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Liu J, Lin X, Wang X, Feng L, Zhu S, Tian R, Fang J, Tao A, Fang P, Qi J, Zhang L, Huang Y, Xu J. Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus). BMC PLANT BIOLOGY 2024; 24:71. [PMID: 38267860 PMCID: PMC10809672 DOI: 10.1186/s12870-024-04739-9] [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: 09/20/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.
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Affiliation(s)
- Jiarui Liu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinyi Lin
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaojie Wang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Shixin Zhu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Runmeng Tian
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Aifen Tao
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pingping Fang
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianmin Qi
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwu Zhang
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongji Huang
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Jiantang Xu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Chase MW, Samuel R, Leitch AR, Guignard MS, Conran JG, Nollet F, Fletcher P, Jakob A, Cauz-Santos LA, Vignolle G, Dodsworth S, Christenhusz MJM, Buril MT, Paun O. Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae). ANNALS OF BOTANY 2023; 131:123-142. [PMID: 35029647 PMCID: PMC9904355 DOI: 10.1093/aob/mcac006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia. METHODS We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework. KEY RESULTS RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids. CONCLUSIONS The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis.
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Affiliation(s)
- Mark W Chase
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | | | - John G Conran
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Felipe Nollet
- Universidade Federal Rural de Pernambuco, Centro de Ciências Biológicas, Departamento de Botânica, Rua Manuel de Medeiros, S/N, Dois Irmãos, 52171-900 Recife, Pernambuco, Brazil
| | - Paul Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Aljaž Jakob
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Gabriel Vignolle
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Maarten J M Christenhusz
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Maria Teresa Buril
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Vozárová R, Wang W, Lunerová J, Shao F, Pellicer J, Leitch IJ, Leitch AR, Kovařík A. Mega-sized pericentromeric blocks of simple telomeric repeats and their variants reveal patterns of chromosome evolution in ancient Cycadales genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:646-663. [PMID: 36065632 PMCID: PMC9827991 DOI: 10.1111/tpj.15969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/19/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Simple telomeric repeats composed of six to seven iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (one newly sequenced), and eight bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10 000-fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non-telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase-sized blocks of telomeric repeats (i.e., billions of copies) were identified. Fluorescent in situ hybridization experiments using variant-specific probes revealed canonical Arabidopsis-type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. The ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads.
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Affiliation(s)
- Radka Vozárová
- Department of Molecular EpigeneticsInstitute of Biophysics, Czech Academy of Sciencesv.v.i., Královopolská 135612 65BrnoCzech Republic
- Department of Experimental Biology, Faculty of ScienceMasaryk University611 37BrnoCzech Republic
| | - Wencai Wang
- Science and Technology Innovation CentreGuangzhou University of Chinese MedicineGuangzhou510405China
| | - Jana Lunerová
- Department of Molecular EpigeneticsInstitute of Biophysics, Czech Academy of Sciencesv.v.i., Královopolská 135612 65BrnoCzech Republic
| | - Fengqing Shao
- Science and Technology Innovation CentreGuangzhou University of Chinese MedicineGuangzhou510405China
| | - Jaume Pellicer
- Royal Botanic GardensKew, RichmondSurreyTW9 3ABUK
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia sn08038BarcelonaSpain
| | | | - Andrew R. Leitch
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
| | - Aleš Kovařík
- Department of Molecular EpigeneticsInstitute of Biophysics, Czech Academy of Sciencesv.v.i., Královopolská 135612 65BrnoCzech Republic
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Fernández P, Hidalgo O, Juan A, Leitch IJ, Leitch AR, Palazzesi L, Pegoraro L, Viruel J, Pellicer J. Genome Insights into Autopolyploid Evolution: A Case Study in Senecio doronicum (Asteraceae) from the Southern Alps. PLANTS 2022; 11:plants11091235. [PMID: 35567236 PMCID: PMC9099586 DOI: 10.3390/plants11091235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
Polyploidy is a widespread phenomenon across angiosperms, and one of the main drivers of diversification. Whilst it frequently involves hybridisation, autopolyploidy is also an important feature of plant evolution. Minority cytotypes are frequently overlooked due to their lower frequency in populations, but the development of techniques such as flow cytometry, which enable the rapid screening of cytotype diversity across large numbers of individuals, is now providing a more comprehensive understanding of cytotype diversity within species. Senecio doronicum is a relatively common daisy found throughout European mountain grasslands from subalpine to almost nival elevations. We have carried out a population-level cytotype screening of 500 individuals from Tête Grosse (Alpes-de-Haute-Provence, France), confirming the coexistence of tetraploid (28.2%) and octoploid cytotypes (71.2%), but also uncovering a small number of hexaploid individuals (0.6%). The analysis of repetitive elements from short-read genome-skimming data combined with nuclear (ITS) and whole plastid DNA sequences support an autopolyploid origin of the polyploid S. doronicum individuals and provide molecular evidence regarding the sole contribution of tetraploids in the formation of hexaploid individuals. The evolutionary impact and resilience of the new cytotype have yet to be determined, although the coexistence of different cytotypes may indicate nascent speciation.
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Affiliation(s)
- Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Correspondence: (P.F.); (J.P.); Tel.: +34-932890611 (P.F. & J.P.)
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Ana Juan
- Departamento de Ciencias Ambientales y Recursos Naturales, Universidad de Alicante, 03080 Alicante, Spain;
| | - Ilia J. Leitch
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK;
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales, CONICET, División Paleobotánica, Buenos Aires C1405DJR, Argentina;
| | - Luca Pegoraro
- Biodiversity and Conservation Biology Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Bimensdorf, Switzerland;
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
- Correspondence: (P.F.); (J.P.); Tel.: +34-932890611 (P.F. & J.P.)
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Amosova AV, Yurkevich OY, Bolsheva NL, Samatadze TE, Zoshchuk SA, Muravenko OV. Repeatome Analyses and Satellite DNA Chromosome Patterns in Deschampsia sukatschewii, D. cespitosa, and D. antarctica (Poaceae). Genes (Basel) 2022; 13:genes13050762. [PMID: 35627148 PMCID: PMC9141916 DOI: 10.3390/genes13050762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 02/05/2023] Open
Abstract
Subpolar and polar ecotypes of Deschampsia sukatschewii (Popl.) Roshev, D. cespitosa (L.) P. Beauv, and D. antarctica E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants for genetic research and breeding. For the first time, the comparative repeatome analyses of subpolar and polar D. sukatschewii, D. cespitosa, and D. antarctica was performed using RepeatExplorer/TAREAN pipelines and FISH-based chromosomal mapping of the identified satellite DNA families (satDNAs). In the studied species, mobile genetic elements of class 1 made up the majority of their repetitive DNA; interspecific variations in the total amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were revealed; 12–18 high confident and 7–9 low confident putative satDNAs were identified. According to BLAST, most D. sukatschewii satDNAs demonstrated sequence similarity with satDNAs of D. antarctica and D. cespitosa indicating their common origin. Chromosomal mapping of 45S rDNA, 5S rDNA, and satDNAs of D. sukatschewii allowed us to construct the species karyograms and detect new molecular chromosome markers important for Deschampsia species. Our findings confirmed that genomes of D. sukatschewii and D. cespitosa were more closely related compared to D. antarctica according to repeatome composition and patterns of satDNA chromosomal distribution.
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Oliveira MAS, Nunes T, Dos Santos MA, Ferreira Gomes D, Costa I, Van-Lume B, Marques Da Silva SS, Oliveira RS, Simon MF, Lima GSA, Gissi DS, Almeida CCDS, Souza G, Marques A. High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae). Front Genet 2021; 12:727314. [PMID: 34630521 PMCID: PMC8495327 DOI: 10.3389/fgene.2021.727314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.
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Affiliation(s)
| | - Tomáz Nunes
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | | | | | - Iara Costa
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | | | - Ronaldo Simão Oliveira
- Campus Xique Xique, Federal Institute of Education, Science and Technology of Bahia, Xique-Xique, Brazil
| | | | - Gaus S A Lima
- Center of Agronomic Sciences, Federal University of Alagoas, Rio Largo, Brazil
| | - Danilo Soares Gissi
- Department of Biostatistics, Institute of Biosciences-IBB, Plant Biology, Parasitology and Zoology, São Paulo State University-UNESP, Botucatu, Brazil
| | | | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil.,Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Becher H, Powell RF, Brown MR, Metherell C, Pellicer J, Leitch IJ, Twyford AD. The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights. ANNALS OF BOTANY 2021; 128:639-651. [PMID: 34318876 PMCID: PMC8422891 DOI: 10.1093/aob/mcab102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.
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Affiliation(s)
- Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Max R Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, Harpenden, Hertfordshire, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
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Giraud D, Lima O, Huteau V, Coriton O, Boutte J, Kovarik A, Leitch AR, Leitch IJ, Aïnouche M, Salmon A. Evolutionary dynamics of transposable elements and satellite DNAs in polyploid Spartina species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110671. [PMID: 33288000 DOI: 10.1016/j.plantsci.2020.110671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/31/2020] [Accepted: 09/06/2020] [Indexed: 06/12/2023]
Abstract
Repeated sequences and polyploidy play a central role in plant genome dynamics. Here, we analyze the evolutionary dynamics of repeats in tetraploid and hexaploid Spartina species that diverged during the last 10 million years within the Chloridoideae, one of the poorest investigated grass lineages. From high-throughput genome sequencing, we annotated Spartina repeats and determined what sequence types account for the genome size variation among species. We examined whether differential genome size evolution correlated with ploidy levels and phylogenetic relationships. We also examined the tempo of repeat sequence dynamics associated with allopatric speciation over the last 3-6 million years between hexaploid species that diverged on the American and European Atlantic coasts and tetraploid species from North and South America. The tetraploid S. spartinae, whose phylogenetic placement has been debated, exhibits a similar repeat content as hexaploid species, suggesting common ancestry. Genome expansion or contraction resulting from repeat dynamics seems to be explained mostly by the contrasting divergence times between species, rather than by genome changes triggered by ploidy level change per se. One 370 bp satellite may be exhibiting 'meiotic drive' and driving chromosome evolution in S. alterniflora. Our results provide crucial insights for investigating the genetic and epigenetic consequences of such differential repeat dynamics on the ecology and distribution of the meso- and neopolyploid Spartina species.
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Affiliation(s)
- Delphine Giraud
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Oscar Lima
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Virginie Huteau
- Plateforme de cytogénétique moléculaire végétale, INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Olivier Coriton
- Plateforme de cytogénétique moléculaire végétale, INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Julien Boutte
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3DS, UK.
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
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9
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Heitkam T, Weber B, Walter I, Liedtke S, Ost C, Schmidt T. Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:32-52. [PMID: 31981259 DOI: 10.1111/tpj.14705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n = 4x = 36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3-6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles. Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Ines Walter
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Charlotte Ost
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
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10
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Zwyrtková J, Němečková A, Čížková J, Holušová K, Kapustová V, Svačina R, Kopecký D, Till BJ, Doležel J, Hřibová E. Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses. BMC PLANT BIOLOGY 2020; 20:280. [PMID: 32552738 PMCID: PMC7302162 DOI: 10.1186/s12870-020-02495-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/15/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Cultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the development of new cultivars with better quality and greater resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species (Lolium) and diploid and hexaploid fescue species (Festuca). In this work, we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species as well as one fescue and two ryegrass cultivars. RESULTS Partial genome sequences produced by Illumina sequencing technology were used for genome-wide comparative analyses with the RepeatExplorer pipeline. Retrotransposons were the most abundant repeat type in all seven grass species. The Athila element of the Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of the long terminal repeat (LTR) element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of fluorescence in situ hybridization (FISH) with a probe specific to the Fesreba element and immunostaining with centromeric histone H3 (CENH3) antibody showed their co-localization and indicated a possible role of Fesreba in centromere function. CONCLUSIONS Comparative repeatome analyses in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of the LTR element Fesreba. A new LTR element Fesreba was identified and found in abundance in centromeric regions of the fescues and ryegrasses. It may play a role in the function of their centromeres.
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Affiliation(s)
- Jana Zwyrtková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Alžběta Němečková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Veronika Kapustová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Radim Svačina
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Bradley John Till
- Centro de Genómica Nutricional Agroacuícola, Las Heras 350, Temuco, Chile
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
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11
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Lunerová J, Herklotz V, Laudien M, Vozárová R, Groth M, Kovařík A, Ritz CM. Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa. ANNALS OF BOTANY 2020; 125:1025-1038. [PMID: 32095807 PMCID: PMC7262465 DOI: 10.1093/aob/mcaa028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 02/24/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Despite their abundant odd-ploidy (2n = 5x = 35), dogroses (Rosa sect. Caninae) are capable of sexual reproduction due to their unique meiosis. During canina meiosis, two sets of chromosomes form bivalents and are transmitted by male and female gametes, whereas the remaining chromosomes form univalents and are exclusively transmitted by the egg cells. Thus, the evolution of chromosomes is expected to be driven by their behaviour during meiosis. METHODS To gain insight into differential chromosome evolution, fluorescence in situ hybridization was conducted for mitotic and meiotic chromosomes in four dogroses (two subsections) using satellite and ribosomal DNA probes. By exploiting high-throughput sequencing data, we determined the abundance and diversity of the satellite repeats in the genus Rosa by analysing 20 pentaploid, tetraploid and diploid species in total. KEY RESULTS A pericentromeric satellite repeat, CANR4, was found in all members of the genus Rosa, including the basal subgenera Hulthemia and Hesperhodos. The satellite was distributed across multiple chromosomes (5-20 sites per mitotic cell), and its genomic abundance was higher in pentaploid dogroses (2.3 %) than in non-dogrose species (1.3 %). In dogrose meiosis, univalent chromosomes were markedly enriched in CANR4 repeats based on both the number and the intensity of the signals compared to bivalent-forming chromosomes. Single-nucleotide polymorphisms and cluster analysis revealed high intragenomic homogeneity of the satellite in dogrose genomes. CONCLUSIONS The CANR4 satellite arose early in the evolution of the genus Rosa. Its high content and extraordinary homogeneity in dogrose genomes is explained by its recent amplification in non-recombining chromosomes. We hypothesize that satellite DNA expansion may contribute to the divergence of univalent chromosomes in Rosa species with non-symmetrical meiosis.
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Affiliation(s)
- Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Melanie Laudien
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute Zittau (IHI), Chair of Biodiversity of Higher Plants, Zittau, Germany
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
- Masaryk University, Faculty of Science, Brno, Czech Republic
| | - Marco Groth
- Leibniz Institute on Ageing – Fritz Lipmann Institute, Jena, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
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12
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McCann J, Macas J, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Differential Genome Size and Repetitive DNA Evolution in Diploid Species of Melampodium sect. Melampodium (Asteraceae). FRONTIERS IN PLANT SCIENCE 2020; 11:362. [PMID: 32296454 PMCID: PMC7136903 DOI: 10.3389/fpls.2020.00362] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/12/2020] [Indexed: 05/18/2023]
Abstract
Plant genomes vary greatly in composition and size mainly due to the diversity of repetitive DNAs and the inherent propensity for their amplification and removal from the host genome. Most studies addressing repeatome dynamics focus on model organisms, whereas few provide comprehensive investigations across the genomes of related taxa. Herein, we analyze the evolution of repeats of the 13 species in Melampodium sect. Melampodium, representing all but two of its diploid taxa, in a phylogenetic context. The investigated genomes range in size from 0.49 to 2.27 pg/1C (ca. 4.5-fold variation), despite having the same base chromosome number (x = 10) and very strong phylogenetic affinities. Phylogenetic analysis performed in BEAST and ancestral genome size reconstruction revealed mixed patterns of genome size increases and decreases across the group. High-throughput genome skimming and the RepeatExplorer pipeline were utilized to determine the repeat families responsible for the differences in observed genome sizes. Patterns of repeat evolution were found to be highly correlated with phylogenetic position, namely taxonomic series circumscription. Major differences found were in the abundances of the SIRE (Ty1-copia), Athila (Ty3-gypsy), and CACTA (DNA transposon) lineages. Additionally, several satellite DNA families were found to be highly group-specific, although their overall contribution to genome size variation was relatively small. Evolutionary changes in repetitive DNA composition and genome size were complex, with independent patterns of genome up- and downsizing throughout the evolution of the analyzed diploids. A model-based analysis of genome size and repetitive DNA composition revealed evidence for strong phylogenetic signal and differential evolutionary rates of major lineages of repeats in the diploid genomes.
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Affiliation(s)
- Jamie McCann
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czechia
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czechia
| | - Tod F. Stuessy
- Herbarium and Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Jose L. Villaseñor
- Department of Botany, National Autonomous University of Mexico, Mexico City, Mexico
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13
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Dodsworth S, Guignard MS, Pérez-Escobar OA, Struebig M, Chase MW, Leitch AR. Repetitive DNA Restructuring Across Multiple Nicotiana Allopolyploidisation Events Shows a Lack of Strong Cytoplasmic Bias in Influencing Repeat Turnover. Genes (Basel) 2020; 11:E216. [PMID: 32092894 PMCID: PMC7074350 DOI: 10.3390/genes11020216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following three allotetraploid events, and how these are inherited from the closest extant relatives of the maternal and paternal subgenome donors. In all three cases, there was a lack of clear maternal, cytoplasmic bias in repeat evolution, i.e., lack of a predicted bias towards maternal subgenome-derived repeats, with roughly equal contributions from both parental subgenomes. Different overall repeat dynamics were found across timescales of <0.5 (N. rustica L.), 4 (N. repanda Willd.) and 6 (N. benthamiana Domin) Ma, with nearly additive, genome upsizing, and genome downsizing, respectively. Lower copy repeats were inherited in similar abundance to the parental subgenomes, whereas higher copy repeats contributed the most to genome size change in N. repanda and N. benthamiana. Genome downsizing post-polyploidisation may be a general long-term trend across angiosperms, but at more recent timescales there is species-specific variance as found in Nicotiana.
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Affiliation(s)
- Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton LU1 3JU, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
| | - Maïté S. Guignard
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, UK; (O.A.P.-E.); (M.W.C.)
| | | | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, UK; (O.A.P.-E.); (M.W.C.)
- Department of Environment and Agriculture, Curtin University, Bentley 6102, Western Australia, Australia
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
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14
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Garcia S, Wendel JF, Borowska-Zuchowska N, Aïnouche M, Kuderova A, Kovarik A. The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants. FRONTIERS IN PLANT SCIENCE 2020; 11:41. [PMID: 32117380 PMCID: PMC7025596 DOI: 10.3389/fpls.2020.00041] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups. RESULTS (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures. CONCLUSION We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC - Ajuntament de Barcelona), Barcelona, Spain
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Jonathan F. Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, United States
| | - Natalia Borowska-Zuchowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, Rennes, France
| | - Alena Kuderova
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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15
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Renny-Byfield S, Baumgarten A. Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci. BMC Genomics 2020; 21:98. [PMID: 32000670 PMCID: PMC6993463 DOI: 10.1186/s12864-020-6517-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 01/20/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Repetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes has limited large-scale intraspecific comparisons to a handful of model organisms where multiple reference genomes are available. RESULTS We examine repeat content variation in the genomes of 94 elite inbred maize lines using graph-based repeat clustering, a reference-free and rapid assay of repeat content. We examine population structure using genome-wide repeat profiles, and demonstrate the stiff-stalk and non-stiff-stalk heterotic populations are homogenous with regard to global repeat content. In contrast, and similar to previously reported results, the same individuals show clear differentiation, and aggregate into two populations when examining population structure using genome-wide SNPs. Additionally, we develop a novel kmer based technique to examine the chromosomal distribution of repeat clusters in silico and show a cluster dependent association with gene density. CONCLUSION Our results indicate global repeat content variation in the heterotic populations of maize has not diverged, and is uncoupled from population stratification at SNP loci. We show that repeat families exhibit divergent patterns with regard to chromosomal distribution, some repeat clusters accumulate in regions of high gene density, whereas others aggregate in regions of low gene density.
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16
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Ventimilla D, Domingo C, González-Ibeas D, Talon M, Tadeo FR. Differential expression of IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like genes in Nicotiana benthamiana during corolla abscission, stem growth and water stress. BMC PLANT BIOLOGY 2020; 20:34. [PMID: 31959115 PMCID: PMC6971993 DOI: 10.1186/s12870-020-2250-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/14/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like signaling peptides and the associated HAE (HAESA)-like family of receptor kinases were originally reported in the model plant Arabidopsis thaliana (Arabidopsis) to be deeply involved in the regulation of abscission. Actually, IDA peptides, as cell-to-cell communication elements, appear to be implicated in many developmental processes that rely on cell separation events, and even in the responses to abiotic stresses. However, the knowledge related to the molecular machinery regulating abscission in economically important crops is scarce. In this work, we determined the conservation and phylogeny of the IDA-like and HAE-like gene families in relevant species of the Solanaceae family and analyzed the expression of these genes in the allopolyploid Nicotiana benthamiana, in order to identify members involved in abscission, stem growth and in the response to drought conditions. RESULTS The phylogenetic relationships among the IDA-like members of the Solanaceae studied, grouped the two pairs of NbenIDA1 and NbenIDA2 protein homeologs with the Arabidopsis prepropeptides related to abscission. Analysis of promoter regions searching for regulatory elements showed that these two pairs of homeologs contained both hormonal and drought response elements, although NbenIDA2A lacked the hormonal regulatory elements. Expression analyses showed that the pair of NbenIDA1 homeologs were upregulated during corolla abscission. NbenIDA1 and NbenIDA2 pairs showed tissue differential expression under water stress conditions, since NbenIDA1 homeologs were highly expressed in stressed leaves while NbenIDA2 homeologs, especially NbenIDA2B, were highly expressed in stressed roots. In non-stressed active growing plants, nodes and internodes were the tissues with the highest expression levels of all members of the IDA-like family and their putative HAE-like receptors. CONCLUSION Our results suggest that the pair of NbenIDA1 homeologs are involved in the natural process of corolla abscission while both pairs of NbenIDA1 and NbenIDA2 homeologs are implicated in the response to water stress. The data also suggest that IDA peptides may be important during stem growth and development. These results provide additional evidence that the functional module formed by IDA peptides and its receptor kinases, as defined in Arabidopsis, may also be conserved in Solanaceae.
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Affiliation(s)
- Daniel Ventimilla
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113 Valencia, Spain
| | - Concha Domingo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113 Valencia, Spain
| | - Daniel González-Ibeas
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113 Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113 Valencia, Spain
| | - Francisco R. Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113 Valencia, Spain
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17
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Ventimilla D, Domingo C, González-Ibeas D, Talon M, Tadeo FR. Differential expression of IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like genes in Nicotiana benthamiana during corolla abscission, stem growth and water stress. BMC PLANT BIOLOGY 2020; 20:34. [PMID: 31959115 DOI: 10.1186/s12870-020-2250-2258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/14/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like signaling peptides and the associated HAE (HAESA)-like family of receptor kinases were originally reported in the model plant Arabidopsis thaliana (Arabidopsis) to be deeply involved in the regulation of abscission. Actually, IDA peptides, as cell-to-cell communication elements, appear to be implicated in many developmental processes that rely on cell separation events, and even in the responses to abiotic stresses. However, the knowledge related to the molecular machinery regulating abscission in economically important crops is scarce. In this work, we determined the conservation and phylogeny of the IDA-like and HAE-like gene families in relevant species of the Solanaceae family and analyzed the expression of these genes in the allopolyploid Nicotiana benthamiana, in order to identify members involved in abscission, stem growth and in the response to drought conditions. RESULTS The phylogenetic relationships among the IDA-like members of the Solanaceae studied, grouped the two pairs of NbenIDA1 and NbenIDA2 protein homeologs with the Arabidopsis prepropeptides related to abscission. Analysis of promoter regions searching for regulatory elements showed that these two pairs of homeologs contained both hormonal and drought response elements, although NbenIDA2A lacked the hormonal regulatory elements. Expression analyses showed that the pair of NbenIDA1 homeologs were upregulated during corolla abscission. NbenIDA1 and NbenIDA2 pairs showed tissue differential expression under water stress conditions, since NbenIDA1 homeologs were highly expressed in stressed leaves while NbenIDA2 homeologs, especially NbenIDA2B, were highly expressed in stressed roots. In non-stressed active growing plants, nodes and internodes were the tissues with the highest expression levels of all members of the IDA-like family and their putative HAE-like receptors. CONCLUSION Our results suggest that the pair of NbenIDA1 homeologs are involved in the natural process of corolla abscission while both pairs of NbenIDA1 and NbenIDA2 homeologs are implicated in the response to water stress. The data also suggest that IDA peptides may be important during stem growth and development. These results provide additional evidence that the functional module formed by IDA peptides and its receptor kinases, as defined in Arabidopsis, may also be conserved in Solanaceae.
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Affiliation(s)
- Daniel Ventimilla
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113, Valencia, Spain
| | - Concha Domingo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113, Valencia, Spain
| | - Daniel González-Ibeas
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113, Valencia, Spain
| | - Francisco R Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315, Km 10,7 Moncada, E-46113, Valencia, Spain.
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18
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Identification and characterization of abundant repetitive sequences in Allium cepa. Sci Rep 2019; 9:16756. [PMID: 31727905 PMCID: PMC6856378 DOI: 10.1038/s41598-019-52995-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 10/26/2019] [Indexed: 01/01/2023] Open
Abstract
Species of the genus Allium are well known for their large genomes. Allium cepa is of great economic significance. Among vegetables, it ranks second after tomato in terms of the global production value. However, there is limited genomics information available on A. cepa. In this study, we sequenced the A. cepa genome at low-coverage and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. Nearly 92% of 16 Gb haploid onion genome were defined as repetitive sequences, organized in 162 clusters of at least 0.01 percent of the genome. Of these, a proportion representing 40.5% of the genome were further analyzed in detail to obtain an overview of representative repetitive elements present in the A. cepa genome. Few representative satellite repeats were studied by fluorescence in situ hybridization (FISH) and southern blotting. These results provided a basis for evolutionary cytogenomics within the Allium genus.
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Majka J, Bzdęga K, Janiak A, Ćwiek-Kupczyńska H, Krajewski P, Książczyk T, Zwierzykowski Z. Cytogenetic and molecular genotyping in the allotetraploid Festuca pratensis × Lolium perenne hybrids. BMC Genomics 2019; 20:367. [PMID: 31088367 PMCID: PMC6518686 DOI: 10.1186/s12864-019-5766-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/03/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids can merge in their genomes agronomically important characteristics. However, in polyploid plants, especially in allopolyploids, the hybridization of divergent genomes could contribute to various abnormalities, such as variability in chromosome number, structural rearrangements, and/or disorders in inheritance patterns. Here we studied these issues in allotetraploid Festuca pratensis × Lolium perenne hybrids. RESULTS Cytogenetic procedures, including fluorescent in situ hybridization, genomic in situ hybridization, and molecular markers - inter-simple sequence repeats (ISSR) were exploited. This cytogenetic approach indicated the dynamics in the number and distribution of ribosomal RNA genes and structural rearrangements for both parental genomes (Festuca and Lolium) in hybrid karyotypes. The separate analysis of F. pratensis and L. perenne chromosomes in hybrid plants (F2-F3 generations of F. pratensis × L. perenne) revealed the asymmetrical level of rearrangements. Recognized structural changes were mainly located in the distal part of chromosome arms, and in chromosomes bearing ribosomal DNA, they were more frequently mapped in arms without this sequence. Based on the ISSR markers distribution, we found that the tetrasomic type of inheritance was characteristic for the majority of ISSR loci, but the disomic type was also observed. Nonetheless, no preference in the transmission of either Festuca or Lolium alleles to the following generations of allotetraploid F. pratensis × L. perenne hybrid was observed. CONCLUSION Our study reports cytogenetic and molecular genotyping of the F. pratensis × L. perenne hybrid and its following F2-F3 progenies. The analysis of 137 allotetraploid F. pratensis × L. perenne hybrids revealed the higher level of recombination in chromosomes derived from F. pratensis genome. The results of ISSR markers indicated a mixed model of inheritance, which may be characteristic for these hybrids.
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Affiliation(s)
- Joanna Majka
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Katarzyna Bzdęga
- Department of Botany and Nature Protection, University of Silesia in Katowice, Katowice, Poland
| | - Agnieszka Janiak
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Hanna Ćwiek-Kupczyńska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz Książczyk
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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20
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Mhiri C, Parisod C, Daniel J, Petit M, Lim KY, Dorlhac de Borne F, Kovarik A, Leitch AR, Grandbastien MA. Parental transposable element loads influence their dynamics in young Nicotiana hybrids and allotetraploids. THE NEW PHYTOLOGIST 2019; 221:1619-1633. [PMID: 30220091 DOI: 10.1111/nph.15484] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/06/2018] [Indexed: 05/29/2023]
Abstract
The genomic shock hypothesis suggests that allopolyploidy is associated with genome changes driven by transposable elements, as a response to imbalances between parental insertion loads. To explore this hypothesis, we compared three allotetraploids, Nicotiana arentsii, N. rustica and N. tabacum, which arose over comparable time frames from hybridisation between increasingly divergent diploid species. We used sequence-specific amplification polymorphism (SSAP) to compare the dynamics of six transposable elements in these allopolyploids, their diploid progenitors and in corresponding synthetic hybrids. We show that element-specific dynamics in young Nicotiana allopolyploids reflect their dynamics in diploid progenitors. Transposable element mobilisation is not concomitant with immediate genome merger, but occurs within the first generations of allopolyploid formation. In natural allopolyploids, such mobilisations correlate with imbalances in the repeat profile of the parental species, which increases with their genetic divergence. Other restructuring leading to locus loss is immediate, nonrandom and targeted at specific subgenomes, independently of cross orientation. The correlation between transposable element mobilisation in allopolyploids and quantitative imbalances in parental transposable element loads supports the genome shock hypothesis proposed by McClintock.
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Affiliation(s)
- Corinne Mhiri
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Christian Parisod
- Ecological Genomics, Institute of Plant Sciences, University of Bern, Bern, CH-3013, Switzerland
| | - Julien Daniel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Maud Petit
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - K Yoong Lim
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | | | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Marie-Angèle Grandbastien
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
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21
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Effect of Hybridization on Somatic Mutations and Genomic Rearrangements in Plants. Int J Mol Sci 2018; 19:ijms19123758. [PMID: 30486351 PMCID: PMC6320998 DOI: 10.3390/ijms19123758] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022] Open
Abstract
Hybridization has been routinely practiced in agriculture to enhance the crop yield. Principally, it can cause hybrid vigor where hybrid plants display increased size, biomass, fertility, and resistance to diseases, when compared to their parents. During hybridization, hybrid offspring receive a genomic shock due to mixing of distant parental genomes, which triggers a myriad of genomic rearrangements, e.g., transpositions, genome size changes, chromosomal rearrangements, and other effects on the chromatin. Recently, it has been reported that, besides genomic rearrangements, hybridization can also alter the somatic mutation rates in plants. In this review, we provide in-depth insights about hybridization triggered genomic rearrangements and somatic mutations in plants.
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22
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Mccann J, Jang TS, Macas J, Schneeweiss GM, Matzke NJ, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae). Syst Biol 2018; 67:1010-1024. [PMID: 29562303 PMCID: PMC6193527 DOI: 10.1093/sysbio/syy024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 02/17/2018] [Accepted: 03/15/2018] [Indexed: 12/04/2022] Open
Abstract
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multispecies coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, Melampodium strigosum, and its two allohexaploid derivatives, Melampodium pringlei and Melampodium sericeum, which share both parentage and the direction of the cross, to the Pleistocene ($<$1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids' genomes. The repetitive elements most affected by the postpolyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
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Affiliation(s)
- Jamie Mccann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Jiři Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Tod F Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Herbarium and Department of Evolution, Ecology and Organismal Biology, 1315 Kinnear Road, The Ohio State University, Columbus, Ohio, USA
| | - José L Villaseñor
- Department of Botany, UNAM, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, MX-04510 México, D.F., México
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
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23
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Orzechowska M, Majka M, Weiss-Schneeweiss H, Kovařík A, Borowska-Zuchowska N, Kolano B. Organization and evolution of two repetitive sequences, 18-24J and 12-13P, in the genome of Chenopodium (Amaranthaceae). Genome 2018; 61:643-652. [PMID: 30067084 DOI: 10.1139/gen-2018-0044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The abundance and chromosomal organization of two repetitive sequences named 12-13P and 18-24J were analyzed in 24 diploid and nine polyploid species of Chenopodium s.l., with special attention to Chenopodium s.s. Both sequences were predominantly present in species of Chenopodium s.s.; however, differences in the amplification levels were observed among the species. The 12-13P repeat was highly amplified in all of the analyzed Eurasian species, whereas the American diploids showed a marked variation in the amplification levels. The 12-13P repeat contains a tandemly arranged 40 bp minisatellite element forming a large proportion of the genome of Chenopodium (up to 3.5%). FISH revealed its localization to the pericentromeric regions of the chromosomes. The chromosomal distribution of 12-13P delivered additional chromosomal marker for B-genome diploids. The 18-24J repeat showed a dispersed organization in all of the chromosomes of the analyzed diploid species and the Eurasian tetraploids. In the American allotetraploids (C. quinoa, C. berlandieri) and Eurasian allohexaploids (e.g., C. album) very intense hybridization signals of 18-24J were observed only on 18 chromosomes that belong to the B subgenome of these polyploids. Combined cytogenetic and molecular analyses suggests that reorganization of these two repeats accompanied the diversification and speciation of diploid (especially A genome) and polyploid species of Chenopodium s.s.
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Affiliation(s)
- Maja Orzechowska
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
| | - Maciej Majka
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
| | - Hanna Weiss-Schneeweiss
- b Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Ales Kovařík
- c Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Natalia Borowska-Zuchowska
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
| | - Bozena Kolano
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
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24
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Chen S, Ren F, Zhang L, Liu Y, Chen X, Li Y, Zhang L, Zhu B, Zeng P, Li Z, Larkin RM, Kuang H. Unstable Allotetraploid Tobacco Genome due to Frequent Homeologous Recombination, Segmental Deletion, and Chromosome Loss. MOLECULAR PLANT 2018; 11:914-927. [PMID: 29734001 DOI: 10.1016/j.molp.2018.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 05/20/2023]
Abstract
The types of mutations and their corresponding frequencies are difficult to measure in complex genomes. In this study, a high-throughput method was developed to identify spontaneous loss-of-function alleles for the resistance gene N and the transgenic avirulence gene P50 in allotetraploid tobacco. A total of 2134 loss-of-function alleles of the N gene were identified after screening 14 million F1 hybrids. Analysis of these mutants revealed striking evolutionary patterns for genes in polyploids. Only 14 of the loss-of-function mutations were caused by spontaneous point mutations or indels, while the others were caused by homeologous recombination (with a frequency of ∼1/12 000) or chromosome loss (∼1/15 000). Loss of the chromosome with the P50 insertion occurred at a similar frequency (∼1/13 000), and the frequency of spontaneous segmental deletion in this chromosome was ∼1/16 000. Both homeologous recombination and chromosome loss considerably decreased the viability of the mutants. Our data suggest that the high mutation rate in polyploids is probably due to the occurrence of homeologous recombination and the tolerance of large mutations such as chromosome loss in polyploid genomes. Frequent mutations tend to drive polyploids to extinction unless a novel mutation helps the polyploid to effectively compete with diploids or find a new ecological niche.
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Affiliation(s)
- Shumin Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan 430070, People's Republic of China
| | - Feihong Ren
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan 430070, People's Republic of China
| | - Lei Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan 430070, People's Republic of China
| | - Yong Liu
- Yunan Academy of Tobacco Agricultural Science, Kunming, Yunnan Province, People's Republic of China
| | - Xuejun Chen
- Yunan Academy of Tobacco Agricultural Science, Kunming, Yunnan Province, People's Republic of China
| | - Yuanmei Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan 430070, People's Republic of China
| | - Liang Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan 430070, People's Republic of China
| | - Bin Zhu
- Yunan Academy of Tobacco Agricultural Science, Kunming, Yunnan Province, People's Republic of China
| | - Pan Zeng
- College of Plant Science, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Zaiyun Li
- College of Plant Science, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan 430070, People's Republic of China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, College of Horticulture and Forestry Sciences, Huazhong Agricultural University Wuhan 430070, People's Republic of China.
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25
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Bateman RM, Guy JJ, Rudall PJ, Leitch IJ, Pellicer J, Leitch AR. Evolutionary and functional potential of ploidy increase within individual plants: somatic ploidy mapping of the complex labellum of sexually deceptive bee orchids. ANNALS OF BOTANY 2018; 122:133-150. [PMID: 29672665 PMCID: PMC6025197 DOI: 10.1093/aob/mcy048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/15/2018] [Indexed: 05/07/2023]
Abstract
Background and Aims Recent tissue-level observations made indirectly via flow cytometry suggest that endoreplication (duplication of the nuclear genome within the nuclear envelope in the absence of subsequent cell division) is widespread within the plant kingdom. Here, we also directly observe ploidy variation among cells within individual petals, relating size of nucleus to cell micromorphology and (more speculatively) to function. Methods We compared the labella (specialized pollinator-attracting petals) of two European orchid genera: Dactylorhiza has a known predisposition to organismal polyploidy, whereas Ophrys exhibits exceptionally complex epidermal patterning that aids pseudocopulatory pollination. Confocal microscopy using multiple staining techniques allowed us to observe directly both the sizes and the internal structures of individual nuclei across each labellum, while flow cytometry was used to test for progressively partial endoreplication. Key Results In Dactylorhiza, endoreplication was comparatively infrequent, reached only low levels, and appeared randomly located across the labellum, whereas in Ophrys endoreplication was commonplace, being most frequent in large peripheral trichomes. Endoreplicated nuclei reflected both endomitosis and endocycling, the latter reaching the third round of genome doubling (16C) to generate polytene nuclei. All Ophrys individuals studied exhibited progressively partial endoreplication. Conclusions Comparison of the two genera failed to demonstrate the hypothesized pattern of frequent polyploid speciation in genera showing extensive endoreplication. Endoreplication in Ophrys appears more strongly positively correlated with cell size/complexity than with cell location or secretory role. Epigenetic control of gene overexpression by localized induction of endoreplication within individual plant organs may represent a significant component of a plant's developmental programme, contributing substantially to organ plasticity.
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Affiliation(s)
| | - Jessica J Guy
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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26
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Evans BJ, Upham NS, Golding GB, Ojeda RA, Ojeda AA. Evolution of the Largest Mammalian Genome. Genome Biol Evol 2018; 9:1711-1724. [PMID: 28854639 PMCID: PMC5569995 DOI: 10.1093/gbe/evx113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/31/2022] Open
Abstract
The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects—including during the evolution of hypersaline dietary tolerance in T. barrerae.
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Affiliation(s)
- Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Nathan S Upham
- Biology Department, McMaster University, Hamilton, Ontario, Canada.,Field Museum of Natural History, Chicago, IL.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | | | - Ricardo A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
| | - Agustina A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
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27
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Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res 2017. [PMID: 28402514 DOI: 10.1093/nar/gkx257.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
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Affiliation(s)
- Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Laura Ávila Robledillo
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Andrea Koblížková
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Iva Vrbová
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Jirí Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
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28
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Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res 2017; 45:e111. [PMID: 28402514 PMCID: PMC5499541 DOI: 10.1093/nar/gkx257] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/23/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
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Affiliation(s)
- Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Laura Ávila Robledillo
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Andrea Koblížková
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Iva Vrbová
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Jirí Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
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Pont C, Salse J. Wheat paleohistory created asymmetrical genomic evolution. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:29-37. [PMID: 28182971 DOI: 10.1016/j.pbi.2017.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/12/2016] [Accepted: 01/04/2017] [Indexed: 05/26/2023]
Abstract
Following the triplication reported in Brassiceae ∼10million years ago, and at the basis of rosids ∼100million years ago, bias in organization and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestors of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic control between the A, B and D subgenomes.
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Affiliation(s)
- Caroline Pont
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Jérôme Salse
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France*.
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Garcia S, Kovařík A, Leitch AR, Garnatje T. Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1020-1030. [PMID: 27943584 DOI: 10.1111/tpj.13442] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 05/09/2023]
Abstract
The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Ales Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, 612 65, Czech Republic
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
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Kirov IV, Kiseleva AV, Van Laere K, Van Roy N, Khrustaleva LI. Tandem repeats of Allium fistulosum associated with major chromosomal landmarks. Mol Genet Genomics 2017; 292:453-464. [PMID: 28150039 DOI: 10.1007/s00438-016-1286-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 12/30/2016] [Indexed: 01/22/2023]
Abstract
Tandem repeats are often associated with important chromosomal landmarks, such as centromeres, telomeres, subtelomeric, and other heterochromatic regions, and can be good candidates for molecular cytogenetic markers. Tandem repeats present in many plant species demonstrate dramatic differences in unit length, proportion in the genome, and chromosomal organization. Members of genus Allium with their large genomes represent a challenging task for current genetics. Using the next generation sequencing data, molecular, and cytogenetic methods, we discovered two tandemly organized repeats in the Allium fistulosum genome (2n = 2C = 16), HAT58 and CAT36. Together, these repeats comprise 0.25% of the bunching onion genome with 160,000 copies/1 C of HAT58 and 93,000 copies/1 C of CAT36. Fluorescent in situ hybridization (FISH) and C-banding showed that HAT58 and CAT36 associated with the interstitial and pericentromeric heterochromatin of the A. fistulosum chromosomes 5, 6, 7, and 8. FISH with HAT58 and CAT36 performed on A. cepa (2n = 2C = 16) and A. wakegi (2n = 2C = 16), a natural allodiploid hybrid between A. fistulosum and A. cepa, revealed that these repeats are species specific and produced specific hybridization patterns only on A. fistulosum chromosomes. Thus, the markers can be used in interspecific breeding programs for monitoring of alien genetic material. We applied Non-denaturing FISH that allowed detection of the repeat bearing chromosomes within 3 h. A polymorphism of the HAT58 chromosome location was observed. This finding suggests that the rapid evolution of the HAT58 repeat is still ongoing.
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Affiliation(s)
- Ilya V Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium.
| | - Anna V Kiseleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Katrijn Van Laere
- Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | - Nadine Van Roy
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Ludmila I Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. .,Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.
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Dodsworth S, Jang TS, Struebig M, Chase MW, Weiss-Schneeweiss H, Leitch AR. Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae). PLANT SYSTEMATICS AND EVOLUTION = ENTWICKLUNGSGESCHICHTE UND SYSTEMATIK DER PFLANZEN 2017; 303:1013-1020. [PMID: 32009724 PMCID: PMC6961477 DOI: 10.1007/s00606-016-1356-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/23/2016] [Indexed: 05/02/2023]
Abstract
Nicotiana sect. Repandae is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of N. nudicaulis as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing (N. nudicaulis) from those with genome upsizing (N. repanda, N. nesophila, N. stocktonii). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between N. nudicaulis and the Revillagigedo Island taxa (N. nesophila and N. stocktonii), thereby placing N. repanda as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for N. nudicaulis as sister to the rest of the section, with N. repanda sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original (N. nudicaulis (N. repanda (N. nesophila + N. stocktonii))) hypothesis. Furthermore, overall repeat dynamics in the island species N. nesophila and N. stocktonii confirm their similarity to N. repanda and the distinctive patterns between these three species and N. nudicaulis. Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance.
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Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS UK
| | - Tae-Soo Jang
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | - Mark W. Chase
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Hanna Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
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Renny-Byfield S, Page JT, Udall JA, Sanders WS, Peterson DG, Arick MA, Grover CE, Wendel JF. Independent Domestication of Two Old World Cotton Species. Genome Biol Evol 2016; 8:1940-7. [PMID: 27289095 PMCID: PMC4943200 DOI: 10.1093/gbe/evw129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/16/2022] Open
Abstract
Domesticated cotton species provide raw material for the majority of the world's textile industry. Two independent domestication events have been identified in allopolyploid cotton, one in Upland cotton (Gossypium hirsutum L.) and the other to Egyptian cotton (Gossypium barbadense L.). However, two diploid cotton species, Gossypium arboreum L. and Gossypium herbaceum L., have been cultivated for several millennia, but their status as independent domesticates has long been in question. Using genome resequencing data, we estimated the global abundance of various repetitive DNAs. We demonstrate that, despite negligible divergence in genome size, the two domesticated diploid cotton species contain different, but compensatory, repeat content and have thus experienced cryptic alterations in repeat abundance despite equivalence in genome size. Evidence of independent origin is bolstered by estimates of divergence times based on molecular evolutionary analysis of f7,000 orthologous genes, for which synonymous substitution rates suggest that G. arboreum and G. herbaceum last shared a common ancestor approximately 0.4-2.5 Ma. These data are incompatible with a shared domestication history during the emergence of agriculture and lead to the conclusion that G. arboreum and G. herbaceum were each domesticated independently.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University DuPont Pioneer, Johnston, IA
| | - Justin T Page
- Plant and Wildlife Science Department, Brigham Young University
| | - Joshua A Udall
- Plant and Wildlife Science Department, Brigham Young University
| | - William S Sanders
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Computer Science and Engineering, Mississippi State University
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Plant and Soil Sciences, Mississippi State University
| | - Mark A Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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Salse J. Deciphering the evolutionary interplay between subgenomes following polyploidy: A paleogenomics approach in grasses. AMERICAN JOURNAL OF BOTANY 2016; 103:1167-1174. [PMID: 27425631 DOI: 10.3732/ajb.1500459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/01/2016] [Indexed: 06/06/2023]
Abstract
How did plant species emerge from their most recent common ancestors (MRCAs) 250 million years ago? Modern plant genomes help to address such key questions in unveiling precise species genealogies. The field of paleogenomics is undergoing a paradigm shift for investigating species evolution from the study of ancestral genomes from extinct species to deciphering the evolutionary forces (in terms of duplication, fusion, fission, deletion, and translocation) that drove present-day plant diversity (in terms of chromosome/gene number and genome size). In this review, inferred ancestral karyotype genomes are shown to be powerful tools to (1) unravel the past history of extant species by recovering the variations of ancestral genomic compartments and (2) accelerate translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.
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Affiliation(s)
- Jérôme Salse
- INRA/UBP UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Laboratory of Paleogenomics & Evolution, 5 chemin de Beaulieu 63100 Clermont Ferrand, France
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Han YY, Ma YQ, Li DZ, Yao JW, Xu ZQ. Characterization and phylogenetic analysis of fifteen NtabSPL genes in Nicotiana tabacum L. cv. Qinyan95. Dev Genes Evol 2016; 226:1-14. [PMID: 26635304 DOI: 10.1007/s00427-015-0522-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/23/2015] [Indexed: 11/29/2022]
Abstract
Fifteen SPL (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE) genes were identified and characterized in Nicotiana tabacum L. cv. Qinyan95. The exon-intron structures of these genes were determined according to the coding sequences confirmed by RT-PCR and the genomic DNA sequences downloaded from the databases in Sol Genomics Network, and thirteen of them were found to carry the response element of miR156. To elucidate the origin of the validated NtabSPL genes, multiple alignments of the nucleotide sequences encompassing the open reading frames were conducted by using the orthologs in N. tabacum, Nicotiana sylvestris, Nicotiana tomentosiformis, and Nicotiana otophora. The results showed that six NtabSPL genes were derived from a progenitor of N. sylvestris, and nine NtabSPL genes were derived from a progenitor of N. tomentosiformis, further corroborating that N. tabacum came from the interspecific hybridization between the ancestors of N. sylvestris and N. tomentosiformis. In contrast to previous statements about highly repetitive sequences, the genome of N. tabacum mainly retained the paternal-derived SPL genes in diploidization process. Phylogenetic analyses based on the highly conserved SBP (SQUAMOSA PROMOTER BINDING PROTEIN) domains and the full-length amino acid sequences reveal that the SPL proteins of tobacco, tomato, and Arabidopsis can be categorized into eight groups. It is worth noting that N. tabacum contains seven NtabSPL6 genes originated from two parental genomes and NtabSPL6-2 possesses a GC-AG intron. In addition, transgenic tobacco plants harboring Arabidopsis Pri-miR156A were generated by Agrobacterium-mediated transformation method, and the constitutive expression of miR156 could obviously inhibit the activity of the NtabSPL genes containing its target site, suggesting the function of miR156 is conservative in tobacco and Arabidopsis.
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Affiliation(s)
- Yao-Yao Han
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Yan-Qin Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Dian-Zhen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Jing-Wen Yao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Zi-Qin Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China.
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Tungkajiwangkoon S, Shirakawa J, Azumatani M, Hoshi Y. Breeding and Cytogenetic Characterizations of New Hexaploid Drosera Strains Colchicine-Induced from Triploid Hybrid of D. rotundifolia and D. spatulata. CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | | | - Yoshikazu Hoshi
- Department of Plant Science, School of Agriculture, Tokai University
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Olanj N, Garnatje T, Sonboli A, Vallès J, Garcia S. The striking and unexpected cytogenetic diversity of genus Tanacetum L. (Asteraceae): a cytometric and fluorescent in situ hybridisation study of Iranian taxa. BMC PLANT BIOLOGY 2015; 15:174. [PMID: 26152193 PMCID: PMC4494159 DOI: 10.1186/s12870-015-0564-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/26/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Although karyologically well studied, the genus Tanacetum (Asteraceae) is poorly known from the perspective of molecular cytogenetics. The prevalence of polyploidy, including odd ploidy warranted an extensive cytogenetic study. We studied several species native to Iran, one of the most important centres of diversity of the genus. We aimed to characterise Tanacetum genomes through fluorochrome banding, fluorescent in situ hybridisation (FISH) of rRNA genes and the assessment of genome size by flow cytometry. We appraise the effect of polyploidy and evaluate the existence of intraspecific variation based on the number and distribution of GC-rich bands and rDNA loci. Finally, we infer ancestral genome size and other cytogenetic traits considering phylogenetic relationships within the genus. RESULTS We report first genome size (2C) estimates ranging from 3.84 to 24.87 pg representing about 11 % of those recognised for the genus. We found striking cytogenetic diversity both in the number of GC-rich bands and rDNA loci. There is variation even at the population level and some species have undergone massive heterochromatic or rDNA amplification. Certain morphometric data, such as pollen size or inflorescence architecture, bear some relationship with genome size. Reconstruction of ancestral genome size, number of CMA+ bands and number of rDNA loci show that ups and downs have occurred during the evolution of these traits, although genome size has mostly increased and the number of CMA+ bands and rDNA loci have decreased in present-day taxa compared with ancestral values. CONCLUSIONS Tanacetum genomes are highly unstable in the number of GC-rich bands and rDNA loci, although some patterns can be established at the diploid and tetraploid levels. In particular, aneuploid taxa and some odd ploidy species show greater cytogenetic instability than the rest of the genus. We have also confirmed a linked rDNA arrangement for all the studied Tanacetum species. The labile scenario found in Tanacetum proves that some cytogenetic features previously regarded as relatively constant, or even diagnostic, can display high variability, which is better interpreted within a phylogenetic context.
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Affiliation(s)
- Nayyereh Olanj
- Department of Biology, Faculty of Basic Science, Malayer University, Malayer, Iran.
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Joan XXIII s/n, 08028, Barcelona, Catalonia, Spain.
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, 08038, Barcelona, Catalonia, Spain.
| | - Ali Sonboli
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, 1983963113, Tehran, Iran.
| | - Joan Vallès
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Joan XXIII s/n, 08028, Barcelona, Catalonia, Spain.
| | - Sònia Garcia
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Joan XXIII s/n, 08028, Barcelona, Catalonia, Spain.
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Wang X, Bennetzen JL. Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes. Mol Genet Genomics 2015; 290:11-21. [PMID: 25582664 DOI: 10.1007/s00438-015-0989-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 01/05/2015] [Indexed: 12/31/2022]
Abstract
Nicotiana, a member of the Solanaceae family, is one of the most important research model plants, and of high agricultural and economic value worldwide. To better understand the substantial and rapid research progress with Nicotiana in recent years, its genomics, genetics, and nicotine gene studies are summarized, with useful web links. Several important genetic maps, including a high-density map of N. tabacum consisting of ~2,000 markers published in 2012, provide tools for genetics research. Four whole genome sequences are from allotetraploid species, including N. benthamiana in 2012, and three N. tabacum cultivars (TN90, K326, and BX) in 2014. Three whole genome sequences are from diploids, including progenitors N. sylvestris and N. tomentosiformis in 2013 and N. otophora in 2014. These and additional studies provide numerous insights into genome evolution after polyploidization, including changes in gene composition and transcriptome expression in N. tabacum. The major genes involved in the nicotine biosynthetic pathway have been identified and the genetic basis of the differences in nicotine levels among Nicotiana species has been revealed. In addition, other progress on chloroplast, mitochondrial, and NCBI-registered projects on Nicotiana are discussed. The challenges and prospects for genomic, genetic and application research are addressed. Hence, this review provides important resources and guidance for current and future research and application in Nicotiana.
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Affiliation(s)
- Xuewen Wang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, People's Republic of China,
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Dodsworth S, Chase MW, Kelly LJ, Leitch IJ, Macas J, Novák P, Piednoël M, Weiss-Schneeweiss H, Leitch AR. Genomic repeat abundances contain phylogenetic signal. Syst Biol 2015; 64:112-26. [PMID: 25261464 PMCID: PMC4265144 DOI: 10.1093/sysbio/syu080] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.
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Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Mark W Chase
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Ilia J Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Jiří Macas
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Petr Novák
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Mathieu Piednoël
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Plant Biology, The University of Western Australia, Crawley WA 6009, Australia; Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic; Systematic Botany and Mycology, University of Munich (LMU), Menzinger Straße 67, 80638 München, Germany; and Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Hong Y, Pandey MK, Liu Y, Chen X, Liu H, Varshney RK, Liang X, Huang S. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:1068. [PMID: 26697032 PMCID: PMC4667090 DOI: 10.3389/fpls.2015.01068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 11/16/2015] [Indexed: 05/06/2023]
Abstract
The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.
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Affiliation(s)
- Yanbin Hong
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Ying Liu
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoping Chen
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hong Liu
- College of Agriculture, South China Agricultural UniversityGuangzhou, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - Xuanqiang Liang
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shangzhi Huang
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
- *Correspondence: Shangzhi Huang
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Chen K, Dorlhac de Borne F, Szegedi E, Otten L. Deep sequencing of the ancestral tobacco species Nicotiana tomentosiformis reveals multiple T-DNA inserts and a complex evolutionary history of natural transformation in the genus Nicotiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:669-82. [PMID: 25219519 DOI: 10.1111/tpj.12661] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 07/30/2014] [Accepted: 08/29/2014] [Indexed: 05/21/2023]
Abstract
Nicotiana species carry cellular T-DNA sequences (cT-DNAs), acquired by Agrobacterium-mediated transformation. We characterized the cT-DNA sequences of the ancestral Nicotiana tabacum species Nicotiana tomentosiformis by deep sequencing. N. tomentosiformis contains four cT-DNA inserts derived from different Agrobacterium strains. Each has an incomplete inverted-repeat structure. TA is similar to part of the Agrobacterium rhizogenes 1724 mikimopine-type T-DNA, but has unusual orf14 and mis genes. TB carries a 1724 mikimopine-type orf14-mis fragment and a mannopine-agropine synthesis region (mas2-mas1-ags). The mas2' gene codes for an active enzyme. TC is similar to the left part of the A. rhizogenes A4 T-DNA, but also carries octopine synthase-like (ocl) and c-like genes normally found in A. tumefaciens. TD shows a complex rearrangement of T-DNA fragments similar to the right end of the A4 TL-DNA, and including an orf14-like gene and a gene with unknown function, orf511. The TA, TB, TC and TD insertion sites were identified by alignment with N. tabacum and Nicotiana sylvestris sequences. The divergence values for the TA, TB, TC and TD repeats provide an estimate for their relative introduction times. A large deletion has occurred in the central part of the N. tabacum cv. Basma/Xanthi TA region, and another deletion removed the complete TC region in N. tabacum. Nicotiana otophora lacks TA, TB and TD, but contains TC and another cT-DNA, TE. This analysis, together with that of Nicotiana glauca and other Nicotiana species, indicates multiple sequential insertions of cT-DNAs during the evolution of the genus Nicotiana.
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Affiliation(s)
- Ke Chen
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du C. N. R. S., Rue du Général Zimmer 12, 67084, Strasbourg, France
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Renny-Byfield S, Wendel JF. Doubling down on genomes: polyploidy and crop plants. AMERICAN JOURNAL OF BOTANY 2014; 101:1711-25. [PMID: 25090999 DOI: 10.3732/ajb.1400119] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidy, or whole genome multiplication, is ubiquitous among angiosperms. Many crop species are relatively recent allopolyploids, resulting from interspecific hybridization and polyploidy. Thus, an appreciation of the evolutionary consequences of (allo)polyploidy is central to our understanding of crop plant domestication, agricultural improvement, and the evolution of angiosperms in general. Indeed, many recent insights into plant biology have been gleaned from polyploid crops, including, but not limited to wheat, tobacco, sugarcane, apple, and cotton. A multitude of evolutionary processes affect polyploid genomes, including rapid and substantial genome reorganization, transgressive gene expression alterations, gene fractionation, gene conversion, genome downsizing, and sub- and neofunctionalization of duplicate genes. Often these genomic changes are accompanied by heterosis, robustness, and the improvement of crop yield, relative to closely related diploids. Historically, however, the genome-wide analysis of polyploid crops has lagged behind those of diploid crops and other model organisms. This lag is partly due to the difficulties in genome assembly, resulting from the genomic complexities induced by combining two or more evolutionarily diverged genomes into a single nucleus and by the significant size of polyploid genomes. In this review, we explore the role of polyploidy in angiosperm evolution, the domestication process and crop improvement. We focus on the potential of modern technologies, particularly next-generation sequencing, to inform us on the patterns and processes governing polyploid crop improvement and phenotypic change subsequent to domestication.
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Affiliation(s)
- Simon Renny-Byfield
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
| | - Jonathan F Wendel
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
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44
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Yuan Z, Liu M, Ouyang Y, Zeng X, Hao M, Zhang L, Ning S, Yan Z, Liu D. The detection of a de novo allele of the Glu-1Dx gene in wheat-rye hybrid offspring. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2173-2182. [PMID: 25119869 DOI: 10.1007/s00122-014-2370-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
This study provides a link between a de novo gene and novel phenotype in wheat-rye hybrids that can be used as a model for induced de novo genetic variation. Wide hybridization can produce de novo DNA variation that may cause novel phenotypes. However, there is still a lack of specific links between changed genes and novel phenotypes in wide hybrids. The well-studied high-molecular-weight glutenin subunit (HMW-GS) genes in tribe Triticeae provide a useful model for addressing this issue. In this study, we investigated the feasibility of a wheat-rye hybridization method for inducing de novo phenotypes using the Glu-1Dx2.2 subunit as an example. We developed three hexaploid wheat lines with normal fertility and a Glu-1Dx2.2 variant, named Glu-1Dx2.2 (v) , derived from three F1 hybrids. The wild-type Glu-1Dx2.2 has two direct repeats of 295 bp length separated by an intervening 101 bp in its central repetitive region. In the mutant Glu-1Dx2.2 (v) , one copy of the repeats and the intervening sequence were deleted, probably through homology-dependent illegitimate recombination (IR). This study provides a direct link between a de novo allele and novel phenotype. Our results indicate that the wheat-rye method may be a useful tool to induce de novo genetic variations that broaden the genetic diversity for wheat improvement.
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Affiliation(s)
- Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
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Gottula J, Lewis R, Saito S, Fuchs M. Allopolyploidy and the evolution of plant virus resistance. BMC Evol Biol 2014; 14:149. [PMID: 24992820 PMCID: PMC4226957 DOI: 10.1186/1471-2148-14-149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The relationship between allopolyploidy and plant virus resistance is poorly understood. To determine the relationship of plant evolutionary history and basal virus resistance, a panel of Nicotiana species from diverse geographic regions and ploidy levels was assessed for resistance to non-coevolved viruses from the genus Nepovirus, family Secoviridae. The heritability of resistance was tested in a panel of synthetic allopolyploids. Leaves of different positions on each inoculated plant were tested for virus presence and a subset of plants was re-inoculated and assessed for systemic recovery. RESULTS Depending on the host-virus combination, plants displayed immunity, susceptibility or intermediate levels of resistance. Synthetic allopolyploids showed an incompletely dominant resistance phenotype and manifested systemic recovery. Plant ploidy was weakly negatively correlated with virus resistance in Nicotiana species, but this trend did not hold when synthetic allopolyploids were taken into account. Furthermore, a relationship between resistance and geographical origin was observed. CONCLUSION The gradients of resistance and virulence corresponded to a modified matching allele model of resistance. Intermediate resistance responses of allopolyploids corresponded with a model of multi-allelic additive resistance. The variable virus resistance of extant allopolyploids suggested that selection-based mechanisms surpass ploidy with respect to evolution of basal resistance to viruses.
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Affiliation(s)
- John Gottula
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Ramsey Lewis
- Department of Crop Science, North Carolina State University, 4310 Williams Hall Campus, Box 7620, Raleigh, NC 27695-7620, USA
| | - Seiya Saito
- Kearney Agricultural Research Center, University of California, Parlier, CA 93648, USA
| | - Marc Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
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Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol 2014; 6:559-71. [PMID: 24558256 PMCID: PMC3971588 DOI: 10.1093/gbe/evu037] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/25/2022] Open
Abstract
Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼ 2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Joseph P. Gallagher
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Emmanuel Szadkowski
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia
| | | | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
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Shapiro JA. How life changes itself: the Read-Write (RW) genome. Phys Life Rev 2013; 10:287-323. [PMID: 23876611 DOI: 10.1016/j.plrev.2013.07.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/02/2013] [Indexed: 01/06/2023]
Abstract
The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
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Affiliation(s)
- James A Shapiro
- Dept. of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA. http://www.huffingtonpost.com/james-a-shapiro
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Weiss-Schneeweiss H, Emadzade K, Jang TS, Schneeweiss G. Evolutionary consequences, constraints and potential of polyploidy in plants. Cytogenet Genome Res 2013; 140:137-50. [PMID: 23796571 PMCID: PMC3859924 DOI: 10.1159/000351727] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
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Affiliation(s)
- H. Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - K. Emadzade
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - T.-S. Jang
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - G.M. Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
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49
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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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Renny-Byfield S, Kovarik A, Kelly LJ, Macas J, Novak P, Chase MW, Nichols RA, Pancholi MR, Grandbastien MA, Leitch AR. Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:829-39. [PMID: 23517128 DOI: 10.1111/tpj.12168] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 02/23/2013] [Accepted: 03/01/2013] [Indexed: 05/18/2023]
Abstract
Recent advances have highlighted the ubiquity of whole-genome duplication (polyploidy) in angiosperms, although subsequent genome size change and diploidization (returning to a diploid-like condition) are poorly understood. An excellent system to assess these processes is provided by Nicotiana section Repandae, which arose via allopolyploidy (approximately 5 million years ago) involving relatives of Nicotiana sylvestris and Nicotiana obtusifolia. Subsequent speciation in Repandae has resulted in allotetraploids with divergent genome sizes, including Nicotiana repanda and Nicotiana nudicaulis studied here, which have an estimated 23.6% genome expansion and 19.2% genome contraction from the early polyploid, respectively. Graph-based clustering of next-generation sequence data enabled assessment of the global genome composition of these allotetraploids and their diploid progenitors. Unexpectedly, in both allotetraploids, over 85% of sequence clusters (repetitive DNA families) had a lower abundance than predicted from their diploid relatives; a trend seen particularly in low-copy repeats. The loss of high-copy sequences predominantly accounts for the genome downsizing in N. nudicaulis. In contrast, N. repanda shows expansion of clusters already inherited in high copy number (mostly chromovirus-like Ty3/Gypsy retroelements and some low-complexity sequences), leading to much of the genome upsizing predicted. We suggest that the differential dynamics of low- and high-copy sequences reveal two genomic processes that occur subsequent to allopolyploidy. The loss of low-copy sequences, common to both allopolyploids, may reflect genome diploidization, a process that also involves loss of duplicate copies of genes and upstream regulators. In contrast, genome size divergence between allopolyploids is manifested through differential accumulation and/or deletion of high-copy-number sequences.
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Affiliation(s)
- Simon Renny-Byfield
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK
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