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Li H, Che R, Zhu J, Yang X, Li J, Fernie AR, Yan J. Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:999-1017. [PMID: 38009661 DOI: 10.1111/tpj.16545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.
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Affiliation(s)
- Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ronghui Che
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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2
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Makarenko MS, Azarin KV, Gavrilova VA. Mitogenomic Research of Silverleaf Sunflower ( Helianthus argophyllus) and Its Interspecific Hybrids. Curr Issues Mol Biol 2023; 45:4841-4849. [PMID: 37367057 DOI: 10.3390/cimb45060308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Interspecific hybridization is widespread for sunflowers, both in wild populations and commercial breeding. One of the most common species that can efficiently cross with Helianthus annuus is the Silverleaf sunflower-Helianthus argophyllus. The current study carried out structural and functional organization analyses of mitochondrial DNA in H. argophyllus and the interspecific hybrid, H. annuus (VIR114A line) × H. argophyllus. The complete mitogenome of H. argophyllus counts 300,843 bp, has a similar organization to the mitogenome of cultivated sunflower, and holds SNPs typical for wild sunflowers. RNA editing analysis predicted 484 sites in H. argophyllus mitochondrial CDS. The mitochondrial genome of the H. annuus × H. argophyllus hybrid is identical to the maternal line (VIR114A). We expected that significant rearrangements in the mitochondrial DNA of the hybrid would occur, due to the frequent recombination. However, the hybrid mitogenome lacks rearrangements, presumably due to the preservation of nuclear-cytoplasmic interaction paths.
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Affiliation(s)
- Maksim S Makarenko
- The Laboratory of Plant Genomics, The Institute for Information Transmission Problems, 127051 Moscow, Russia
| | - Kirill V Azarin
- The Laboratory of Molecular Genetics, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Vera A Gavrilova
- Oil and Fiber Crops Genetic Resources Department, The N.I. Vavilov All Russian Institute of Plant Genetic Resources, 190031 Saint Petersburg, Russia
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3
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Bahmani K, Robinson A, Majumder S, LaVardera A, Dowell JA, Goolsby EW, Mason CM. Broad diversity in monoterpene-sesquiterpene balance across wild sunflowers: Implications of leaf and floral volatiles for biotic interactions. AMERICAN JOURNAL OF BOTANY 2022; 109:2051-2067. [PMID: 36317693 DOI: 10.1002/ajb2.16093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
PREMISE As plant lineages diversify across environmental gradients, species are predicted to encounter divergent biotic pressures. This study investigated the evolution of volatile secondary metabolism across species of Helianthus. METHODS Leaves and petals of 40 species of wild Helianthus were analyzed via gas chromatography-mass spectrometry to determine volatile secondary metabolite profiles. RESULTS Across all species, 500 compounds were identified; 40% were sesquiterpenes, 18% monoterpenes, 3% diterpenes, 4% fatty acid derivatives, and 35% other compounds such as phenolics and small organic molecules. Qualitatively, annuals and species from more arid western climates had leaf compositions with a higher proportion of total monoterpenes, while erect perennials and species from more mesic eastern habitats contained a higher proportion of total sesquiterpenes. Among species, mass-based leaf monoterpene and sesquiterpene abundance were identified as largely orthogonal axes of variation by principal component analysis. Profiles for leaves were not strongly correlated with those of petals. CONCLUSIONS Volatile metabolites were highly diverse among wild Helianthus, indicating the value of this genus as a model system and rich genetic resource. The independence of leaf and petal volatile profiles indicates a low level of phenotypic integration between vegetative and reproductive structures, implying vegetative defense and reproductive defense or pollinator attraction functions mediated by terpene profiles in these two organs can evolve without major trade-offs. The major biosynthetic pathways for the major terpenes in wild Helianthus are already well described, providing a road map to deeper inquiry into the drivers of this diversity.
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Affiliation(s)
- Keivan Bahmani
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | | | - Sambadi Majumder
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | | | - Jordan A Dowell
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Eric W Goolsby
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | - Chase M Mason
- Department of Biology, University of Central Florida, Orlando, FL, USA
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4
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Bercovich N, Genze N, Todesco M, Owens GL, Légaré JS, Huang K, Rieseberg LH, Grimm DG. HeliantHOME, a public and centralized database of phenotypic sunflower data. Sci Data 2022; 9:735. [PMID: 36450875 PMCID: PMC9712528 DOI: 10.1038/s41597-022-01842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used model plant system for the study of population genomics, adaptation, and speciation. Moreover, cultivated sunflower, domesticated from a wild relative (Helianthus annuus) is a global oil crop, ranking fourth in production of vegetable oils worldwide. Public availability of data resources both for the plant research community and for the associated agricultural sector, are extremely valuable. We have created HeliantHOME ( http://www.helianthome.org ), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals. Additionally, the database is enriched with external genomic data and results of genome-wide association studies. Finally, being a community open-source platform, HeliantHOME is expected to expand as new knowledge and resources become available.
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Affiliation(s)
- Natalia Bercovich
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Nikita Genze
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany
| | - Marco Todesco
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Gregory L. Owens
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.143640.40000 0004 1936 9465Department of Biology, University of Victoria, Victoria, BC Canada
| | - Jean-Sébastien Légaré
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.17091.3e0000 0001 2288 9830Department of Computer Science, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Data Science Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - Kaichi Huang
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Loren H. Rieseberg
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Dominik G. Grimm
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany ,grid.6936.a0000000123222966Technical University of Munich, Department of Informatics, Garching, Germany
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5
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Rushworth CA, Wagner MR, Mitchell-Olds T, Anderson JT. The Boechera model system for evolutionary ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1939-1961. [PMID: 36371714 DOI: 10.1002/ajb2.16090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.
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Affiliation(s)
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
| | | | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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6
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Cai X, Li X, Qi L. Genomic Insights Into Sclerotinia Basal Stalk Rot Resistance Introgressed From Wild Helianthus praecox Into Cultivated Sunflower ( Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:840954. [PMID: 35665155 PMCID: PMC9158519 DOI: 10.3389/fpls.2022.840954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Crop wild relatives of the cultivated sunflower (Helianthus annuus L.) are a valuable resource for its sustainable production. Helianthus praecox ssp. runyonii is a wild sunflower known for its resistance against diseases caused by the fungus, Sclerotinia sclerotiorum (Lib.) de Bary, which infects over 400 broadleaf hosts including many important food crops. The objective of this research was to dissect the Sclerotinia basal stalk rot (BSR) resistance introgressed from H. praecox ssp. runyonii into cultivated sunflower. An advanced backcross quantitative trait loci (AB-QTL) mapping population was developed from the cross of a H. praecox accession with cultivated sunflower lines. The AB-QTL population was evaluated for BSR resistance in the field during the summers of 2017-2018 and in the greenhouse in the spring of 2018. Highly significant genetic variations (p < 0.001) were observed for the BSR disease in the field and greenhouse with a moderately high broad-sense heritability (H 2) ranging from 0.66 to 0.73. Genotyping-by-sequencing approach was used to genotype the parents and the progeny lines of the AB-QTL population. A genetic linkage map spanning 1,802.95 cM was constructed using 1,755 single nucleotide polymorphism (SNP) markers mapped on 17 sunflower chromosomes. A total of 19 BSR resistance QTL were detected on nine sunflower chromosomes, each explaining 2.21%-16.99% of the phenotypic variance for resistance in the AB-QTL population. Sixteen of the 19 QTL had alleles conferring increased BSR resistance derived from the H. praecox parent. SNP markers flanking the identified QTL will facilitate marker-assisted breeding to combat the disease in sunflower.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - William Underwood
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gerald J. Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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7
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Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F. Arabis alpina: A perennial model plant for ecological genomics and life-history evolution. Mol Ecol Resour 2021; 22:468-486. [PMID: 34415668 PMCID: PMC9293087 DOI: 10.1111/1755-0998.13490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 01/03/2023]
Abstract
Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.
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Affiliation(s)
- Stefan Wötzel
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS, Rome, Italy
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - George Coupland
- Department of Plant Development Biology, MPI for Plant Breeding Research, Cologne, Germany
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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8
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Fanelli V, Ngo KJ, Thompson VL, Silva BR, Tsai H, Sabetta W, Montemurro C, Comai L, Harmer SL. A TILLING by sequencing approach to identify induced mutations in sunflower genes. Sci Rep 2021; 11:9885. [PMID: 33972605 PMCID: PMC8110748 DOI: 10.1038/s41598-021-89237-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
The Targeting Induced Local Lesions in Genomes (TILLING) technology is a reverse genetic strategy broadly applicable to every kind of genome and represents an attractive tool for functional genomic and agronomic applications. It consists of chemical random mutagenesis followed by high-throughput screening of point mutations in targeted genomic regions. Although multiple methods for mutation discovery in amplicons have been described, next-generation sequencing (NGS) is the tool of choice for mutation detection because it quickly allows for the analysis of a large number of amplicons. The aim of the present work was to screen a previously generated sunflower TILLING population and identify alterations in genes involved in several important and complex physiological processes. Twenty-one candidate sunflower genes were chosen as targets for the screening. The TILLING by sequencing strategy allowed us to identify multiple mutations in selected genes and we subsequently validated 16 mutations in 11 different genes through Sanger sequencing. In addition to addressing challenges posed by outcrossing, our detection and validation of mutations in multiple regulatory loci highlights the importance of this sunflower population as a genetic resource.
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Affiliation(s)
- Valentina Fanelli
- grid.7644.10000 0001 0120 3326Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, 70124 Bari, Italy ,grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Kathie J. Ngo
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Veronica L. Thompson
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Brennan R. Silva
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Helen Tsai
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Wilma Sabetta
- grid.5326.20000 0001 1940 4177National Research Council, Institute of Bioscience and BioResources-IBBR, 70124 Bari, Italy
| | - Cinzia Montemurro
- grid.7644.10000 0001 0120 3326Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, 70124 Bari, Italy
| | - Luca Comai
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Stacey L. Harmer
- grid.27860.3b0000 0004 1936 9684Department of Plant Biology, University of California, Davis, CA 95616 USA
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9
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Azarin K, Usatov A, Makarenko M, Khachumov V, Gavrilova V. Comparative analysis of chloroplast genomes of seven perennial Helianthus species. Gene 2021; 774:145418. [PMID: 33444687 DOI: 10.1016/j.gene.2021.145418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/15/2020] [Accepted: 01/05/2021] [Indexed: 10/25/2022]
Abstract
Sequencing and a comparative analysis of the complete chloroplast genomes of seven perennial Helianthus species were carried out. The chloroplast genomes have a typical quadripartite structure, including large and small single regions and a pair of inverted repeats. Genome sizes were between 151,152 bp and 151,289 bp. The genome of H. grosseserratus was the smallest, while that of H. microcephalus was the largest. The size variation of the chloroplast genomes is substantially due to the change in the length of simple sequence repeats (SSRs) in non-coding regions. An analysis of these SSRs revealed 35 polymorphic loci (average PIC value > 0.5) that can be used to examine ecological and evolutionary processes in wild Helianthus species. Eight divergence hotspots, including five intergenic regions (petN-psbM, clpP intron, rps3-rpl16, ndhD-ccsA, and ndhF-rpl32) and three gene regions (rbcL, ycf1, and ndhF) were also identified in Helianthus chloroplast genomes. The evolutionary selection pressure analysis revealed a strong purifying selection. Only the rbcL gene experienced efficiency of positive selection at the annual/perennial transitions. The inverted repeat (IR)/single copy (SC) boundaries were identical in all of these (Helianthus) species. In general, the comparison of the genomes revealed low levels of sequence variability (Pi = 0.00051). This indicates that the chloroplast genomes of the studied perennial species of Helianthus, in addition to purifying selection, are closely related and have a recent divergence time.
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Affiliation(s)
- Kirill Azarin
- Southern Federal University, Rostov-on-Don, Russian Federation; Agricultural Research Center "Donskoy", Zernograd, Russian Federation.
| | | | - Maksim Makarenko
- Institute for Information Transmission Problems, Moscow, Russian Federation
| | | | - Vera Gavrilova
- Vavilov All Russian Institute of Plant Genetic Resources, Saint Petersburg, Russian Federation
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10
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Horváth G, Slíz-Balogh J, Horváth Á, Egri Á, Virágh B, Horváth D, Jánosi IM. Sunflower inflorescences absorb maximum light energy if they face east and afternoons are cloudier than mornings. Sci Rep 2020; 10:21597. [PMID: 33299003 PMCID: PMC7725789 DOI: 10.1038/s41598-020-78243-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/17/2020] [Indexed: 11/09/2022] Open
Abstract
The mature inflorescence of sunflowers (Helianthus annuus) orients eastward after its anthesis (the flowering period, especially the maturing of the stamens), from which point it no longer tracks the Sun. Although several hypothetical explanations have been proposed for the ecological functions of this east facing, none have been tested. Here we propose an atmospheric-optical explanation. Using (i) astronomical data of the celestial motion of the Sun, (ii) meteorological data of diurnal cloudiness for Boone County located in the region from which domesticated sunflowers originate, (iii) time-dependent elevation angle of mature sunflower heads, and (iv) absorption spectra of the inflorescence and the back of heads, we computed the light energy absorbed separately by the inflorescence and the back between anthesis and senescence. We found that the inflorescences facing east absorb the maximum radiation, being advantageous for seed production and maturation, furthermore west facing would be more advantageous than south facing. The reason for these is that afternoons are cloudier than mornings in the cultivation areas of sunflowers. Since the photosynthesizing green back of mature heads absorbs maximal energy when the inflorescence faces west, maximizing the energy absorbed by the back cannot explain the east facing of inflorescences. The same results were obtained for central Italy and Hungary, where mornings are also less cloudy than afternoons. In contrast, in south Sweden, where mornings are cloudier than afternoons, west-facing mature inflorescences would absorb the maximum light energy. We suggest that the domesticated Helianthus annuus developed an easterly final orientation of its mature inflorescence, because it evolved in a region with cloudier afternoons.
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Affiliation(s)
- Gábor Horváth
- Environmental Optics Laboratory, Department of Biological Physics, ELTE Eötvös Loránd University, Pázmány sétány 1, 1117, Budapest, Hungary.
| | - Judit Slíz-Balogh
- Environmental Optics Laboratory, Department of Biological Physics, ELTE Eötvös Loránd University, Pázmány sétány 1, 1117, Budapest, Hungary.,Department of Astronomy, ELTE Eötvös Loránd University, Pázmány sétány 1, 1117, Budapest, Hungary
| | - Ákos Horváth
- Meteorological Institute, Universität Hamburg, Bundesstrasse 55, 20146, Hamburg, Germany
| | - Ádám Egri
- Danube Research Institute, MTA Centre for Ecological Research, Karolina út 29-31, 1113, Budapest, Hungary
| | - Balázs Virágh
- Environmental Optics Laboratory, Department of Biological Physics, ELTE Eötvös Loránd University, Pázmány sétány 1, 1117, Budapest, Hungary
| | - Dániel Horváth
- Environmental Optics Laboratory, Department of Biological Physics, ELTE Eötvös Loránd University, Pázmány sétány 1, 1117, Budapest, Hungary
| | - Imre M Jánosi
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány sétány 1, 1117, Budapest, Hungary
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11
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M Morsi M, Abdelmgid HM, M Hammad D. Genetic Variation Analysis for Breeding Purposes in Wild and Cultivated Sunflower Germplasm (<i>Helianthus annuus</i> Sp.). Pak J Biol Sci 2020; 23:1539-1550. [PMID: 33274886 DOI: 10.3923/pjbs.2020.1539.1550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Molecular genetic methods show conclusive turn in phylogeny investigations and therefore, understanding the allocation and extension of genetic diversity inside and among species. The current study aims to evaluate genetic diversity using molecular markers (5 SSR and 5 ISSR) on 13 sunflowers (Helianthus annuus) genotypes from different regions. MATERIALS AND METHODS The data acquired with the highest degree of polymorphism were confirmed. Polymorphic bands (24 and 55) were demonstrated totally through SSR and ISSR, respectively. Nevertheless, ISSR was superior in exhibiting polymorphism rate (97.37%) compared to SSR markers (90.83%). A range from 2-21 of amplified fragments, with molecular weights varying from 34-1331 bp, was noticeable. The genetic similarity coefficient was employed to set UPGMA dendrogram. RESULTS Dissimilarity was found in genotypes clustering within groups, whilst the manner of clustering in genotypes kept adjacent in ISSR and aggregated results of SSR and ISSR. Dice similarity ranged from 0.058-0.792, 0.168-0.770 and 0.154-0.847 with SSR, ISSR and the combined phylogeny dendrogram, respectively. The genetic variance of sunflower accessions of wild and cultivated cultivars from different geographic regions was established. CONCLUSION Knowledge of these results could be applied to confirm a wide genetic basis for outlook sunflower and manage germplasm breeding programs.
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The Investigation of Perennial Sunflower Species ( Helianthus L.) Mitochondrial Genomes. Genes (Basel) 2020; 11:genes11090982. [PMID: 32846894 PMCID: PMC7565312 DOI: 10.3390/genes11090982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022] Open
Abstract
The genus Helianthus is a diverse taxonomic group with approximately 50 species. Most sunflower genomic investigations are devoted to economically valuable species, e.g., H. annuus, while other Helianthus species, especially perennial, are predominantly a blind spot. In the current study, we have assembled the complete mitogenomes of two perennial species: H. grosseserratus (273,543 bp) and H. strumosus (281,055 bp). We analyzed their sequences and gene profiles in comparison to the available complete mitogenomes of H. annuus. Except for sdh4 and trnA-UGC, both perennial sunflower species had the same gene content and almost identical protein-coding sequences when compared with each other and with annual sunflowers (H. annuus). Common mitochondrial open reading frames (ORFs) (orf117, orf139, and orf334) in sunflowers and unique ORFs for H. grosseserratus (orf633) and H. strumosus (orf126, orf184, orf207) were identified. The maintenance of plastid-derived coding sequences in the mitogenomes of both annual and perennial sunflowers and the low frequency of nonsynonymous mutations point at an extremely low variability of mitochondrial DNA (mtDNA) coding sequences in the Helianthus genus.
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Skim-Sequencing Reveals the Likely Origin of the Enigmatic Endangered Sunflower Helianthus schweinitzii. Genes (Basel) 2019; 10:genes10121040. [PMID: 31847493 PMCID: PMC6947582 DOI: 10.3390/genes10121040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/05/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022] Open
Abstract
Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the origin of Helianthus schweinitzii, an endangered tetraploid sunflower that is endemic to the Piedmont Plateau in the eastern United States. We surveyed four accessions representing four populations of H. schweinitzii and 38 accessions of six purported parental species. Using de novo approaches, we assembled 87,004 bp of the chloroplast genome and 6770 bp of the nuclear 35S rDNA. Phylogenetic reconstructions based on the chloroplast genome revealed no reciprocal monophyly of taxa. In contrast, nuclear rDNA data strongly supported the currently accepted sections of the genus Helianthus. Information from combined cpDNA and rDNA provided evidence that H. schweinitzii is likely an allo-tetraploid that formed as a result of hybridization between the diploids Helianthus giganteus and Helianthus microcephalus.
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Castillo-Lorenzo E, Pritchard HW, Finch-Savage WE, Seal CE. Comparison of seed and seedling functional traits in native Helianthus species and the crop H. annuus (sunflower). PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:533-543. [PMID: 30353985 DOI: 10.1111/plb.12928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
Seed functional traits of native Helianthus species contribute towards ecosystem services but limitations to their use in managed programmes exist. Many perennial Helianthus possess seed dormancy. The ability for germination to occur under different temperature and drought conditions, as well as the capacity of germinated seeds to convert into normal seedlings is rarely considered. Our aim was to identify and quantify these constraints through functional trait analyses. In five seed lots of native Helianthus (four perennial and one annual) and five genotypes of sunflower (H. annuus) for comparison, dormancy, thermal and hydro thresholds and times, morphology, mass, oil content and conversion into normal seedlings were quantified. The influence of the seed collection site environment on these traits was also explored. Seed dormancy of the perennial species was overcome by scarification followed by germination in 5 mm GA3 . Thermal and hydro-time analyses revealed slower germination for the native seed lots (>1350 °Ch) in comparison to the sunflower genotypes (<829.9 °Ch). However, native seed lots had a higher capacity to convert into normal seedlings at high temperatures and low water potentials than sunflower genotypes. For the native seed lots, the average monthly temperature of the collection site was negatively correlated with thermal time. Variability in seed functional traits of native Helianthus and greater capacity for germinated seeds to convert into normal seedlings suggests they are better equipped to cope with high temperature and drought scenarios than sunflower. Effective dormancy alleviation is required to facilitate the use of native Helianthus species.
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Affiliation(s)
- E Castillo-Lorenzo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Ardingly, West Sussex, UK
- School of Life Sciences, Warwick University, Wellesbourne, Warwick, UK
| | - H W Pritchard
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Ardingly, West Sussex, UK
| | - W E Finch-Savage
- School of Life Sciences, Warwick University, Wellesbourne, Warwick, UK
| | - C E Seal
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Ardingly, West Sussex, UK
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15
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Qiu F, Baack EJ, Whitney KD, Bock DG, Tetreault HM, Rieseberg LH, Ungerer MC. Phylogenetic trends and environmental correlates of nuclear genome size variation in Helianthus sunflowers. THE NEW PHYTOLOGIST 2019; 221:1609-1618. [PMID: 30368824 DOI: 10.1111/nph.15465] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Flowering plants serve as a powerful model for studying the evolution of nuclear genome size (GS) given the tremendous GS variation that exists both within and across angiosperm lineages. Helianthus sunflowers consist of c. 50 species native to North America that occupy diverse habitats and vary in ploidy level. In the current study, we generated a comprehensive GS database for 49 Helianthus species using flow cytometric approaches. We examined variability across the genus and present a comparative phylogenetic analysis of GS evolution in diploid Helianthus species. Results demonstrated that different clades of diploid Helianthus species showed evolutionary patterns of GS contraction, expansion and relative stasis, with annual diploid species evolving smaller GS with the highest rate of evolution. Phylogenetic comparative analyses of diploids revealed significant negative associations of GS with temperature seasonality and cell production rate, indicating that the evolution of larger GS in Helianthus diploids may be more permissible in habitats with longer growing seasons where selection for more rapid growth may be relaxed. The Helianthus GS database presented here and corresponding analyses of environmental and phenotypic correlates will facilitate ongoing and future research on the ultimate drivers of GS evolution in this well-studied North American plant genus.
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Affiliation(s)
- Fan Qiu
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Eric J Baack
- Department of Biology, Luther College, Decorah, IA, 52101, USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Dan G Bock
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark C Ungerer
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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16
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Mangin B, Pouilly N, Boniface MC, Langlade NB, Vincourt P, Vear F, Muños S. Molecular diversity of sunflower populations maintained as genetic resources is affected by multiplication processes and breeding for major traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1099-1112. [PMID: 28255669 DOI: 10.1007/s00122-017-2872-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/04/2017] [Indexed: 05/20/2023]
Abstract
SNP genotyping of 114 cultivated sunflower populations showed that the multiplication process and the main traits selected during breeding of sunflower cultivars drove molecular diversity of the populations. The molecular diversity in a set of 114 cultivated sunflower populations was studied by single-nucleotide polymorphism genotyping. These populations were chosen as representative of the 400 entries in the INRA collection received or developed between 1962 and 2011 and made up of land races, open-pollinated varieties, and breeding pools. Mean allele number varied from 1.07 to 1.90. Intra-population variability was slightly reduced according to the number of multiplications since entry but some entries were probably largely homozygous when received. A principal component analysis was used to study inter-population variability. The first 3 axes accounted for 17% of total intra-population variability. The first axis was significantly correlated with seed oil content, more closely than just the distinction between oil and confectionary types. The second axis was related to the presence or absence of restorer genes and the third axis to flowering date and possibly to adaptation to different climates. Our results provide arguments highlighting the effect of the maintenance process on the within population genetic variability as well as on the impact of breeding for major agronomic traits on the between population variability of the collection. Propositions are made to improve sunflower population maintenance procedures to keep maximum genetic variability for future breeding.
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Affiliation(s)
- Brigitte Mangin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Pouilly
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | | | - Patrick Vincourt
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Felicity Vear
- GDEC, INRA, Université Clermont II Blaise Pascal, Clermont-Ferrand, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
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17
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Leff JW, Lynch RC, Kane NC, Fierer N. Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus. THE NEW PHYTOLOGIST 2017; 214:412-423. [PMID: 27879004 DOI: 10.1111/nph.14323] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/09/2016] [Indexed: 05/21/2023]
Abstract
Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds. Neither root nor rhizosphere bacterial communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere fungal communities. In particular, more modern sunflower strains had lower relative abundances of putative fungal pathogens. Seed-associated fungal communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Our results indicate that plant-associated fungal communities are more strongly influenced by host genetic factors and plant breeding than bacterial communities, a finding that could influence strategies for optimizing microbial communities to improve crop yields.
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Affiliation(s)
- Jonathan W Leff
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Ryan C Lynch
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Medicinal Genomics, 12 Gill St, Woburn, MA, 01801, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
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18
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Guo S, Zuo Y, Zhang Y, Wu C, Su W, Jin W, Yu H, An Y, Li Q. Large-scale transcriptome comparison of sunflower genes responsive to Verticillium dahliae. BMC Genomics 2017; 18:42. [PMID: 28061745 PMCID: PMC5219742 DOI: 10.1186/s12864-016-3386-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/07/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Sunflower Verticillium wilt (SVW) is a vascular disease caused by root infection with Verticillium dahliae (V. dahlia). It is a serious threat to the yield and quality of sunflower. However, chemical and agronomic measures for controlling this disease are not effective. The selection of more resistant genotypes is a desirable strategy to reduce contamination. A deeper knowledge of the molecular mechanisms and genetic basis underlying sunflower Verticillium wilt is necessary to accelerate breeding progress. RESULTS An RNA-Seq approach was used to perform global transcriptome profiling on the roots of resistant (S18) and susceptible (P77) sunflower genotypes infected with V. dahlia. Different pairwise transcriptome comparisons were examined over a time course (6, 12 and 24 h, and 2, 3, 5 and 10 d post inoculation). In RD, SD and D datasets, 1231 genes were associated with SVW resistance in a genotype-common transcriptional pattern. Moreover, 759 and 511 genes were directly related to SVW resistance in the resistant and susceptible genotypes, respectively, in a genotype-specific transcriptional pattern. Most of the genes were demonstrated to participate in plant defense responses; these genes included peroxidase (POD), glutathione peroxidase, aquaporin PIP, chitinase, L-ascorbate oxidase, and LRR receptors. For the up-regulated genotype-specific differentially expressed genes (DEGs) in the resistant genotype, higher average fold-changes were observed in the resistant genotype compared to those in the susceptible genotype. An inverse effect was observed in the down-regulated genotype-specific DEGs in the resistant genotype. KEGG analyses showed that 98, 112 and 52 genes were classified into plant hormone signal transduction, plant-pathogen interaction and flavonoid biosynthesis categories, respectively. Many of these genes, such as CNGC, RBOH, FLS2, JAZ, MYC2 NPR1 and TGA, regulate crucial points in defense-related pathway and may contribute to V. dahliae resistance in sunflower. CONCLUSIONS The transcriptome profiling results provided a clearer understanding of the transcripts associated with the crosstalk between sunflower and V. dahliae. The results identified several differentially expressed unigenes involved in the hyper sensitive response (HR) and the salicylic acid (SA)/jasmonic acid (JA)-mediated signal transduction pathway for resistance against V. dahliae. These results are useful for screening resistant sunflower genotypes.
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Affiliation(s)
- Shuchun Guo
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.,Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yongchun Zuo
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.,The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, College of life sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Yanfang Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Chengyan Wu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Wenxia Su
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Wen Jin
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Haifeng Yu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yulin An
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Qianzhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
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19
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Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. G3-GENES GENOMES GENETICS 2016; 6:2299-308. [PMID: 27233667 PMCID: PMC4978885 DOI: 10.1534/g3.116.029082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny.
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20
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Bowsher AW, Miller BJ, Donovan LA. Evolutionary divergences in root system morphology, allocation, and nitrogen uptake in species from high- versus low-fertility soils. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:129-140. [PMID: 32480447 DOI: 10.1071/fp15162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 10/29/2015] [Indexed: 06/11/2023]
Abstract
Root morphology and nutrient uptake processes are essential for acquisition of mineral resources from soil. However, our understanding of how root form and function have diverged across environments is limited. In this study, we addressed hypotheses of adaptive differentiation using three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrients. Under controlled environmental conditions, root morphology, allocation, and nitrogen (N) uptake (using a 15N tracer) were assessed for seedlings under both high and low N treatments. Species native to low nutrient soils (LNS) had lower total root length than those native to high nutrient soils (HNS), reflecting the slower growth rates of species from less fertile environments. Contrary to expectations, species did not consistently differ in specific root length, root tissue density, or root system plasticity, and species native to LNS had lower root:total mass ratio and higher 15N uptake rates than species native to HNS. Overall, these evolutionary divergences provide support for adaptive differentiation among species, with repeated evolution of slow-growing root systems suited for low resource availability in LNS. However, species native to LNS maintain a high capacity for N uptake, potentially as a means of maximising nutrient acquisition from transient pulses.
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Affiliation(s)
- Alan W Bowsher
- 2502 Miller Plant Sciences, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Benjamin J Miller
- 400 Biosciences Building, Division of Biological Sciences, University of Georgia, Athens, GA 30602, USA
| | - Lisa A Donovan
- 2502 Miller Plant Sciences, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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21
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Bowsher AW, Mason CM, Goolsby EW, Donovan LA. Fine root tradeoffs between nitrogen concentration and xylem vessel traits preclude unified whole-plant resource strategies in Helianthus. Ecol Evol 2016; 6:1016-31. [PMID: 26941942 PMCID: PMC4761775 DOI: 10.1002/ece3.1947] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/11/2015] [Accepted: 12/14/2015] [Indexed: 12/25/2022] Open
Abstract
Recent work suggests variation in plant growth strategies is governed by a tradeoff in resource acquisition and use, ranging from a rapid resource acquisition strategy to a resource-conservative strategy. While evidence for this tradeoff has been found in leaves, knowledge of root trait strategies, and whether they reflect adaptive differentiation across environments, is limited. In the greenhouse, we investigated variation in fine root morphology (specific root length and tissue density), chemistry (nitrogen concentration and carbon:nitrogen), and anatomy (root cross-sectional traits) in populations of 26 Helianthus species and sister Phoebanthus tenuifolius. We also compared root trait variation in this study with leaf trait variation previously reported in a parallel study of these populations. Root traits varied widely and exhibited little phylogenetic signal, suggesting high evolutionary lability. Specific root length and root tissue density were weakly negatively correlated, but neither was associated with root nitrogen, providing little support for a single axis of root trait covariation. Correlations between traits measured in the greenhouse and native site characteristics were generally weak, suggesting a variety of equally viable root trait combinations exist within and across environments. However, high root nitrogen was associated with lower xylem vessel number and cross-sectional area, suggesting a tradeoff between nutrient investment and water transport capacity. This led to correlations between root and leaf traits that were not always consistent with an acquisition-conservation tradeoff at the whole-plant level. Given that roots must balance acquisition of water and nutrients with functions like anchorage, exudation, and microbial symbioses, the varied evidence for root trait covariation likely reflects the complexity of interacting selection pressures belowground. Similarly, the lack of evidence for a single acquisition-conservation tradeoff at the whole-plant level likely reflects the vastly different selection pressures shaping roots and leaves, and the resources they are optimized to obtain.
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Affiliation(s)
- Alan W. Bowsher
- Department of Plant BiologyUniversity of Georgia2502 Miller Plant SciencesAthensGeorgia30602
| | - Chase M. Mason
- Department of Plant BiologyUniversity of Georgia2502 Miller Plant SciencesAthensGeorgia30602
| | - Eric W. Goolsby
- Interdisciplinary Toxicology ProgramUniversity of GeorgiaAthensGeorgia
| | - Lisa A. Donovan
- Interdisciplinary Toxicology ProgramUniversity of GeorgiaAthensGeorgia
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22
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Bowsher AW, Ali R, Harding SA, Tsai CJ, Donovan LA. Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species. PLoS One 2016; 11:e0148280. [PMID: 26824236 PMCID: PMC4733055 DOI: 10.1371/journal.pone.0148280] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/16/2016] [Indexed: 11/18/2022] Open
Abstract
Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments.
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Affiliation(s)
- Alan W. Bowsher
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Rifhat Ali
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
| | - Scott A. Harding
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Lisa A. Donovan
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
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23
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Low Temperature Tolerance in the Perennial Sunflower Helianthus maximiliani. AMERICAN MIDLAND NATURALIST 2016. [DOI: 10.1674/amid-175-01-91-102.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Stephens JD, Rogers WL, Mason CM, Donovan LA, Malmberg RL. Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment. AMERICAN JOURNAL OF BOTANY 2015; 102:910-20. [PMID: 26101417 DOI: 10.3732/ajb.1500031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/08/2015] [Indexed: 05/02/2023]
Abstract
PREMISE OF THE STUDY The sunflower genus Helianthus has long been recognized as economically significant, containing species of agricultural and horticultural importance. Additionally, this genus displays a large range of phenotypic and genetic variation, making Helianthus a useful system for studying evolutionary and ecological processes. Here we present the most robust Helianthus phylogeny to date, laying the foundation for future studies of this genus. METHODS We used a target enrichment approach across 37 diploid Helianthus species/subspecies with a total of 103 accessions. This technique garnered 170 genes used for both coalescent and concatenation analyses. The resulting phylogeny was additionally used to examine the evolution of life history and growth form across the genus. KEY RESULTS Coalescent and concatenation approaches were largely congruent, resolving a large annual clade and two large perennial clades. However, several relationships deeper within the phylogeny were more weakly supported and incongruent among analyses including the placement of H. agrestis, H. cusickii, H. gracilentus, H. mollis, and H. occidentalis. CONCLUSIONS The current phylogeny supports three major clades including a large annual clade, a southeastern perennial clade, and another clade of primarily large-statured perennials. Relationships among taxa are more consistent with early phylogenies of the genus using morphological and crossing data than recent efforts using single genes, which highlight the difficulties of phylogenetic estimation in genera known for reticulate evolution. Additionally, conflict and low support at the base of the perennial clades may suggest a rapid radiation and/or ancient introgression within the genus.
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Affiliation(s)
- Jessica D Stephens
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States
| | - Willie L Rogers
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States
| | - Chase M Mason
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States
| | - Lisa A Donovan
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States
| | - Russell L Malmberg
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States
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25
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Kantar MB, Sosa CC, Khoury CK, Castañeda-Álvarez NP, Achicanoy HA, Bernau V, Kane NC, Marek L, Seiler G, Rieseberg LH. Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2015; 6:841. [PMID: 26500675 PMCID: PMC4597133 DOI: 10.3389/fpls.2015.00841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 09/24/2015] [Indexed: 05/22/2023]
Abstract
Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation.
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Affiliation(s)
- Michael B. Kantar
- Biodiversity Research Centre and Department of Botany, University of British ColumbiaVancouver, BC, Canada
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, USA
- *Correspondence: Michael B. Kantar
| | | | - Colin K. Khoury
- International Center for Tropical AgricultureCali, Colombia
- Centre for Crop Systems Analysis, Wageningen UniversityWageningen, Netherlands
| | - Nora P. Castañeda-Álvarez
- International Center for Tropical AgricultureCali, Colombia
- School of Biosciences, University of BirminghamBirmingham, UK
| | | | - Vivian Bernau
- International Center for Tropical AgricultureCali, Colombia
- Department of Horticulture and Crop Science, The Ohio State UniversityColumbus, OH, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of Colorado at BoulderBoulder, CO, USA
| | - Laura Marek
- Agronomy Department, North Central Regional Plant Introduction Station, Iowa State University and United States Department of Agriculture Agricultural Research ServiceAmes, IA, USA
| | - Gerald Seiler
- Northern Crop Science Laboratory, United States Department of Agriculture Agricultural Research ServiceFargo, ND, USA
| | - Loren H. Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British ColumbiaVancouver, BC, Canada
- Department of Biology, Indiana UniversityBloomington, IN, USA
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Vandenbrink JP, Brown RI, Harmer SL, Blackman BK. Turning heads: the biology of solar tracking in sunflower. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:20-6. [PMID: 24908502 DOI: 10.1016/j.plantsci.2014.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/22/2014] [Accepted: 04/07/2014] [Indexed: 05/25/2023]
Abstract
Solar tracking in the common sunflower, Helianthus annuus, is a dramatic example of a diurnal rhythm in plants. During the day, the shoot apex continuously reorients, following the sun's relative position so that the developing heads track from east to west. At night, the reverse happens, and the heads return and face east in anticipation of dawn. This daily cycle dampens and eventually stops at anthesis, after which the sunflower head maintains an easterly orientation. Although shoot apical heliotropism has long been the subject of physiological studies in sunflower, the underlying developmental, cellular, and molecular mechanisms that drive the directional growth and curvature of the stem in response to extrinsic and perhaps intrinsic cues are not known. Furthermore, the ecological functions of solar tracking and the easterly orientation of mature heads have been the subject of significant but unresolved speculation. In this review, we discuss the current state of knowledge about this complex, dynamic trait. Candidate mechanisms that may contribute to daytime and nighttime movement are highlighted, including light signaling, hormonal action, and circadian regulation of growth pathways. The merits of the diverse hypotheses advanced to explain the adaptive significance of heliotropism in sunflower are also considered.
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Affiliation(s)
- Joshua P Vandenbrink
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA 22904, USA.
| | - Robin Isadora Brown
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA 22904, USA.
| | - Stacey L Harmer
- Department of Plant Biology, University of California, One Shields Avenue, Davis, CA 95616, USA.
| | - Benjamin K Blackman
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA 22904, USA.
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Kawakami T, Darby BJ, Ungerer MC. Transcriptome resources for the perennial sunflowerHelianthus maximilianiobtained from ecologically divergent populations. Mol Ecol Resour 2014; 14:812-9. [DOI: 10.1111/1755-0998.12227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Takeshi Kawakami
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Brian J. Darby
- Department of Biology; University of North Dakota; Grand Forks ND 58202 USA
| | - Mark C. Ungerer
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
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Kantar MB, Baute GJ, Bock DG, Rieseberg LH. Genomic variation in Helianthus: learning from the past and looking to the future. Brief Funct Genomics 2014; 13:328-40. [DOI: 10.1093/bfgp/elu004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Garcia S, Leitch IJ, Anadon-Rosell A, Canela MÁ, Gálvez F, Garnatje T, Gras A, Hidalgo O, Johnston E, Mas de Xaxars G, Pellicer J, Siljak-Yakovlev S, Vallès J, Vitales D, Bennett MD. Recent updates and developments to plant genome size databases. Nucleic Acids Res 2013; 42:D1159-66. [PMID: 24288377 PMCID: PMC3965065 DOI: 10.1093/nar/gkt1195] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols.
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Affiliation(s)
- Sònia Garcia
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
- *To whom correspondence should be addressed. Sònia Garcia: Tel: +34 934 024490; Fax: +34 934 025879;
| | - Ilia J. Leitch
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
- Correspondence may be also addressed to Ilia J. Leitch. Tel: +44 208 332 5329; Fax: +44 208 332 5310;
| | - Alba Anadon-Rosell
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Miguel Á. Canela
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Francisco Gálvez
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Teresa Garnatje
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Airy Gras
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Oriane Hidalgo
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Emmeline Johnston
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Gemma Mas de Xaxars
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Jaume Pellicer
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Sonja Siljak-Yakovlev
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Joan Vallès
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Daniel Vitales
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Michael D. Bennett
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
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Lobréaux S, Manel S, Melodelima C. Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery. Mol Ecol Resour 2013; 14:411-8. [PMID: 24128264 DOI: 10.1111/1755-0998.12189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/28/2022]
Abstract
The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A. alpina genomic fragments using next-generation sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analysed and 127,041 single-nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.
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Affiliation(s)
- Stéphane Lobréaux
- Laboratoire d'Ecologie Alpine, Université Joseph Fourier, UMR-CNRS 5553, BP53 38041, Grenoble, France
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