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Ferraz ME, Ribeiro T, Sader M, Nascimento T, Pedrosa-Harand A. Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans. Chromosome Res 2023; 31:30. [PMID: 37812264 DOI: 10.1007/s10577-023-09739-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species present relatively stable karyotypes with 2n = 22 chromosomes, the karyotypes of species of the Leptostachyus group show high rates of structural rearrangements, including a nested chromosome fusion that led to the dysploid chromosome number of the group (2n = 20). We examined the roles of repetitive landscapes in the rearrangements of species of the Leptostachyus group using genome-skimming data to characterize the repeatome in a range of Phaseolus species and compared them to species of that group (P. leptostachyus and P. macvaughii). LTR retrotransposons, especially the Ty3/gypsy lineage Chromovirus, were the most abundant elements in the genomes. Differences in the abundance of Tekay, Retand, and SIRE elements between P. macvaughii and P. leptostachyus were reflected in their total amounts of Ty3/gypsy and Ty1/copia. The satellite DNA fraction was the most divergent among the species, varying both in abundance and distribution, even between P. leptostachyus and P. macvaughii. The rapid turnover of repeats in the Leptostachyus group may be associated with the several rearrangements observed.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Tiago Ribeiro
- Integrative Plant Research Lab, Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Mariela Sader
- Multidisciplinary Institute of Plant Biology, National Council for Scientific and Technical Research, National University of Córdoba, Córdoba, Argentina
| | - Thiago Nascimento
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil.
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de Assis R, Gonçalves LSA, Guyot R, Vanzela ALL. Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. Genome 2023; 66:269-280. [PMID: 37364373 DOI: 10.1139/gen-2022-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition, and genomic distribution has been provided. Here, we exploited the noncoding repetitive fraction, represented by satellite sequences, that tends to accumulate in blocks along chromosomes, especially near the chromosome ends of peppers. Two satellite DNA sequences were identified (CDR-1 and CDR-2), characterized and mapped in silico in three Capsicum genomes (C. annuum, C. chinense, and C. baccatum) using data from the published high-coverage sequencing and repeats finding bioinformatic tools. Localization using FISH in the chromosomes of these species and in two others (C. frutescens and C. chacoense), totaling five species, showed signals adjacent to the rDNA sites. A sequence comparison with existing Solanaceae repeats showed that CDR-1 and CDR-2 have different origins but without homology to rDNA sequences. Satellites occupied subterminal chromosomal regions, sometimes collocated with or adjacent to 35S rDNA sequences. Our results expand knowledge about the diversity of subterminal regions of Capsicum chromosomes, showing different amounts and distributions within and between karyotypes. In addition, these sequences may be useful for future phylogenetic studies.
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Affiliation(s)
- Rafael de Assis
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina 86097-570, Paraná, Brazil
| | | | - Romain Guyot
- Institute de Recherche pour le Développement, CIRAD, Université de Montpellier, UMR DIADE, Montpellier, France
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3
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Kirov I, Kolganova E, Dudnikov M, Yurkevich OY, Amosova AV, Muravenko OV. A Pipeline NanoTRF as a New Tool for De Novo Satellite DNA Identification in the Raw Nanopore Sequencing Reads of Plant Genomes. PLANTS (BASEL, SWITZERLAND) 2022; 11:2103. [PMID: 36015406 PMCID: PMC9413040 DOI: 10.3390/plants11162103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
High-copy tandemly organized repeats (TRs), or satellite DNA, is an important but still enigmatic component of eukaryotic genomes. TRs comprise arrays of multi-copy and highly similar tandem repeats, which makes the elucidation of TRs a very challenging task. Oxford Nanopore sequencing data provide a valuable source of information on TR organization at the single molecule level. However, bioinformatics tools for de novo identification of TRs in raw Nanopore data have not been reported so far. We developed NanoTRF, a new python pipeline for TR repeat identification, characterization and consensus monomer sequence assembly. This new pipeline requires only a raw Nanopore read file from low-depth (<1×) genome sequencing. The program generates an informative html report and figures on TR genome abundance, monomer sequence and monomer length. In addition, NanoTRF performs annotation of transposable elements (TEs) sequences within or near satDNA arrays, and the information can be used to elucidate how TR−TE co-evolve in the genome. Moreover, we validated by FISH that the NanoTRF report is useful for the evaluation of TR chromosome organization—clustered or dispersed. Our findings showed that NanoTRF is a robust method for the de novo identification of satellite repeats in raw Nanopore data without prior read assembly. The obtained sequences can be used in many downstream analyses including genome assembly assistance and gap estimation, chromosome mapping and cytogenetic marker development.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, Moscow 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Elizaveta Kolganova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, Moscow 127550, Russia
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, Moscow 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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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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Andreev IO, Parnikoza IY, Konvalyuk II, Metcheva R, Kozeretska IA, Kunakh VA. Genetic divergence of Deschampsia antarctica (Poaceae) population groups in the maritime Antarctic. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
We used inter-simple sequence repeats and inter-retrotransposon amplified polymorphism markers to assess genetic variation in Deschampsia antarctica populations in the context of its uneven distribution in the northern and central maritime Antarctic. Genetic diversity and population structure and differentiation were assessed in nine populations from geographically isolated population groups of D. antarctica, including the South Shetland Islands, Anvers Island and the Argentine Islands regions. In total, 265 amplified DNA fragments were scored, of which 220 (83.0%) were polymorphic. The total sample showed low genetic diversity (unbiased expected heterozygosity = 0.081 and Shannon diversity index = 0.115) and high population differentiation (molecular variance among populations = 0.659). We also found a trend toward a decrease in genetic diversity and an increase in population differentiation toward the southern edge of the species range. Principal coordinates analysis of polymerase chain reaction data and Bayesian population structure analysis showed three main clusters, which included plants originating from three spatially isolated population groups. The unweighted pair group method with arithmetic mean clustering of populations based on Nei’s genetic distances was mainly in agreement with this pattern. Testing of isolation by distance using the Mantel test demonstrated a significant correlation between genetic and ln-transformed geographical distance (r = 0.703). The data obtained indicate that the geographically isolated D. antarctica populations in the maritime Antarctic might form genetic clusters within the total range.
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Affiliation(s)
- Igor O Andreev
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Ivan Yu Parnikoza
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
- National Antarctic Scientific Centre of Ukraine, Kyiv, Ukraine
| | - Iryna I Konvalyuk
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | | | | | - Viktor A Kunakh
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
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González ML, Chiapella JO, Urdampilleta JD. Chromosomal Differentiation of Deschampsia (Poaceae) Based on Four Satellite DNA Families. Front Genet 2021; 12:728664. [PMID: 34621294 PMCID: PMC8490763 DOI: 10.3389/fgene.2021.728664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022] Open
Abstract
Diverse families of satellite DNA (satDNA) were detected in heterochromatin regions of Deschampsia. This kind of repetitive DNA consists of tandem repeat sequences forming big arrays in genomes, and can contribute to lineages differentiation. The differentiation between types of satDNA is related to their sequence identity, the size and number of monomers forming the array, and their chromosomal location. In this work, four families of satDNA (D2, D3, D12, D13), previously isolated by genomic analysis, were studied on chromosomal preparations of 12 species of Deschampsia (D. airiformis, D. antarctica, D. cespitosa, D. cordillerarum, D. elongata, D. kingii, D. laxa, D. mendocina, D. parvula, D. patula, D. venustula, and Deschampsia sp) and one of Deyeuxia (D. eminens). Despite the number of satDNA loci showing interspecific variation, the general distribution pattern of each satDNA family is maintained. The four satDNA families are AT-rich and associated with DAPI + heterochromatin regions. D2, D3, and D12 have mainly subterminal distribution, while D13 is distributed in intercalary regions. Such conservation of satDNA patterns suggests a not random distribution in genomes, where the variation between species is mainly associated with the array size and the loci number. The presence of satDNA in all species studied suggests a low genetic differentiation of sequences. On the other hand, the variation of the distribution pattern of satDNA has no clear association with phylogeny. This may be related to high differential amplification and contraction of sequences between lineages, as explained by the library model.
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Affiliation(s)
- María Laura González
- Instituto Multidisciplinario de Biología Vegetal (Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - Jorge Oscar Chiapella
- Instituto de Investigaciones en Biodiversidad y Medioambiente (Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional Del Comahue), Bariloche, Argentina
| | - Juan Domingo Urdampilleta
- Instituto Multidisciplinario de Biología Vegetal (Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Córdoba), Córdoba, Argentina
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Cytogenomics of Deschampsia P. Beauv. (Poaceae) Species Based on Sequence Analyses and FISH Mapping of CON/COM Satellite DNA Families. PLANTS 2021; 10:plants10061105. [PMID: 34070920 PMCID: PMC8229069 DOI: 10.3390/plants10061105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023]
Abstract
The genus Deschampsia P. Beauv. (Poaceae) involves a group of widespread polymorphic species, and many of them are highly tolerant to stressful environmental conditions. Genome diversity and chromosomal phylogeny within the genus are still insufficiently studied. Satellite DNAs, including CON/COM families, are the main components of the plant repeatome, which contribute to chromosome organization. For the first time, using PCR-based (Polymerase Chain Reaction) techniques and sequential BLAST (Basic Local Alignment Search Tool) and MSA (Multiple Sequence Alignment) analyses, we identified and classified CON/COM repeats in genomes of eleven Deschampsia accessions and three accessions from related genera. High homology of CON/COM sequences were revealed in the studied species though differences in single-nucleotide alteration profiles detected in homologous CON/COM regions indicated that they tended to diverge independently. The performed chromosome mapping of 45S rDNA, 5S rDNA, and CON/COM repeats in six Deschampsia species demonstrated interspecific variability in localization of these cytogenetic markers and facilitated the identification of different chromosomal rearrangements. Based on the obtained data, the studied Deschampsia species were distinguished into karyological groups, and MSA-based schematic trees were built, which could clarify the relationships within the genus. Our findings can be useful for further genetic and phylogenetic studies.
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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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Cuadra P, Guajardo J, Carrasco-Orellana C, Stappung Y, Fajardo V, Herrera R. Differential expression after UV-B radiation and characterization of chalcone synthase from the Patagonian hairgrass Deschampsia antarctica. PHYTOCHEMISTRY 2020; 169:112179. [PMID: 31669976 DOI: 10.1016/j.phytochem.2019.112179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 06/10/2023]
Abstract
Deschampsiaantarctica inhabits the maritime territory of Antarctica and South Patagonia. It grows under very harsh environmental conditions. The survival of this species in low freezing temperatures and under high levels of UV-B radiation may constitute some of the most remarkable adaptive plant responses and suggests that this plant possesses genes associated with cold and UV tolerance. Frequently, increased levels of flavonoids have been linked to highly UV-B irradiated plants. Studies examining the biosynthesis of flavonoids in D. antarctica may provide clues to its success in this extreme environment. In this study, we characterized the family of genes encoding chalcone synthase, a key enzyme of the flavonoid biosynthetic pathway. DaCHS was cloned, sequenced and characterized by using software tools. CHS contains two domains, the N-terminal domain ranges from amino acid 8 to 231 and the C-terminal domain ranges from amino acid 241 to 391. Sequence analysis of the three family members revealed a high degree of identity after comparison with other monocotyledons such as Oryza sativa L., Zea mays L. and Hordeum vulgare L. According to these results, DaCHS can be grouped together with H. vulgare CHS1 in the same branch. The phylogenetic tree was built using MEGA software and the neighbour join method with 1000 bootstrap replicates. A model of DaCHS was constructed by way of structural tools and key amino acid residues were identified at the active motif site.
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Affiliation(s)
- Pedro Cuadra
- Universidad de Magallanes, Laboratorio de Productos Naturales, P.O. Box 113-D, Punta Arenas, Chile.
| | - Joselin Guajardo
- Universidad de Talca, Instituto de Ciencias Biológicas, 2 norte 685, P.O. Box 747, Talca, Chile
| | | | - Yazmina Stappung
- Universidad de Talca, Instituto de Ciencias Biológicas, 2 norte 685, P.O. Box 747, Talca, Chile
| | - Víctor Fajardo
- Universidad de Magallanes, Laboratorio de Productos Naturales, P.O. Box 113-D, Punta Arenas, Chile
| | - Raúl Herrera
- Universidad de Talca, Instituto de Ciencias Biológicas, 2 norte 685, P.O. Box 747, Talca, Chile.
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Van-Lume B, Mata-Sucre Y, Báez M, Ribeiro T, Huettel B, Gagnon E, Leitch IJ, Pedrosa-Harand A, Lewis GP, Souza G. Evolutionary convergence or homology? Comparative cytogenomics of Caesalpinia group species (Leguminosae) reveals diversification in the pericentromeric heterochromatic composition. PLANTA 2019; 250:2173-2186. [PMID: 31696317 DOI: 10.1007/s00425-019-03287-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/25/2019] [Indexed: 05/02/2023]
Abstract
We demonstrated by cytogenomic analysis that the proximal heterochromatin of the Northeast Brazilian species of Caesalpinia group is enriched with phylogenetically conserved Ty3/Gypsy-Tekay RT, but diverge in the presence of Ty3/Gypsy-Athila RT and satDNA. The Caesalpinia Group includes 225 species and 27 monophyletic genera of which four occur in Northeastern Brazil: Erythrostemon (1 sp.), Cenostigma (7 spp.), Libidibia (1 sp.), and Paubrasilia (1 sp.). The last three genera are placed in different clades in the Caesalpinia Group phylogeny, and yet they are characterized by having a numerically stable karyotype 2n = 24 (16 M+8A) and GC-rich heterochromatic bands (chromomycin A3 positive/CMA+ bands) in the proximal chromosome regions. To characterize the composition of their heterochromatin and test for the homology of these chromosomal regions, genomic DNA was extracted from Cenostigma microphyllum, Libidibia ferrea, and Paubrasilia echinata, and sequenced at low coverage using the Illumina platform. The genomic repetitive fractions were characterized using a Galaxy/RepeatExplorer-Elixir platform. The most abundant elements of each genome were chromosomally located by fluorescent in situ hybridization (FISH) and compared to the CMA+ heterochromatin distribution. The repetitive fraction of the genomes of C. microphyllum, L. ferrea, and P. echinata were estimated to be 41.70%, 38.44%, and 72.51%, respectively. Ty3/Gypsy retrotransposons (RT), specifically the Tekay lineage, were the most abundant repeats in each of the three genomes. FISH mapping revealed species-specific patterns for the Tekay elements in the proximal regions of the chromosomes, co-localized with CMA+ bands. Other species-specific patterns were observed, e.g., for the Ty3/Gypsy RT Athila elements which were found in all the proximal heterochromatin of L. ferrea or restricted to the acrocentric chromosomes of C. microphyllum. This Athila labeling co-localized with satellite DNAs (satDNAs). Although the Caesalpinia Group diverged around 55 Mya, our results suggest an ancestral colonization of Tekay RT in the proximal heterochromatin. Thus, the present-day composition of the pericentromeric heterochromatin in these Northeast Brazilian species is a combination of the maintenance of an ancestral Tekay distribution with a species-specific accumulation of other repeats.
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Affiliation(s)
- Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Tiago Ribeiro
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
- Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Av. Fernando Correa da Costa, 2.367, Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | | | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Gwilym P Lewis
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil.
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Bolsheva NL, Melnikova NV, Kirov IV, Dmitriev AA, Krasnov GS, Amosova АV, Samatadze TE, Yurkevich OY, Zoshchuk SA, Kudryavtseva AV, Muravenko OV. Characterization of repeated DNA sequences in genomes of blue-flowered flax. BMC Evol Biol 2019; 19:49. [PMID: 30813893 PMCID: PMC6391757 DOI: 10.1186/s12862-019-1375-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Members of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes. Since such variability is determined mainly by the amount and composition of repeated sequences, we conducted a comparative study of the repeatomes of species from four sections forming a clade of blue-flowered flax. Based on the results of high-throughput genome sequencing performed in this study as well as available WGS data, bioinformatic analyses of repeated sequences from 12 flax samples were carried out using a graph-based clustering method. RESULTS It was found that the genomes of closely related species, which have a similar karyotype structure, are also similar in the repeatome composition. In contrast, the repeatomes of karyologically distinct species differed significantly, and no similar tandem-organized repeats have been identified in their genomes. At the same time, many common mobile element families have been identified in genomes of all species, among them, Athila Ty3/gypsy LTR retrotransposon was the most abundant. The 30-chromosome members of the sect. Linum (including the cultivated species L. usitatissimum) differed significantly from other studied species by a great number of satellite DNA families as well as their relative content in genomes. CONCLUSIONS The evolution of studied flax species was accompanied by waves of amplification of satellite DNAs and LTR retrotransposons. The observed inverse correlation between the total contents of dispersed repeats and satellite DNAs allowed to suggest a relationship between both classes of repeating sequences. Significant interspecific differences in satellite DNA sets indicated a high rate of evolution of this genomic fraction. The phylogenetic relationships between the investigated flax species, obtained by comparison of the repeatomes, agreed with the results of previous molecular phylogenetic studies.
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Affiliation(s)
- Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Аlexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Mlinarec J, Skuhala A, Jurković A, Malenica N, McCann J, Weiss-Schneeweiss H, Bohanec B, Besendorfer V. The Repetitive DNA Composition in the Natural Pesticide Producer Tanacetum cinerariifolium: Interindividual Variation of Subtelomeric Tandem Repeats. FRONTIERS IN PLANT SCIENCE 2019; 10:613. [PMID: 31156676 PMCID: PMC6532368 DOI: 10.3389/fpls.2019.00613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/25/2019] [Indexed: 05/02/2023]
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.), a plant species endemic to the east Adriatic coast, is used worldwide for production of the organic insecticide, pyrethrin. Most studies concerning Dalmatian pyrethrum have focused on its morphological and biochemical traits relevant for breeding. However, little is known about the chromosomal evolution and genome organization of this species. Our study aims are to identify, classify, and characterize repetitive DNA in the T. cinerariifolium genome using clustering analysis of a low coverage genomic dataset. Repetitive DNA represents about 71.63% of the genome. T. cinerariifolium exhibits linked 5S and 35S rDNA configuration (L-type). FISH reveals amplification of interstitial telomeric repeats (ITRs) in T. cinerariifolium. Of the three newly identified satellite DNA families, TcSAT1 and TcSAT2 are located subterminally on most of T. cinerariifolium chromosomes, while TcSAT3 family is located intercalary within the longer arm of two chromosome pairs. FISH reveals high levels of polymorphism of the TcSAT1 and TcSAT2 sites by comparative screening of 28 individuals. TcSAT2 is more variable than TcSAT1 regarding the number and position of FISH signals. Altogether, our data highlights the dynamic nature of DNA sequences associated with subtelomeres in T. cinerariifolium and suggests that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
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Affiliation(s)
- Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | - Ana Skuhala
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Jamie McCann
- Institute of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | | | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
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Ishchenko OO, Panchuk ІІ, Andreev ІO, Kunakh VA, Volkov RA. Molecular Organization of 5S Ribosomal DNА of Deschapmpsia antarctica. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718060105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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