculales. RT-PCR expression data suggest that gene duplication and diversification in Fumariaceae and Papaveraceae s.str. was accompanied by divergence in expression patterns.
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Affiliation(s)
- A Kölsch
- Institut für Spezielle Botanik, Johannes-Gutenberg-Universität, Bentzelweg 9 a, 55099 Mainz, Germany
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Carolan JC, Hook ILI, Chase MW, Kadereit JW, Hodkinson TR. Phylogenetics of Papaver and related genera based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers. Ann Bot 2006; 98:141-55. [PMID: 16675606 PMCID: PMC2803553 DOI: 10.1093/aob/mcl079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Representatives from Papaver, Roemeria, Stylomecon and Meconopsis were studied to elucidate phylogenetic relationships between Papaver and these closely allied genera. METHODS Two molecular data sets were used individually and combined and included sequences from the internally transcribed spacer region (ITS) of 18S-26S nuclear ribosomal DNA and the trnL intron and the trnL-trnF intergenic spacer region of plastid DNA. KEY RESULTS Parsimony analysis demonstrated that the genus is not monophyletic unless the closely related Roemeria, Stylomecon and Meconopsis cambrica are included in a revised circumscription of Papaver. Three distinct clades are resolved in a combined ITS and trnL-F analysis. Clade 1 consists of Papaver sect. Meconella and Asian Meconopsis. Clade 2 contains a group here identified as Papaver s.s., comprising sections Carinatae, Meconidium, Oxytona, Papaver, Pilosa, Pseudopilosa and Rhoeadium. Clade 3 consists of Papaver sect. Argemonidium and Roemeria refracta. A number of diagnostic indels support these groupings. Within clade 2, sects. Papaver and Rhoeadium are either not monophyletic or lack evidence supporting their monophyly. CONCLUSIONS The results of this molecular analysis indicate that a number of morphological characters such as valvate capsule dehiscence, dark or light filaments and sessile stigmatic discs have arisen in parallel. The phylogenetic trees are incongruent with the existing taxonomy of Papaver, and a revised classification is suggested.
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Affiliation(s)
- James C Carolan
- Department of Botany, School of Natural Sciences, University of Dublin, Trinity College, Ireland.
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Groot EP, Sinha N, Gleissberg S. Expression patterns of STM-like KNOX and Histone H4 genes in shoot development of the dissected-leaved basal eudicot plants Chelidonium majus and Eschscholzia californica (Papaveraceae). Plant Mol Biol 2005; 58:317-31. [PMID: 16021398 DOI: 10.1007/s11103-005-4548-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2004] [Accepted: 03/24/2005] [Indexed: 05/03/2023]
Abstract
Knotted-like homeobox (KNOX) genes encode important regulators of shoot development in flowering plants. In Arabidopsis, class I KNOX genes are part of a regulatory system that contributes to indeterminacy of shoot development, delimitation of leaf primordia and internode development. In other species, class I KNOX genes have also been recruited in the control of marginal blastozone fractionation during dissected leaf development. Here we report the isolation of class I KNOX genes from two species of the basal eudicot family Papaveraceae, Chelidonium majus and Eschscholzia californica. Sequence comparisons and expression patterns indicate that these genes are orthologs of SHOOTMERISTEMLESS (STM), a class I KNOX gene from Arabidopsis. Both genes are expressed in the center of vegetative and floral shoot apical meristems (SAM), but downregulated at leaf or floral organ initiating sites. While Eschscholzia californica STM (EcSTM) is again upregulated during acropetal pinna formation, in situ hybridization could not detect Chelidonium majus STM (CmSTM) transcripts at any stage of basipetal leaf development, indicating divergent evolution of STM gene function in leaves within Papaveraceae. Immunolocalization of KNOX proteins indicate that other gene family members may control leaf dissection in both species. The contrasting direction of pinna initiation in the two species was also investigated using Histone H4 expression. Leaves at early stages of development did not reveal notable differences in cell division activity of the elongating leaf axis, suggesting that differential meristematic growth may not play a role in determining the observed dissection patterns.
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Affiliation(s)
- Edwin P Groot
- Institut für Spezielle Botanik, Johannes-Gutenberg-Universität Mainz, Bentzelweg 9a, 55099 Mainz, Germany
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Yuan CC, Li PX, Wang YF, Shi SH. [The confirmation of putative natural hybrid species Meconopsis x cookei G. Taylor (Papaveraceae) based on nuclear ribosomal DNA ITS region sequence]. Yi Chuan Xue Bao 2004; 31:901-7. [PMID: 15493139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The Nuclear Ribosomal DNA internal transcribed spacers (ITS) region sequences from a putative natural hybrid species Meconopsis x cookei and its possible parents M. punicea and M. quintuplinervia were obtained by using direct sequencing method. The sequence length of ITS region (including ITS1, 5.8S and ITS2) is 667 bp for M. punicea, 668 bp for M. x cookei, and 668 bp for M. quintuplinervia. The sequences were aligned by the software Clustal X, and the bases per locus were compared by using software with manual method. The aligned sequence length is 688 bp, of which ITS1 is 254 bp, 5.8S is 162 bp, and ITS2 is 252 bp. 16 variable loci were detected from the aligned sequence, approximately 2.40% to the whole sequence length, of which ITS1 has nine variable loci (56.25%), ITS2 has six variable loci (37.50%), and 5.8S has one variable locus (6.25%). The results show that M. x cookei have two kinds of ITS sequences contributed from two species M. puniceaa and M. quintuplinervia, i.e. the variation of ITS gene among M. x cookei, M. punicea and M. quintuplinervia is congruence with the Mendel's genetics law. Therefore, the molecular evidences indicate that M. x cookei is a hybrid origin from M. punicea and M. quintuplinervia.
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Affiliation(s)
- Chang-Chun Yuan
- Life Science and Chemistry School, Zhanjiang Normal University, Zhanjiang 524048, China.
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Abstract
In a common garden, we investigated genetic and environmental influences on alkaloid production using Sanguinaria canadensis as a model. Nutrient and shade regimes were applied to replicated clones over one growing season, and induction of alkaloid production in bloodroot was tested on a whole-plant basis using jasmonic acid as an elicitor. Alkaloid concentrations increased with decreasing light intensity and fertilizer levels. Induction was not achieved by foliar application of jasmonic acid. Genetic influences represented by clone effects may be indicated by variation in alkaloid concentration by clone, but this experimental design did not allow us to distinguish genetic from pre-experiment environmental influences on the rhizomes.
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Affiliation(s)
- A K Salmore
- Institute of Ecology, University of Georgia, Athens 30602, USA
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