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Ibiapino A, Báez M, García MA, Costea M, Stefanović S, Pedrosa-Harand A. Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition. Chromosome Res 2022; 30:91-107. [PMID: 35089455 DOI: 10.1007/s10577-021-09683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022]
Abstract
Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 127-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.
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Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.,Plant Breeding Department, University of Bonn, Bonn, Germany
| | | | - Mihai Costea
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
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Ibiapino A, García MA, Amorim B, Baez M, Costea M, Stefanović S, Pedrosa-Harand A. The Evolution of Cytogenetic Traits in Cuscuta (Convolvulaceae), the Genus With the Most Diverse Chromosomes in Angiosperms. FRONTIERS IN PLANT SCIENCE 2022; 13:842260. [PMID: 35432411 PMCID: PMC9011109 DOI: 10.3389/fpls.2022.842260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/03/2022] [Indexed: 05/17/2023]
Abstract
Karyotypes are characterized by traits such as chromosome number, which can change through whole-genome duplication and dysploidy. In the parasitic plant genus Cuscuta (Convolvulaceae), chromosome numbers vary more than 18-fold. In addition, species of this group show the highest diversity in terms of genome size among angiosperms, as well as a wide variation in the number and distribution of 5S and 35S ribosomal DNA (rDNA) sites. To understand its karyotypic evolution, ancestral character state reconstructions were performed for chromosome number, genome size, and position of 5S and 35S rDNA sites. Previous cytogenetic data were reviewed and complemented with original chromosome counts, genome size estimates, and rDNA distribution assessed via fluorescence in situ hybridization (FISH), for two, seven, and 10 species, respectively. Starting from an ancestral chromosome number of x = 15, duplications were inferred as the prevalent evolutionary process. However, in holocentric clade (subgenus Cuscuta), dysploidy was identified as the main evolutionary mechanism, typical of holocentric karyotypes. The ancestral genome size of Cuscuta was inferred as approximately 1C = 12 Gbp, with an average genome size of 1C = 2.8 Gbp. This indicates an expansion of the genome size relative to other Convolvulaceae, which may be linked to the parasitic lifestyle of Cuscuta. Finally, the position of rDNA sites varied mostly in species with multiple sites in the same karyotype. This feature may be related to the amplification of rDNA sites in association to other repeats present in the heterochromatin. The data suggest that different mechanisms acted in different subgenera, generating the exceptional diversity of karyotypes in Cuscuta.
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Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | | | - Bruno Amorim
- Postgraduate Program of Biotechnology and Natural Resources of the Amazonia (PPGMBT), State University of Amazonas, Manaus, Brazil
| | - Mariana Baez
- Plant Breeding Department, University of Bonn, Bonn, Germany
| | - Mihai Costea
- Department of Biology, University of Wilfrid Laurier, Waterloo, ON, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
- *Correspondence: Miguel A. García,
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Melo NFDE, Guerra M. The karyotype of Adenia and the origin of the base number x = 12 in Passifloroideae (Passifloraceae). AN ACAD BRAS CIENC 2021; 93:e20201852. [PMID: 34614089 DOI: 10.1590/0001-3765202120201852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/04/2021] [Indexed: 11/21/2022] Open
Abstract
Adenia is an Old World genus of Passifloroideae closely related to Passiflora. The two genera comprise the large majority of Passifloroideae species, although most studies are concentrated on Passiflora. Cytological analyses reveal that changes in chromosome numbers played an important role in the evolution of Passiflora, whereas in the remaining genera little is known, hindering the identification of the base number of the family. Here we analyzed the chromosome number and the 35S rDNA sites of three species of Adenia and reevaluated the base number (x) of the subfamily Passifloroideae and the family Passifloraceae, including chromosome data for Turneroideae and Malesherbioideae. The chromosome number of Adenia species seemed to be stable with 2n = 24 or 48 and one or two pairs of rDNA sites, very similar to Passiflora subgenus Astrophea, suggesting a common ancestral karyotype with x = 12. Differently, Turneroideae and Malesherbioideae present x = 7. A whole genomic duplication detected after the separation of Passifloroideae and Malesherbioideae suggests that the base number of Passifloraceae most probably was x = 7, which by dysploidy and polyploidy generated x = 12 for the subfamily Passifloroideae.
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Affiliation(s)
- Natoniel Franklin DE Melo
- Embrapa Semiárido, Laboratório de Biotecnologia, BR-428, km 152, Caixa Postal 23, 56302-970 Petrolina, PE, Brazil
| | - Marcelo Guerra
- Universidade Federal de Pernambuco, CB, Departamento de Botânica, Rua Prof. Nelson Chaves, s/n, Cidade Universitária, 50670-420 Recife, PE, Brazil
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Ibiapino A, García MÁ, Costea M, Stefanović S, Guerra M. Intense proliferation of rDNA sites and heterochromatic bands in two distantly related Cuscuta species (Convolvulaceae) with very large genomes and symmetric karyotypes. Genet Mol Biol 2020; 43:e20190068. [PMID: 32542306 PMCID: PMC7295182 DOI: 10.1590/1678-4685-gmb-2019-0068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/06/2020] [Indexed: 11/21/2022] Open
Abstract
The genome size varies widely among angiosperms but only a few clades present huge variation at a low phylogenetic level. Among diploid species of the genus Cuscuta the genome size increased enormously in at least two independent lineages: in species of subgenus Monogynella and in at least one species (C. indecora) of the subgenus Grammica. Curiously, the independent events lead to similar karyotypes, with 2n = 30 mostly metacentric chromosomes. In this paper we compared the patterns of heterochromatic bands and rDNA sites of C. indecora and C. monogyna, aiming to evaluate the role of these repetitive fractions in these karyotypes. We found out that the large genomes of these species were incremented by a huge number of small heterochromatic CMA+ and DAPI+ bands and 5S and 35 rDNA sites, most of them clearly colocalized with CMA+ bands. Silver nitrate impregnation revealed that the maximum number of nucleoli per nucleus was low in both species, suggesting that some of these sites may be inactive. Noteworthy, the tandem repeats did not generate large bands or sites but rather dozens of small blocks dispersed throughout the chromosomes, apparently contributing to conserve the original karyotype symmetry.
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Affiliation(s)
- Amália Ibiapino
- Universidade Federal de Pernambuco, Departamento de Botânica,
Recife, PE, Brazil
| | - Miguel Ángel García
- University of Toronto Mississauga, Department of Biology,
Mississauga, ON, Canada
- Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
| | - Mihai Costea
- Wilfrid Laurier University, Department of Biology, Waterloo, ON,
Canada
| | - Saša Stefanović
- University of Toronto Mississauga, Department of Biology,
Mississauga, ON, Canada
| | - Marcelo Guerra
- Universidade Federal de Pernambuco, Departamento de Botânica,
Recife, PE, Brazil
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Wang J, Qin J, Sun P, Ma X, Yu J, Li Y, Sun S, Lei T, Meng F, Wei C, Li X, Guo H, Liu X, Xia R, Wang L, Ge W, Song X, Zhang L, Guo D, Wang J, Bao S, Jiang S, Feng Y, Li X, Paterson AH, Wang X. Polyploidy Index and Its Implications for the Evolution of Polyploids. Front Genet 2019; 10:807. [PMID: 31552101 PMCID: PMC6746930 DOI: 10.3389/fgene.2019.00807] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
Polyploidy has contributed to the divergence and domestication of plants; however, estimation of the relative roles that different types of polyploidy have played during evolution has been difficult. Unbalanced and balanced gene removal was previously related to allopolyploidies and autopolyploidies, respectively. Here, to infer the types of polyploidies and evaluate their evolutionary effects, we devised a statistic, the Polyploidy-index or P-index, to characterize the degree of divergence between subgenomes of a polyploidy, to find whether there has been a balanced or unbalanced gene removal from the homoeologous regions. Based on a P-index threshold of 0.3 that distinguishes between known or previously inferred allo- or autopolyploidies, we found that 87.5% of 24 angiosperm paleo-polyploidies were likely produced by allopolyploidizations, responsible for establishment of major tribes such as Poaceae and Fabaceae, and large groups such as monocots and eudicots. These findings suggest that >99.7% of plant genomes likely derived directly from allopolyploidies, with autopolyploidies responsible for the establishment of only a few small genera, including Glycine, Malus, and Populus, each containing tens of species. Overall, these findings show that polyploids with high divergence between subgenomes (presumably allopolyploids) established the major plant groups, possibly through secondary contact between previously isolated populations and hybrid vigor associated with their re-joining.
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Affiliation(s)
- Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Qin
- Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xuelian Ma
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Tianyu Lei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaojian Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Ruiyan Xia
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Li Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Di Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinyu Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shoutong Bao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shan Jiang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yishan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xueping Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
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