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Kroupin PY, Yurkina AI, Ulyanov DS, Karlov GI, Divashuk MG. Comparative Characterization of Pseudoroegneria libanotica and Pseudoroegneria tauri Based on Their Repeatome Peculiarities. PLANTS (BASEL, SWITZERLAND) 2023; 12:4169. [PMID: 38140496 PMCID: PMC10747672 DOI: 10.3390/plants12244169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Pseudoroegneria species play an important role among Triticeae grasses, as they are the putative donors of the St genome in many polyploid species. Satellite repeats are widely used as a reliable tool for tracking evolutionary changes because they are distributed throughout the genomes of plants. The aim of our work is to perform a comparative characterization of the repeatomes of the closely related species Ps. libanotica and Ps. tauri, and Ps. spicata was also included in the analysis. The overall repeatome structures of Ps. libanotica, Ps. tauri, and Ps. spicata were similar, with some individual peculiarities observed in the abundance of the SIRE (Ty1/Copia) retrotransposons, Mutator and Harbinger transposons, and satellites. Nine new satellite repeats that have been identified from the whole-genome sequences of Ps. spicata and Ps. tauri, as well as the CL244 repeat that was previously found in Aegilops crassa, were localized to the chromosomes of Ps. libanotica and Ps. tauri. Four satellite repeats (CL69, CL101, CL119, CL244) demonstrated terminal and/or distal localization, while six repeats (CL82, CL89, CL168, CL185, CL192, CL207) were pericentromeric. Based on the obtained results, it can be assumed that Ps. libanotica and Ps. tauri are closely related species, although they have individual peculiarities in their repeatome structures and patterns of satellite repeat localization on chromosomes. The evolutionary fate of the identified satellite repeats and their related sequences, as well as their distribution on the chromosomes of Triticeae species, are discussed. The newly developed St genome chromosome markers developed in the present research can be useful in population studies of Ps. libanotica and Ps. tauri; auto- and allopolyploids that contain the St genome, such as Thinopyrum, Elymus, Kengyilia, and Roegneria; and wide hybrids between wheat and related wild species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
- Federal Research Center “Nemchinovka”, Bolshoi Blvd., 30 Bld. 1, Skolkovo Innovation Center, 121205 Moscow, Russia
- National Research Center “Kurchatov Institute”, Kurchatov Sq., 1, 123182 Moscow, Russia
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Badaeva ED, Kotseruba VV, Fisenko AV, Chikida NN, Belousova MK, Zhurbenko PM, Surzhikov SA, Dragovich AY. Intraspecific divergence of diploid grass Aegilopscomosa is associated with structural chromosome changes. COMPARATIVE CYTOGENETICS 2023; 17:75-112. [PMID: 37304148 PMCID: PMC10252141 DOI: 10.3897/compcytogen.17.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/24/2023] [Indexed: 06/13/2023]
Abstract
Aegilopscomosa Smith in Sibthorp et Smith, 1806 is diploid grass with MM genome constitution occurring mainly in Greece. Two morphologically distinct subspecies - Ae.c.comosa Chennaveeraiah, 1960 and Ae.c.heldreichii (Holzmann ex Boissier) Eig, 1929 are discriminated within Ae.comosa, however, genetic and karyotypic bases of their divergence are not fully understood. We used Fluorescence in situ hybridization (FISH) with repetitive DNA probes and electrophoretic analysis of gliadins to characterize the genome and karyotype of Ae.comosa to assess the level of their genetic diversity and uncover mechanisms leading to radiation of subspecies. We show that two subspecies differ in size and morphology of chromosomes 3M and 6M, which can be due to reciprocal translocation. Subspecies also differ in the amount and distribution of microsatellite and satellite DNA sequences, the number and position of minor NORs, especially on 3M and 6M, and gliadin spectra mainly in the a-zone. Frequent occurrence of hybrids can be caused by open pollination, which, along with genetic heterogeneity of accessions and, probably, the lack of geographic or genetic barrier between the subspecies, may contribute to extremely broad intraspecific variation of GAAn and gliadin patterns in Ae.comosa, which are usually not observed in endemic plant species.
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Affiliation(s)
- Ekaterina D. Badaeva
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, GSP-1, Moscow 119991, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscowRussia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, GSP-1, Moscow 119334, RussiaN.I.Vavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Violetta V. Kotseruba
- Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova str. 2, Saint Petersburg 197376, RussiaKomarov Botanical Institute, Russian Academy of SciencesSaint PetersburgRussia
| | - Andnrey V. Fisenko
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, GSP-1, Moscow 119991, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscowRussia
| | - Nadezhda N. Chikida
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Ministry of Science and Higher Education, Bolshaya Morskaya str. 42-44, Saint Petersburg 190000, RussiaN.I. Vavilov Institute of Plant Genetic Resources (VIR), Ministry of Science and Higher EducationSaint PetersburgRussia
| | - Maria Kh. Belousova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Ministry of Science and Higher Education, Bolshaya Morskaya str. 42-44, Saint Petersburg 190000, RussiaN.I. Vavilov Institute of Plant Genetic Resources (VIR), Ministry of Science and Higher EducationSaint PetersburgRussia
| | - Peter M. Zhurbenko
- Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova str. 2, Saint Petersburg 197376, RussiaKomarov Botanical Institute, Russian Academy of SciencesSaint PetersburgRussia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, GSP-1, Moscow 119334, RussiaN.I.Vavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Alexandra Yu. Dragovich
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, GSP-1, Moscow 119991, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscowRussia
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Šatović-Vukšić E, Plohl M. Satellite DNAs-From Localized to Highly Dispersed Genome Components. Genes (Basel) 2023; 14:genes14030742. [PMID: 36981013 PMCID: PMC10048060 DOI: 10.3390/genes14030742] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes' diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.
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Affiliation(s)
- Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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Divashuk MG, Nikitina EA, Sokolova VM, Yurkina AI, Kocheshkova AA, Razumova OV, Karlov GI, Kroupin PY. qPCR as a Selective Tool for Cytogenetics. PLANTS (BASEL, SWITZERLAND) 2022; 12:80. [PMID: 36616209 PMCID: PMC9824742 DOI: 10.3390/plants12010080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
qPCR is widely used in quantitative studies of plant genomes and transcriptomes. In this article, this method is considered as an auxiliary step in the preparation and selection of markers for FISH analysis. Several cases from the authors' research on populations of the same species were reviewed, and a comparison of the closely related species, as well as the adaptation of the markers, based on satellite tandem repeats (TRs) using quantitative qPCR data was conducted. In the selected cases, TRs with contrast abundance were identified in the cases of the Dasypyrum, Thinopyrum and Aegilops species, and the transfer of TRs between the wheat and related species was demonstrated. TRs with intraspecific copy number variation were revealed in Thinopyrum ponticum and wheat-wheatgrass partial amphidiploids, and the TR showing predominant hybridization to the sea buckthorn Y chromosome was identified. Additionally, problems such as the absence of a reference gene for qPCR, and low-efficiency and self-complementary primers, were illustrated. In the cases considered here, the qPCR results clearly show high correlation with the subsequent results of the FISH analysis, which confirms the value of this method for cytogenetic studies.
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