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Decena MÁ, Sancho R, Inda LA, Pérez-Collazos E, Catalán P. Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis in Brachypodium model grasses. FRONTIERS IN PLANT SCIENCE 2024; 15:1419255. [PMID: 39049853 PMCID: PMC11266827 DOI: 10.3389/fpls.2024.1419255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024]
Abstract
Brachypodium grass species have been selected as model plants for functional genomics of grass crops, and to elucidate the origins of allopolyploidy and perenniality in monocots, due to their small genome sizes and feasibility of cultivation. However, genome sizes differ greatly between diploid or polyploid Brachypodium lineages. We have used genome skimming sequencing data to uncover the composition, abundance, and phylogenetic value of repetitive elements in 44 representatives of the major Brachypodium lineages and cytotypes. We also aimed to test the possible mechanisms and consequences of the "polyploid genome shock hypothesis" (PGSH) under three different evolutionary scenarios of variation in repeats and genome sizes of Brachypodium allopolyploids. Our data indicated that the proportion of the genome covered by the repeatome in the Brachypodium species showed a 3.3-fold difference between the highest content of B. mexicanum-4x (67.97%) and the lowest of B. stacei-2x (20.77%), and that changes in the sizes of their genomes were a consequence of gains or losses in their repeat elements. LTR-Retand and Tekay retrotransposons were the most frequent repeat elements in the Brachypodium genomes, while Ogre retrotransposons were found exclusively in B. mexicanum. The repeatome phylogenetic network showed a high topological congruence with plastome and nuclear rDNA and transcriptome trees, differentiating the ancestral outcore lineages from the recently evolved core-perennial lineages. The 5S rDNA graph topologies had a strong match with the ploidy levels and nature of the subgenomes of the Brachypodium polyploids. The core-perennial B. sylvaticum presents a large repeatome and characteristics of a potential post-polyploid diploidized origin. Our study evidenced that expansions and contractions in the repeatome were responsible for the three contrasting responses to the PGSH. The exacerbated genome expansion of the ancestral allotetraploid B. mexicanum was a consequence of chromosome-wide proliferation of TEs and not of WGD, the additive repeatome pattern of young allotetraploid B. hybridum of stabilized post-WGD genome evolution, and the genomecontraction of recent core-perennials polyploids (B. pinnatum, B. phoenicoides) of repeat losses through recombination of these highly hybridizing lineages. Our analyses have contributed to unraveling the evolution of the repeatome and the genome size variation in model Brachypodium grasses.
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Affiliation(s)
- María Ángeles Decena
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Rubén Sancho
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Luis A. Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Centro de Investigaciones Tecnológicas y Agroalimentarias de Aragón (CITA), Zaragoza, Spain
| | - Ernesto Pérez-Collazos
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
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Hlavatá K, Záveská E, Leong-Škorničková J, Pouch M, Poulsen AD, Šída O, Khadka B, Mandáková T, Fér T. Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1324358. [PMID: 38708400 PMCID: PMC11066291 DOI: 10.3389/fpls.2024.1324358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/12/2024] [Indexed: 05/07/2024]
Abstract
Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analyzed repeat dynamics, and identified potential hybridization events within the genus. Our analysis confirmed the presence of four major infrageneric clades (A-D) within Amomum, with clades A-C exclusively comprising diploid species (2n = 48) and clade D encompassing both diploid and tetraploid species (2n = 48 and 96). We observed an increase in the repeat content within the genus, ranging from 84% to 89%, compared to outgroup species with 75% of the repeatome. The SIRE lineage of the Ty1-Copia repeat superfamily was prevalent in most analyzed ingroup genomes. We identified significant difference in repeatome structure between the basal Amomum clades (A, B, C) and the most diverged clade D. Our investigation revealed evidence of ancient hybridization events within Amomum, coinciding with a substantial proliferation of multiple repeat groups. This finding supports the hypothesis that ancient hybridization is a driving force in the genomic evolution of Amomum. Furthermore, we contextualize our findings within the broader context of genome size variations and repeatome dynamics observed across major monocot lineages. This study enhances our understanding of evolutionary processes within monocots by highlighting the crucial roles of repetitive elements in shaping genome size and suggesting the mechanisms that drive these changes.
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Affiliation(s)
- Kristýna Hlavatá
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Eliška Záveská
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, Czech Academy of Science, Průhonice, Czechia
| | - Jana Leong-Škorničková
- Herbarium, Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Milan Pouch
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Center for Biomolecular Research (NCBR), Masaryk University, Kamenice, Czechia
| | - Axel Dalberg Poulsen
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Otakar Šída
- Department of Botany, National Museum in Prague, Prague, Czechia
| | - Bijay Khadka
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tomáš Fér
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
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Phylogenomics and Systematics of Overlooked Mesoamerican and South American Polyploid Broad-Leaved Festuca Grasses Differentiate F. sects. Glabricarpae and Ruprechtia and F. subgen. Asperifolia, Erosiflorae, Mallopetalon and Coironhuecu (subgen. nov.). PLANTS 2022; 11:plants11172303. [PMID: 36079685 PMCID: PMC9460391 DOI: 10.3390/plants11172303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022]
Abstract
Allopolyploidy is considered a driver of diversity in subtribe Loliinae. We investigate the evolution and systematics of the poorly studied Mesoamerican and South American polyploid broad-leaved Festuca L. species of uncertain origin and unclear taxonomy. A taxonomic study of seven diagnostic morphological traits was conducted on a representation of 22 species. Phylogenomic analyses were performed on a representation of these supraspecific taxa and all other Loliinae lineages using separate data from the entire plastome, nuclear rDNA 45S and 5S genes, and repetitive DNA elements. F. subgen. Mallopetalon falls within the fine-leaved (FL) Loliinae clade, whereas the remaining taxa are nested within the broad-leaved (BL) Loliinae clade forming two separate Mexico–Central–South American (MCSAI, MCSAII) lineages. MCSAI includes representatives of F. sect. Glabricarpae and F. subgen. Asperifolia plus F. superba, and MCSAII of F. subgen. Erosiflorae and F. sect. Ruprechtia plus F. argentina. MCSAII likely had a BL Leucopoa paternal ancestor, MCSAI and MCSAII a BL Meso-South American maternal ancestor, and Mallopetalon FL, American I–II ancestors. Plastome vs. nuclear topological discordances corroborated the hybrid allopolyploid origins of these taxa, some of which probably originated from Northern Hemisphere ancestors. The observed data indicate rapid reticulate radiations in the Central–South American subcontinent. Our systematic study supports the reclassification of some studied taxa in different supraspecific Festuca ranks.
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