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Zuo (左胜) S, Guo (郭新异) X, Mandáková T, Edginton M, Al-Shehbaz IA, Lysak MA. Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution. PLANT PHYSIOLOGY 2022; 190:403-420. [PMID: 35670733 PMCID: PMC9434143 DOI: 10.1093/plphys/kiac268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/09/2022] [Indexed: 05/20/2023]
Abstract
Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted in the extant c. 17 genera and 60 species endemic to Australia and New Zealand (10 species). As postpolyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. In Microlepidieae, different extents of homoeologous recombination between the two parental subgenomes generated clades marked by slow ("cold") versus fast ("hot") genome diploidization. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, we analyzed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. The four recovered intra-tribal clades mirror the varied diploidization of Microlepidieae genomes, suggesting that the intrinsic genomic features underlying the extent of diploidization are shared among genera and species within one clade. Nevertheless, even congeneric species may exert considerable morphological disparity (e.g. in fruit shape), whereas some species within different clades experience extensive morphological convergence despite the different pace of their genome diploidization. We showed that faster genome diploidization is positively associated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, our results confirm the potential of Microlepidieae as a promising subject for the analysis of postpolyploid genome diploidization in Brassicaceae.
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Affiliation(s)
| | | | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Mark Edginton
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Toowong, QLD 4066, Australia
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Garrido-Ramos MA. The Genomics of Plant Satellite DNA. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:103-143. [PMID: 34386874 DOI: 10.1007/978-3-030-74889-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
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Ribeiro T, Vasconcelos E, Dos Santos KGB, Vaio M, Brasileiro-Vidal AC, Pedrosa-Harand A. Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi. Chromosome Res 2019; 28:139-153. [PMID: 31734754 DOI: 10.1007/s10577-019-09618-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/24/2019] [Accepted: 10/15/2019] [Indexed: 01/08/2023]
Abstract
Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within tribe Phaseoleae (Fabaceae), some genera, such as Phaseolus, Vigna, and Cajanus, show small genome and mostly stable chromosome number. Here, we applied a combined computational and cytological approach to study the organization and diversification of repetitive elements in some species of these genera. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons, especially Ogre and Chromovirus elements, making up most of genomes, other than P. acutifolius and Vigna species. Satellite DNAs (SatDNAs) were less representative, but highly diverse among species, showing a clear phylogenetic relationship. In situ localization revealed preferential location at pericentromeres and centromeres for both types of sequences, suggesting a heterogeneous composition, especially for centromeres. Few elements showed subterminal accumulation. Copy number variation among chromosomes within and among species was observed for all nine identified SatDNAs. Altogether, our data pointed two main elements (Ty3/Gypsy retrotransponsons and SatDNAs) to the diversification on the repetitive landscape in Phaseoleae, with a typical set of repeats in each species. The high turnover of these sequences, however, did not affect total genome size.
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Affiliation(s)
- Tiago Ribeiro
- Integrative Plant Research Laboratory, Department of Botany and Ecology, Federal University of Mato Grosso, Av. Fernando Corrêa da Costa, 2367, Boa Esperança, Cuiabá, MT, 78060900, Brazil.
| | - Emanuelle Vasconcelos
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Recife, PE, Brazil
| | - Karla G B Dos Santos
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rêgo, s/n, Cidade Universitária, Recife, PE, 50670420, Brazil
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Ana Christina Brasileiro-Vidal
- Laboratory of Plant Genetics and Biotechnology, Department of Genetics, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Av. Prof. Moraes Rêgo, s/n, Cidade Universitária, Recife, PE, 50670420, Brazil.
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