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Fernie AR, Yan J, Aharoni A, Ma J. Editorial: The past, present and future of The Plant Journal Resource Articles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:967-973. [PMID: 37943112 DOI: 10.1111/tpj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetics, Huazhong Agricultural District, Wuhan, China
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jianxian Ma
- Purdue University, 915 S. University St, West Lafayette, IN, USA
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Ma J, Hancock WG, Nifong JM, Kernodle SP, Lewis RS. Identification and editing of a hybrid lethality gene expands the range of interspecific hybridization potential in Nicotiana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2915-2925. [PMID: 32613263 DOI: 10.1007/s00122-020-03641-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE Identification and inactivation of hybrid lethality genes can be used to expand the available gene pool for improvement of a cultivated crop species. Hybrid lethality is one genetic mechanism that contributes to reproductive isolation in plants and serves as a barrier to use of diverse germplasm for improvement of cultivated species. A classic example is the seedling lethality exhibited by progeny from the Nicotiana tabacum × N. africana interspecific cross. In order to increase the body of knowledge on mechanisms of hybrid lethality in plants, and to potentially develop tools to circumvent them, we utilized a transposon tagging strategy to identify a candidate gene involved in the control of this reaction. N. tabacum gene Nt6549g30 was identified to code for a class of coiled-coil nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) proteins, the largest class of plant defense proteins. Gene editing, along with other experiments, was used to verify that Nt6549g30 is the gene at the N. tabacum Hybrid Lethality 1 (NtHL1) locus controlling the hybrid lethality reaction in crosses with N. africana. Gene editing of Nt6549g30 was also used to reverse interspecific seedling lethality in crosses between N. tabacum and eight of nine additional tested species from section Suaveolentes. Results further implicate the role of disease resistance-like genes in the evolution of plant species and demonstrate the possibility of expanding the gene pool for a crop species through gene editing.
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Affiliation(s)
- Justin Ma
- Department of Crop and Soil Sciences, North Carolina State University, Campus, Box 7620, Raleigh, NC, 27695, USA
| | - Wesley G Hancock
- Department of Crop and Soil Sciences, North Carolina State University, Campus, Box 7620, Raleigh, NC, 27695, USA
| | - Jessica M Nifong
- Department of Crop and Soil Sciences, North Carolina State University, Campus, Box 7620, Raleigh, NC, 27695, USA
| | - Sheri P Kernodle
- Department of Crop and Soil Sciences, North Carolina State University, Campus, Box 7620, Raleigh, NC, 27695, USA
| | - Ramsey S Lewis
- Department of Crop and Soil Sciences, North Carolina State University, Campus, Box 7620, Raleigh, NC, 27695, USA.
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Ma JM, Heim CB, Humphry M, Nifong JM, Lewis RS. Characterization of Phn15.1, a Newly Identified Phytophthora nicotianae Resistance QTL in Nicotiana tabacum. PLANT DISEASE 2020; 104:1638-1646. [PMID: 32310718 DOI: 10.1094/pdis-10-19-2257-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phytophthora nicotianae is an oomycete that causes black shank, one of the most economically important diseases affecting tobacco production worldwide. Identification and introgression of novel genetic variability affecting partial genetic resistance to this pathogen is important because of the increased durability of partial resistance over time as compared with genes conferring immunity. A previous mapping study identified a quantitative trait locus (QTL), hereafter designated as Phn15.1, with a major effect on P. nicotianae resistance in tobacco. In this research, we describe significantly improved resistance of nearly isogenic lines (NILs) of flue-cured tobacco carrying the introgressed Phn15.1 region derived from highly resistant cigar tobacco cultivar Beinhart 1000. The Phn15.1 region appeared to act in an additive or partially dominant manner to positively affect resistance. To more finely resolve the position of the gene or genes underlying the Phn15.1 effect, the QTL was mapped with an increased number of molecular markers (single-nucleotide polymorphisms) identified to reside within the region. Development and evaluation of subNILs containing varying amounts of Beinhart 1000-derived Phn15.1-associated genetic material permitted the localization of the QTL to a genetic interval of approximately 2.7 centimorgans. Importantly, we were able to disassociate the Beinhart 1000 Phn15.1 resistance alleles from a functional NtCPS2 allele(s) which contributes to the accumulation of a diterpene leaf surface exudate considered undesirable for flue-cured and burley tobacco. Information from this research should be of value for marker-assisted introgression of Beinhart 1000-derived partial black shank resistance into flue-cured and burley tobacco breeding programs.
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Affiliation(s)
- Justin M Ma
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, U.S.A
| | - Crystal B Heim
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, U.S.A
| | - Matt Humphry
- Plant Biotechnology Division, British American Tobacco Company, Cambridge, U.K
| | - Jessica M Nifong
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, U.S.A
| | - Ramsey S Lewis
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, U.S.A
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Wang Z, Wang S, Wu M, Li Z, Liu P, Li F, Chen Q, Yang A, Yang J. Evolutionary and functional analyses of the 2-oxoglutarate-dependent dioxygenase genes involved in the flavonoid biosynthesis pathway in tobacco. PLANTA 2019; 249:543-561. [PMID: 30293202 DOI: 10.1007/s00425-018-3019-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/23/2018] [Indexed: 05/27/2023]
Abstract
MAIN CONCLUSION This study illustrates the differences in the gene structure of 2-oxoglutarate-dependent oxygenase involved in flavonoid biosynthesis (2ODD-IFB), and their potential roles in regulating tobacco flavonoid biosynthesis and plant growth. Flavonol synthase (FLS), anthocyanidin synthase (ANS), and flavanone 3β-hydroxylase belong to the 2-oxoglutarate-dependent (2ODD) oxygenase family, and each performs crucial functions in the biosynthesis of flavonoids. We identified two NtFLS genes, two NtANS genes, and four NtF3H genes from Nicotiana tabacum genome, as well as their homologous genes in the N. sylvestris and N. tomentosiformis genomes. Our phylogenetic analysis indicated that these three types of genes split from each other before the divergence of gymnosperms and angiosperms. FLS evolved faster in the eudicot plants, whereas ANS evolved faster in the monocot plants. Gene structure analysis revealed two fragment insertions occurred at different times in the intron one position of tobacco FLS genes. Homologous protein modeling revealed distinct structures in the N terminus of the tobacco 2ODD oxygenases. We found that the expression patterns of genes encoding tobacco 2ODD oxygenases in flavonoids biosynthesis (2ODD-IFB) did not determine the accumulation patterns of flavonoids among various tobacco tissues, but strongly affected the concentration of flavonoids in the tissues, where they were biosynthesized. More carbon resource flowed to the flavonol biosynthesis when NtANS gene was silenced, otherwise more anthocyanidin accumulated when NtFLS gene was repressed. This study illustrates the 2ODD-IFB gene structure evolution, differences among their protein structures, and provides a foundation for regulating plant development and altering flavonoid content and/or composition through the manipulation of plant 2ODD-IFB genes.
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Affiliation(s)
- Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Shanshan Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Mingzhu Wu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Feng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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Gali KK, Tar’an B, Madoui MA, van der Vossen E, van Oeveren J, Labadie K, Berges H, Bendahmane A, Lachagari RVB, Burstin J, Warkentin T. Development of a Sequence-Based Reference Physical Map of Pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:323. [PMID: 30930928 PMCID: PMC6428963 DOI: 10.3389/fpls.2019.00323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/28/2019] [Indexed: 05/13/2023]
Abstract
Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (∼4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.
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Affiliation(s)
| | - Bunyamin Tar’an
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohammed-Amin Madoui
- Atomic Energy and Alternative Energies Commission (CEA), Genomics Institute (IG), Évry, France
| | | | | | | | | | | | | | | | - Tom Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Tom Warkentin,
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Wang X, Yang S, Chen Y, Zhang S, Zhao Q, Li M, Gao Y, Yang L, Bennetzen JL. Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana. BMC Genomics 2018; 19:500. [PMID: 29945549 PMCID: PMC6020451 DOI: 10.1186/s12864-018-4878-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 06/18/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes. RESULTS Here, we initially characterized 2,483,032 SSRs (repeat units of 1-10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis. CONCLUSIONS The present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms. The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.html.
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Affiliation(s)
- Xuewen Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Shuai Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 China
| | - Yongdui Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650223 People’s Republic of China
| | - Shumeng Zhang
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Qingshi Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
| | - Meng Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
| | - Yulong Gao
- Tobacco Breeding Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 Yunnan China
| | - Long Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 China
| | - Jeffrey L. Bennetzen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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Wei X, Xu Z, Wang G, Hou J, Ma X, Liu H, Liu J, Chen B, Luo M, Xie B, Li R, Ruan J, Liu X. pBACode: a random-barcode-based high-throughput approach for BAC paired-end sequencing and physical clone mapping. Nucleic Acids Res 2017; 45:e52. [PMID: 27980066 PMCID: PMC5397170 DOI: 10.1093/nar/gkw1261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022] Open
Abstract
Applications that use Bacterial Artificial Chromosome (BAC) libraries often require paired-end sequences and knowledge of the physical location of each clone in plates. To facilitate obtaining this information in high-throughput, we generated pBACode vectors: a pool of BAC cloning vectors, each with a pair of random barcodes flanking its cloning site. In a pBACode BAC library, the BAC ends and their linked barcodes can be sequenced in bulk. Barcode pairs are determined by sequencing the empty pBACode vectors, which allows BAC ends to be paired according to their barcodes. For physical clone mapping, the barcodes are used as unique markers for their linked genomic sequence. After multi-dimensional pooling of BAC clones, the barcodes are sequenced and deconvoluted to locate each clone. We generated a pBACode library of 94,464 clones for the flounder Paralichthys olivaceus and obtained paired-end sequence from 95.4% of the clones. Incorporating BAC paired-ends into the genome preassembly improved its continuity by over 10-fold. Furthermore, we were able to use the barcodes to map the physical locations of each clone in just 50 pools, with up to 11 808 clones per pool. Our physical clone mapping located 90.2% of BAC clones, enabling targeted characterization of chromosomal rearrangements.
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Affiliation(s)
- Xiaolin Wei
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China.,School of Life Sciences, Peking University, Beijing 100084, China
| | - Zhichao Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China
| | - Guixing Wang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Jilun Hou
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Xiaopeng Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China
| | - Haijin Liu
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Jiadong Liu
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Chen
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jue Ruan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xiao Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Edwards KD, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans AD, Bombarely A, Allen F, Hurst R, White B, Kernodle SP, Bromley JR, Sanchez-Tamburrino JP, Lewis RS, Mueller LA. A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genomics 2017; 18:448. [PMID: 28625162 PMCID: PMC5474855 DOI: 10.1186/s12864-017-3791-6] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. RESULTS Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. CONCLUSIONS Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.
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Affiliation(s)
- K. D. Edwards
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | | | - K. Drake-Stowe
- Crop Science Department, North Carolina State University, Raleigh, NC USA
| | - M. Humphry
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - A. D. Evans
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - A. Bombarely
- Boyce Thompson Institute, Ithaca, NY USA
- Present address Department of Horticulture, Virginia Tech, Blacksburg, VA USA
| | - F. Allen
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - R. Hurst
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - B. White
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - S. P. Kernodle
- Crop Science Department, North Carolina State University, Raleigh, NC USA
| | - J. R. Bromley
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | | | - R. S. Lewis
- Crop Science Department, North Carolina State University, Raleigh, NC USA
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Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, Aury JM. MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. BMC Bioinformatics 2016; 17:115. [PMID: 26936254 PMCID: PMC4776351 DOI: 10.1186/s12859-016-0969-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
Background Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring. Results We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a Whole Genome Profiling™ (WGP) map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the contiguity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase contiguity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency. Conclusions MaGuS is a powerful reference-free evaluator of assembly quality and a WGP map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the contiguity of large and complex genome assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0969-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohammed-Amin Madoui
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Carole Dossat
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Léo d'Agata
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Jan van Oeveren
- Keygene NV, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands.
| | | | - Jean-Marc Aury
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
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10
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Jelínková A, Müller K, Fílová-Pařezová M, Petrášek J. NtGNL1a ARF-GEF acts in endocytosis in tobacco cells. BMC PLANT BIOLOGY 2015; 15:272. [PMID: 26541824 PMCID: PMC4635988 DOI: 10.1186/s12870-015-0621-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 09/18/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Processes of anterograde and retrograde membrane trafficking play an important role in cellular homeostasis and dynamic rearrangements of the plasma membrane (PM) in all eukaryotes. These processes depend on the activity of adenosine ribosylation factors (ARFs), a family of GTP-binding proteins and their guanine exchange factors (GEFs). However, knowledge on the function and specificity of individual ARF-GEFs for individual steps of membrane trafficking pathways is still limited in plants. RESULTS In this work, treatments with various trafficking inhibitors showed that the endocytosis of FM 4-64 is largely dynamin-dependent and relies on proteins containing endocytic tyrosine-based internalization motif and intact cytoskeleton. Interestingly, brefeldin A (BFA), reported previously as an inhibitor of anterograde membrane trafficking in plants, appeared to be the most potent inhibitor of endocytosis in tobacco. In concert with this finding, we demonstrate that the point mutation in the Sec7 domain of the GNOM-LIKE protein1a (NtGNL1a) confers intracellular trafficking pathway-specific BFA resistance. The internalization of FM 4-64 and trafficking of PIN-FORMED1 (PIN1) auxin efflux carrier in BY-2 tobacco cells were studied to reveal the function of the ARF-GEF NtGNL1a in these. CONCLUSIONS Altogether, our observations uncovered the role of NtGNL1a in endocytosis, including endocytosis of PM proteins (as PIN1 auxin efflux carrier). Moreover these data emphasize the need of careful evaluation of mode of action of non-native inhibitors in various species. In addition, they demonstrate the potential of tobacco BY-2 cells for selective mapping of ARF-GEF-regulated endomembrane trafficking pathways.
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Affiliation(s)
- Adriana Jelínková
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 165 02, Prague 6, Czech Republic.
| | - Karel Müller
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 165 02, Prague 6, Czech Republic.
| | - Markéta Fílová-Pařezová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 165 02, Prague 6, Czech Republic.
| | - Jan Petrášek
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 165 02, Prague 6, Czech Republic.
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic.
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Zhang H, Niu D, Wang J, Zhang S, Yang Y, Jia H, Cui H. Engineering a Platform for Photosynthetic Pigment, Hormone and Cembrane-Related Diterpenoid Production in Nicotiana tabacum. PLANT & CELL PHYSIOLOGY 2015; 56:2125-38. [PMID: 26363359 DOI: 10.1093/pcp/pcv131] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/08/2015] [Indexed: 12/16/2023]
Abstract
Plants synthesize a large number of isoprenoids that are of nutritional, medicinal and industrial importance. 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the first committed step for plastidial isoprenoid biosynthesis. Here, we identified two DXR isogenes, designated NtDXR1 and NtDXR2, from tetraploid common tobacco (Nicotiana tabacum L.). Southern blotting and genotyping analysis revealed that two NtDXR genes existed in the tetraploid tobacco genome; NtDXR1 and NtDXR2 were separately derived from N. tomentosiformis and N. sylvestris. Both NtDXRs were localized in chloroplasts. Expression patterns indicated that NtDXR1 and NtDXR2 had similar expression profiles. NtDXR genes were highly expressed in leaves with or without trichomes; expression was relatively reduced in flowers and stems, weak in leaf trichomes and marginal in roots and seeds. Overexpressing NtDXR1 under control of the 35S promoter resulted in longer primary roots and enhancement of various photosynthetic pigments and hormones in leaves. In contrast, there were no significant changes in cembrane-related diterpenoids synthesized in glandular trichomes. To elucidate further the function of DXR in the biosynthesis of diterpenoids, overexpression vectors for NtDXR1 under the control of a trichome-specific CYP promoter were transferred to tobacco plants. CYP:NtDXR1 tobacco exhibited larger glandular cells and increased cembrane-related diterpenoids in leaf glandular trichomes. Moreover, transcripts of eight MEP (2-C-methyl-d-erythritol 4-phosphate) pathway genes were significantly up-regulated in NtDXR1-overexpressing tobacco plants, indicating that overexpression of NtDXR could boost the expression of downstream genes in the MEP pathway. Our results suggested that overexpression of NtDXR1 could increase the levels of photosynthetic pigments, leaf surface exudates and hormones though the MEP pathway.
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Affiliation(s)
- Hongying Zhang
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dexin Niu
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jing Wang
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Songtao Zhang
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongxia Yang
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongfang Jia
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hong Cui
- Key Laboratory for Cultivation of Tobacco Industry, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
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12
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Zhou XM, Zhao P, Wang W, Zou J, Cheng TH, Peng XB, Sun MX. A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues. DNA Res 2015; 22:245-57. [PMID: 26205094 PMCID: PMC4535619 DOI: 10.1093/dnares/dsv012] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/21/2015] [Indexed: 11/14/2022] Open
Abstract
Autophagy is an evolutionarily conserved mechanism in both animals and plants, which has been shown to be involved in various essential developmental processes in plants. Nicotiana tabacum is considered to be an ideal model plant and has been widely used for the study of the roles of autophagy in the processes of plant development and in the response to various stresses. However, only a few autophagy-related genes (ATGs) have been identified in tobacco up to now. Here, we identified 30 ATGs belonging to 16 different groups in tobacco through a genome-wide survey. Comprehensive expression profile analysis reveals an abroad expression pattern of these ATGs, which could be detected in all tissues tested under normal growth conditions. Our series tests further reveal that majority of ATGs are sensitive and responsive to different stresses including nutrient starvation, plant hormones, heavy metal and other abiotic stresses, suggesting a central role of autophagy, likely as an effector, in plant response to various environmental cues. This work offers a detailed survey of all ATGs in tobacco and also suggests manifold functions of autophagy in both normal plant growth and plant response to environmental stresses.
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Affiliation(s)
- Xue-mei Zhou
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Peng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Wei Wang
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Jie Zou
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Tian-he Cheng
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Xiong-bo Peng
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Meng-xiang Sun
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
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Zhao P, Zhou XM, Zou J, Wang W, Wang L, Peng XB, Sun MX. Comprehensive analysis of cystatin family genes suggests their putative functions in sexual reproduction, embryogenesis, and seed formation. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5093-107. [PMID: 24996653 PMCID: PMC4144781 DOI: 10.1093/jxb/eru274] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cystatins are tightly bound and reversible inhibitors of cysteine proteases in C1A and C13 peptidase families, which have been identified in several species and shown to function in vegetative development and response to biotic/abiotic stresses in plants. Recent work revealed their critical role in regulating programmed cell death during embryogenesis in tobacco and suggested their more comprehensive roles in the process of sexual plant reproduction, although little is known about cystatin family genes in the processes. Here, 10 cystatin family genes in Nicotiana tabacum were identified using an expressed sequence tag (EST)-based gene clone strategy. Analysis of their biochemical properties showed that nine of them have the potency to inhibit the activities of both commercial cathepsin L-like proteases and extracted cysteine proteases from seeds, but with different K i values depending on the types of proteases and the developmental stages of the seed tested. This suggests that cystatin-dependent cathepsin L-like proteolytic pathways are probably important for early seed development. Comprehensive expression profile analysis revealed that cystatin family genes showed manifold variations in their transcription levels in different plant cell types, including the sperm, egg, and zygote, especially in the embryo and seed at different developmental stages. More interestingly, intracellular localization analysis of each cystatin revealed that most members of cystatin families are recognized as secretory proteins with signal peptides that direct them to the endoplasmic reticulum. These results suggest their widespread roles in cell fate determination and cell-cell communication in the process of sexual reproduction, especially in gamete and embryo development, as well as in seed formation.
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Affiliation(s)
- Peng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Xue-mei Zhou
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Jie Zou
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Wei Wang
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiong-bo Peng
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Meng-xiang Sun
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
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Poursarebani N, Nussbaumer T, Šimková H, Šafář J, Witsenboer H, van Oeveren J, Doležel J, Mayer KFX, Stein N, Schnurbusch T. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:334-47. [PMID: 24813060 PMCID: PMC4241024 DOI: 10.1111/tpj.12550] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/25/2014] [Accepted: 05/01/2014] [Indexed: 05/08/2023]
Abstract
Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the 'decoration' of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map-based isolation of agronomically important genes/quantitative trait loci located on this chromosome.
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Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mails and )
| | - Thomas Nussbaumer
- MIPS/IBIS German Research Center for Environmental HealthD-85764, Neuherberg, Germany
- † These authors contributed equally to this work
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | | | - Jan van Oeveren
- Keygene N.V.Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | - Klaus FX Mayer
- MIPS/IBIS German Research Center for Environmental HealthD-85764, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mails and )
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Sierro N, Battey JN, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV. The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 2014; 5:3833. [PMID: 24807620 PMCID: PMC4024737 DOI: 10.1038/ncomms4833] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
The allotetraploid plant Nicotiana tabacum (common tobacco) is a major crop species and a model organism, for which only very fragmented genomic sequences are currently available. Here we report high-quality draft genomes for three main tobacco varieties. These genomes show both the low divergence of tobacco from its ancestors and microsynteny with other Solanaceae species. We identify over 90,000 gene models and determine the ancestral origin of tobacco mosaic virus and potyvirus disease resistance in tobacco. We anticipate that the draft genomes will strengthen the use of N. tabacum as a versatile model organism for functional genomics and biotechnology applications.
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Affiliation(s)
- Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - James N.D. Battey
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Sonia Ouadi
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Nicolas Bakaher
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Lucien Bovet
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Adrian Willig
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
- Present address: 25b Quai Charles-Page, CH-1205 Genève, Switzerland
| | - Simon Goepfert
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Manuel C. Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Nikolai V. Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
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16
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Mandáková T, Marhold K, Lysak MA. The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure. THE NEW PHYTOLOGIST 2014; 201:982-992. [PMID: 24400905 DOI: 10.1111/nph.12567] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 09/23/2013] [Indexed: 05/18/2023]
Abstract
The origin of Cardamine flexuosa (Wavy Bittercress) has been a conundrum for more than six decades. Here we identify its parental species, analyse its genome structure in comparison to parental genomes and describe intergenomic structural variations in C. flexuosa. Genomic in situ hybridization (GISH) and comparative chromosome painting (CCP) uncovered the parental genomes and the chromosome composition of C. flexuosa and its presumed diploid progenitors. Cardamine flexuosa is an allotetraploid (2n = 4x = 32), originating from two diploid species, Cardamine amara and Cardamine hirsuta (2n = 2x = 16). The two parental species display almost perfectly conserved chromosomal collinearity for seven out of the eight chromosomes. A 13 Mb pericentric inversion distinguishes chromosome CA1 from CH1. A comparative cytomolecular map was established for C. flexuosa by CCP/GISH. Whereas conserved chromosome collinearity between the C. amara and C. hirsuta subgenomes might have promoted intergenomic rearrangements through homeologous recombination, only one reciprocal translocation between two homeologues has occurred since the origin of C. flexuosa. The genome of C. flexuosa demonstrates that allopolyploids can maintain remarkably stable subgenomes over 10(4) -10(5) yr throughout a wide distribution range. By contrast, the rRNA genes underwent genome-specific elimination towards a diploid-like number of loci.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
| | - Karol Marhold
- Institute of Botany, Slovak Academy of Sciences, SK-84523, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic
| | - Martin A Lysak
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
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Sierro N, Battey JND, Ouadi S, Bovet L, Goepfert S, Bakaher N, Peitsch MC, Ivanov NV. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol 2013; 14:R60. [PMID: 23773524 PMCID: PMC3707018 DOI: 10.1186/gb-2013-14-6-r60] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 05/10/2013] [Accepted: 06/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit different alkaloid and diterpenoid production. N. sylvestris is cultivated largely as an ornamental plant and it has been used as a diploid model system for studies of terpenoid production, plastid engineering, and resistance to biotic and abiotic stress. N. sylvestris and N. tomentosiformis are considered to be modern descendants of the maternal and paternal donors that formed Nicotiana tabacum about 200,000 years ago through interspecific hybridization. Here we report the first genome-wide analysis of these two Nicotiana species. RESULTS Draft genomes of N. sylvestris and N. tomentosiformis were assembled to 82.9% and 71.6% of their expected size respectively, with N50 sizes of about 80 kb. The repeat content was 72-75%, with a higher proportion of retrotransposons and copia-like long terminal repeats in N. tomentosiformis. The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. The key genes involved in terpenoid metabolism, alkaloid metabolism and heavy metal transport showed differential expression in the leaves, roots and flowers of N. sylvestris and N. tomentosiformis. CONCLUSIONS The reference genomes of N. sylvestris and N. tomentosiformis represent a significant contribution to the SOL100 initiative because, as members of the Nicotiana genus of Solanaceae, they strengthen the value of the already existing resources by providing additional comparative information, thereby helping to improve our understanding of plant metabolism and evolution.
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Affiliation(s)
- Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - James ND Battey
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Sonia Ouadi
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Lucien Bovet
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Simon Goepfert
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Nicolas Bakaher
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
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