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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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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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Belyayev A, Josefiová J, Jandová M, Mahelka V, Krak K, Mandák B. Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome. Mob DNA 2020; 11:20. [PMID: 32607133 PMCID: PMC7320549 DOI: 10.1186/s13100-020-00219-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/19/2020] [Indexed: 11/10/2022] Open
Abstract
Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.
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Affiliation(s)
- Alexander Belyayev
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Jiřina Josefiová
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Michaela Jandová
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Václav Mahelka
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Karol Krak
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha, Suchdol Czech Republic
| | - Bohumil Mandák
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha, Suchdol Czech Republic
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Mangelson H, Jarvis DE, Mollinedo P, Rollano‐Penaloza OM, Palma‐Encinas VD, Gomez‐Pando LR, Jellen EN, Maughan PJ. The genome of Chenopodium pallidicaule: An emerging Andean super grain. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11300. [PMID: 31832282 PMCID: PMC6858295 DOI: 10.1002/aps3.11300] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
PREMISE Cañahua is a semi-domesticated crop grown in high-altitude regions of the Andes. It is an A-genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Cañahua seed contains a complete protein, a low glycemic index, and offers a wide variety of nutritionally important vitamins and minerals. METHODS The reference assembly was developed using a combination of short- and long-read sequencing techniques, including multiple rounds of Hi-C-based proximity-guided assembly. RESULTS The final assembly of the ~363-Mbp genome consists of 4633 scaffolds, with 96.6% of the assembly contained in nine scaffolds representing the nine haploid chromosomes of the species. Repetitive element analysis classified 52.3% of the assembly as repetitive, with the most common repeat identified as long terminal repeat retrotransposons. MAKER annotation of the final assembly yielded 22,832 putative gene models. DISCUSSION When compared with quinoa, strong patterns of synteny support the hypothesis that cañahua is a close A-genome diploid relative, and thus potentially a simplified model diploid species for genetic analysis and improvement of quinoa. Resequencing and phylogenetic analysis of a diversity panel of cañahua accessions suggests that coordinated efforts are needed to enhance genetic diversity conservation within ex situ germplasm collections.
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Affiliation(s)
- Hayley Mangelson
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
| | - David E. Jarvis
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
| | - Patricia Mollinedo
- Institute of Natural Product ResearchUniversidad Mayor de San AndrésLa PazBolivia
| | | | | | - Luz Rayda Gomez‐Pando
- Departamento de FitotecniaFacultad de AgronomíaUniversidad Nacional Agraria de La MolinaLa MolinaPeru
| | - Eric N. Jellen
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
| | - Peter J. Maughan
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
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Sun J, Yu L, Cai Z, Zhang A, Jin W, Han Y, Li Z. Comparative karyotype analysis among six species of Ipomoea based on two newly identified repetitive sequences. Genome 2019; 62:243-252. [PMID: 30785785 DOI: 10.1139/gen-2018-0169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sweet potato is one of the most important crops worldwide; however, basic research in this crop is limited. In this study, we aimed to construct a detailed karyotype of six species of Ipomoea (hexaploid Ipomoea batatas and five related species, namely, one tetraploid, I. tabascana and four diploids, I. splendor-sylvae, I. trifida, I. tenuissima, and I. × leucantha) and understand the relationship among these species. Two satellite repeats (viz., Itf_1 and Itf_2) were identified from the diploid I. trifida genome sequence using RepeatExplorer on Galaxy. Together with the ribosomal DNA (rDNA), although without distinguishable chromosomes, a detailed karyotype was constructed for the six species. Our results showed a similar karyotype between I. tenuissima and I. × leucantha, indicating their close relationship. The signal distribution pattern of Itf_1, 45S rDNA combination, detected only in I. trifida, I. tabascana, and I. batatas, implied their close relationships. The chromosomes carrying 5S rDNA could be conserved among the six species as they always carried the Itf_2 signals, which generated a similar signal distribution pattern. The results enabled a detailed comparative cytogenetic analysis, providing valuable information to understand the relationship among these species and help assemble the genome sequence of the six species of Ipomoea.
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Affiliation(s)
- Jianying Sun
- a Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China.,b Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Lixuan Yu
- a Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China.,b Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Zeixi Cai
- c National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Coordinated Research Center for Crop Biology, China Agricultural University, Beijing, China
| | - An Zhang
- d Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou, China
| | - Weiwei Jin
- c National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Coordinated Research Center for Crop Biology, China Agricultural University, Beijing, China
| | - Yonghua Han
- a Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China.,b Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
| | - Zongyun Li
- a Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China.,b Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou, China
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