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Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae). PLANTS 2022; 11:plants11172244. [PMID: 36079625 PMCID: PMC9460151 DOI: 10.3390/plants11172244] [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: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data.
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Moreno-Aguilar MF, Inda LA, Sánchez-Rodríguez A, Arnelas I, Catalán P. Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages. FRONTIERS IN PLANT SCIENCE 2022; 13:901733. [PMID: 35845705 PMCID: PMC9284676 DOI: 10.3389/fpls.2022.901733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses.
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Affiliation(s)
| | - Luis A. Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Instituto Agroalimentario de Aragón, Universidad de Zaragoza, Centro de Investigación y Tecnología Agroalimentaria, Zaragoza, Spain
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Itziar Arnelas
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - 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, Universidad de Zaragoza, Unidad Asociada al CSIC, Zaragoza, Spain
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Yurkevich OY, Samatadze TE, Selyutina IY, Suprun NA, Suslina SN, Zoshchuk SA, Amosova AV, Muravenko OV. Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:865958. [PMID: 35574118 PMCID: PMC9101955 DOI: 10.3389/fpls.2022.865958] [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: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20-24% (Class I) and about 2-2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5-10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia.
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Affiliation(s)
- Olga Yu. Yurkevich
- 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
- Peoples’ Friendship University of Russia, Moscow, Russia
| | - Inessa Yu. Selyutina
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | | | - Alexandra V. Amosova
- 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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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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Zwyrtková J, Blavet N, Doležalová A, Cápal P, Said M, Molnár I, Vrána J, Doležel J, Hřibová E. Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers. Int J Mol Sci 2022; 23:ijms23063191. [PMID: 35328613 PMCID: PMC8948999 DOI: 10.3390/ijms23063191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Crested wheatgrass (Agropyron cristatum), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Its wider use is hampered by limited knowledge of its complex genome. In this work, individual chromosomes were purified by flow sorting, and DNA shotgun sequencing was performed. The annotation of chromosome-specific sequences characterized the DNA-repeat content and led to the identification of genic sequences. Among them, genic sequences homologous to genes conferring plant disease resistance and involved in plant tolerance to biotic and abiotic stress were identified. Genes belonging to the important groups for breeders involved in different functional categories were found. The analysis of the DNA-repeat content identified a new LTR element, Agrocen, which is enriched in centromeric regions. The colocalization of the element with the centromeric histone H3 variant CENH3 suggested its functional role in the grass centromere. Finally, 159 polymorphic simple-sequence-repeat (SSR) markers were identified, with 72 of them being chromosome- or chromosome-arm-specific, 16 mapping to more than one chromosome, and 71 mapping to all the Agropyron chromosomes. The markers were used to characterize orthologous relationships between A. cristatum and common wheat that will facilitate the introgression breeding of wheat using A. cristatum.
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Šimoníková D, Čížková J, Zoulová V, Christelová P, Hřibová E. Advances in the Molecular Cytogenetics of Bananas, Family Musaceae. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040482. [PMID: 35214815 PMCID: PMC8879896 DOI: 10.3390/plants11040482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 05/03/2023]
Abstract
The banana is a staple food crop and represents an important trade commodity for millions of people living in tropical and subtropical countries. The most important edible banana clones originated from natural crosses between diploid Musa balbisiana and various subspecies of M. acuminata. It is worth mentioning that evolution and speciation in the Musaceae family were accompanied by large-scale chromosome structural changes, indicating possible reasons for lower fertility or complete sterility of these vegetatively propagated clones. Chromosomal changes, often accompanied by changes in genome size, are one of the driving forces underlying speciation in plants. They can clarify the genomic constitution of edible bananas and shed light on their origin and on diversification processes in members of the Musaceae family. This article reviews the development of molecular cytogenetic approaches, ranging from classical fluorescence in situ hybridization (FISH) using common cytogenetic markers to oligo painting FISH. We discuss differences in genome size and chromosome number across the Musaceae family in addition to the development of new chromosome-specific cytogenetic probes and their use in genome structure and comparative karyotype analysis. The impact of these methodological advances on our knowledge of Musa genome evolution at the chromosomal level is demonstrated. In addition to citing published results, we include our own new unpublished results and outline future applications of molecular cytogenetics in banana research.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Veronika Zoulová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Pavla Christelová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
- Correspondence: ; Tel.: +420-585-238-713
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Chumová Z, Mandáková T, Trávníček P. On the Origin of Tetraploid Vernal Grasses ( Anthoxanthum) in Europe. Genes (Basel) 2021; 12:966. [PMID: 34202779 PMCID: PMC8308110 DOI: 10.3390/genes12070966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
Polyploidy has played a crucial role in the evolution of many plant taxa, namely in higher latitudinal zones. Surprisingly, after several decades of an intensive research on polyploids, there are still common polyploid species whose evolutionary history is virtually unknown. Here, we addressed the origin of sweet vernal grass (Anthoxanthum odoratum) using flow cytometry, DNA sequencing, and in situ hybridization-based cytogenetic techniques. An allotetraploid and polytopic origin of the species has been verified. The chromosome study reveals an extensive variation between the European populations. In contrast, an autopolyploid origin of the rarer tetraploid vernal grass species, A. alpinum, has been corroborated. Diploid A. alpinum played an essential role in the polyploidization of both European tetraploids studied.
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Affiliation(s)
- Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, CZ-242 53 Průhonice, Czech Republic;
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00 Prague, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, CZ-625 00 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-625 00 Brno, Czech Republic
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, CZ-242 53 Průhonice, Czech Republic;
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Cabral-de-Mello DC, Zrzavá M, Kubíčková S, Rendón P, Marec F. The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths. Front Genet 2021; 12:661417. [PMID: 33859676 PMCID: PMC8042265 DOI: 10.3389/fgene.2021.661417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.
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Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, Brazil.,Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Magda Zrzavá
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | | | - Pedro Rendón
- IAEA-TCLA-Consultant-USDA-APHIS-Moscamed Program Guatemala, Guatemala City, Guatemala
| | - František Marec
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
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Kuo YT, Ishii T, Fuchs J, Hsieh WH, Houben A, Lin YR. The Evolutionary Dynamics of Repetitive DNA and Its Impact on the Genome Diversification in the Genus Sorghum. FRONTIERS IN PLANT SCIENCE 2021; 12:729734. [PMID: 34475879 PMCID: PMC8407070 DOI: 10.3389/fpls.2021.729734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/23/2021] [Indexed: 05/11/2023]
Abstract
Polyploidization is an evolutionary event leading to structural changes of the genome(s), particularly allopolyploidization, which combines different genomes of distinct species. The tetraploid species, Sorghum halepense, is assumed an allopolyploid species formed by hybridization between diploid S. bicolor and S. propinquum. The repeat profiles of S. bicolor, S. halepense, and their relatives were compared to elucidate the repeats' role in shaping their genomes. The repeat frequencies and profiles of the three diploid accessions (S. bicolor, S. bicolor ssp. verticilliflorum, and S. bicolor var. technicum) and two tetraploid accessions (S. halepense) are similar. However, the polymorphic distribution of the subtelomeric satellites preferentially enriched in the tetraploid S. halepense indicates drastic genome rearrangements after the allopolyploidization event. Verified by CENH3 chromatin immunoprecipitation (ChIP)-sequencing and fluorescence in situ hybridization (FISH) analysis the centromeres of S. bicolor are mainly composed of the abundant satellite SorSat137 (CEN38) and diverse CRMs, Athila of Ty3_gypsy and Ty1_copia-SIRE long terminal repeat (LTR) retroelements. A similar centromere composition was found in S. halepense. The potential contribution of S. bicolor in the formation of tetraploid S. halepense is discussed.
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Affiliation(s)
- Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Wei-Hsun Hsieh
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- *Correspondence: Andreas Houben,
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- World Vegetable Center, Tainan, Taiwan
- Yann-Rong Lin,
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