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Luo X, Liu Y, Gong X, Ye M, Xiao Q, Zeng Z. Karyotype Description and Comparative Chromosomal Mapping of 5S rDNA in 42 Species. Genes (Basel) 2024; 15:647. [PMID: 38790276 PMCID: PMC11121585 DOI: 10.3390/genes15050647] [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: 02/29/2024] [Revised: 04/29/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
This study was conducted to evaluate the 5S rDNA site number, position, and origin of signal pattern diversity in 42 plant species using fluorescence in situ hybridization. The species were selected based on the discovery of karyotype rearrangement, or because 5S rDNA had not yet been explored the species. The chromosome number varied from 14 to 160, and the chromosome length ranged from 0.63 to 6.88 μm, with 21 species having small chromosomes (<3 μm). The chromosome numbers of three species and the 5S rDNA loci of nineteen species are reported for the first time. Six 5S rDNA signal pattern types were identified. The 5S rDNA varied and was abundant in signal site numbers (2-18), positions (distal, proximal, outside of chromosome arms), and even in signal intensity. Variation in the numbers and locations of 5S rDNA was observed in 20 species, whereas an extensive stable number and location of 5S rDNA was found in 22 species. The potential origin of the signal pattern diversity was proposed and discussed. These data characterized the variability of 5S rDNA within the karyotypes of the 42 species that exhibited chromosomal rearrangements and provided anchor points for genetic physical maps.
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Affiliation(s)
- Xiaomei Luo
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.G.); (M.Y.)
| | - Yunke Liu
- Chengdu Academy of Agriculture and Forestry Sciences, Nongke Road 200, Wenjiang District, Chengdu 611130, China; (Y.L.); (Q.X.); (Z.Z.)
| | - Xiao Gong
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.G.); (M.Y.)
| | - Meng Ye
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.G.); (M.Y.)
| | - Qiangang Xiao
- Chengdu Academy of Agriculture and Forestry Sciences, Nongke Road 200, Wenjiang District, Chengdu 611130, China; (Y.L.); (Q.X.); (Z.Z.)
| | - Zhen Zeng
- Chengdu Academy of Agriculture and Forestry Sciences, Nongke Road 200, Wenjiang District, Chengdu 611130, China; (Y.L.); (Q.X.); (Z.Z.)
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Amosova AV, Gnutikov AA, Rodionov AV, Loskutov IG, Nosov NN, Yurkevich OY, Samatadze TE, Zoshchuk SA, Muravenko OV. Genome Variability in Artificial Allopolyploid Hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu Based on Marker Sequences of Satellite DNA and the ITS1-5.8S rDNA Region. Int J Mol Sci 2024; 25:5534. [PMID: 38791572 PMCID: PMC11122565 DOI: 10.3390/ijms25105534] [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: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S-ITS1-5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes in the studied karyotypes, determine their subgenomic affiliation, and detect several chromosome rearrangements. Based on the obtained cytogenomic data, we revealed differences between two A. macrostachya subgenomes and demonstrated that only one of them was inherited in the studied octoploid hybrids. Ribotype analyses showed that the second major ribotype of A. macrostachya was species-specific and was not represented in rDNA pools of the octoploids, which could be related to the allopolyploid origin of this species. Our results indicate that the use of marker satDNAs in cytogenomic studies can provide important data on genomic relationships within Avena allopolyploid species and hybrids, and also expand the potential for interspecific crosses for breeding.
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Affiliation(s)
- Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander A. Gnutikov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Alexander V. Rodionov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Igor G. Loskutov
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Nikolai N. Nosov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
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Park HW, Sevilleno SS, Ha MKTT, Cabahug-Braza RA, Yi JH, Lim KB, Cho W, Hwang YJ. The Application of Fluorescence In Situ Hybridization in the Prescreening of Veronica Hybrids. PLANTS (BASEL, SWITZERLAND) 2024; 13:1264. [PMID: 38732480 PMCID: PMC11085602 DOI: 10.3390/plants13091264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Fluorescence in situ hybridization (FISH), a molecular cytogenetic technique that enables the visualization and identification of specific DNA sequences within chromosomes, has emerged as a pivotal tool in plant breeding programs, particularly in the case of Veronica species. Veronica, a genus with a complex reproductive system, often poses challenges in accurately identifying hybrids because of its tendency to hybridize, which leads to intricate genetic variation. This study focused on the use of FISH as a prescreening method to identify true hybrids in Veronica breeding programs. FISH analysis was first performed on the parents to identify their 45S and 5S rDNA signals, along with their respective chromosome numbers. The signals were then compared with those of the twenty progenies with reference to their supposed parents. Five true hybrids, seven self-pollinated progenies, and eight false hybrids were identified through FISH. The findings highlight the significance of FISH as a screening method that contributes significantly to the efficiency of Veronica breeding programs by ensuring the preservation of desired genetic traits and minimizing the inadvertent inclusion of misidentified hybrids. To conclude, this study underscores the vital role of FISH in enhancing the precision and success of breeding programs and opens new avenues for improved breeding strategies and crop development.
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Affiliation(s)
- Hye-Wan Park
- Department of Convergence Science, Sahmyook University, Seoul 01795, Republic of Korea; (H.-W.P.); (S.S.S.)
| | - Samantha Serafin Sevilleno
- Department of Convergence Science, Sahmyook University, Seoul 01795, Republic of Korea; (H.-W.P.); (S.S.S.)
| | - My Khanh Tran Thi Ha
- Institute for Global Health Innovations, Duy Tan University, Danang 550000, Vietnam;
| | | | - Ji-Hun Yi
- Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea;
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Wonwoo Cho
- Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea;
| | - Yoon-Jung Hwang
- Department of Convergence Science, Sahmyook University, Seoul 01795, Republic of Korea; (H.-W.P.); (S.S.S.)
- Plant Genetics and Breeding Institute, Sahmyook University, Seoul 01795, Republic of Korea;
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Kalfusová R, Herklotz V, Kumke K, Houben A, Kovařík A, Ritz CM, Lunerová J. Epigenetic histone H3 phosphorylation marks discriminate between univalent- and bivalent-forming chromosomes during canina asymmetrical meiosis. ANNALS OF BOTANY 2024; 133:435-446. [PMID: 38127060 PMCID: PMC11006542 DOI: 10.1093/aob/mcad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND AND AIMS Dogroses (Rosa sect. Caninae) are mostly pentaploid, bearing 2n = 5x = 35 chromosomes in somatic cells. They evolved a unique form of asymmetrical meiosis characterized by two types of chromosomes: (1) chromosomes forming bivalents and distributed in the normal sexual way; and (2) chromosomes occurring as univalents and transferred by a female gamete only. In the mature pollen of pentaploid species, seven bivalent-derived chromosomes are transmitted to offspring, and 21 unpaired univalent chromosomes are eliminated during microsporogenesis. To discriminate between bivalent- and univalent-forming chromosomes, we studied histone H3 phosphorylation patterns regulating meiotic chromosome condensation and segregation. METHODS We analysed histone modification patterns during male canina meiosis in two representative dogrose species, 5x Rosa canina and 5x Rosa rubiginosa, by immunohistochemical and molecular cytogenetics approaches. Immunostaining of meiotic cells included α-tubulin, histone H3 phosphorylation (H3S10p, H3S28p and H3T3p) and methylation (H3K4me3 and H3K27me3) marks. In addition, fluorescent in situ hybridization was carried out with an 18S rDNA probe. KEY RESULTS In the first meiotic division, univalent chromosomes underwent equational division into chromatids, while homologues in bivalents were segregated as regular dyads. In diakinesis, bivalent chromosomes displayed strong H3 phosphorylation signals in proximal regions, spreading to the rest of the chromosome. In contrast, in univalents, the H3 phosphorylation signals were weaker, occurring mostly outside proximal regions largely overlapping with the H3K4me3 signals. Reduced phosphorylation was associated with relative under-condensation of the univalent chromosomes, particularly at early diakinesis. CONCLUSIONS We hypothesize that the absence of pairing and/or recombination in univalent chromosomes negatively affects the histone H3 phosphorylation of their chromatin and perhaps the loading of meiotic-specific cohesins. This apparently destabilizes cohesion of sister chromatids, leading to their premature split in the first meiotic division.
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Affiliation(s)
- Radka Kalfusová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Veit Herklotz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Christiane M Ritz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
- Chair of Biodiversity of Higher Plants, Technical University Dresden, D-01069, Dresden, Germany
| | - Jana Lunerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
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Cardinali I, Ceccarelli M. Molecular and cytogenetic analyses in Geranium macrorrhizum L. wild Italian plants. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240035. [PMID: 38601032 PMCID: PMC11004676 DOI: 10.1098/rsos.240035] [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: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Geranium macrorrhizum L. is a herbaceous species native to southern Europe and was introduced in central Europe and North America. It is also widely distributed in Italy. In this study, molecular and cytogenetic analyses were carried out on 22 wild plants, collected in central and southern Italy, compared with five cultivated plants, with the main purpose to identify those living near the Marmore waterfalls in central Italy, recently described as the new species Geranium lucarinii. Four barcoding markers (rbcL, matK, trnH-psbA intergenic spacer and internal transcribed spacer region) were sequenced and their variability among the plants was evaluated. Chromosome numbers were determined and 45S rDNA was physically mapped by fluorescence in situ hybridization. Moreover, genomic affinity between wild and cultivated plants was evaluated by genomic in situ hybridization. The results of this study supported that all the plants belong to G. macrorrhizum, including the Marmore population. Barcoding analyses showed a close similarity among the wild plants, and a differentiation, although not significant, between the wild plants on one hand and the cultivated plants on the other. Integrated studies focusing on morphological, genetic and ecological characterization of a larger number of wild populations would allow us to know the extent of the variability within the species.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
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Garcia S, Kovarik A, Maiwald S, Mann L, Schmidt N, Pascual-Díaz JP, Vitales D, Weber B, Heitkam T. The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics. Mol Biol Evol 2024; 41:msae025. [PMID: 38306580 PMCID: PMC10946416 DOI: 10.1093/molbev/msae025] [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: 06/12/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Sophie Maiwald
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | | | - Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Beatrice Weber
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Austria
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7
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Jiang S, Cai Z, Wang Y, Zeng C, Zhang J, Yu W, Su C, Zhao S, Chen Y, Shen Y, Ma Y, Cai Y, Dai J. High plasticity of ribosomal DNA organization in budding yeast. Cell Rep 2024; 43:113742. [PMID: 38324449 DOI: 10.1016/j.celrep.2024.113742] [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] [Received: 07/20/2023] [Revised: 12/12/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
In eukaryotic genomes, rDNA generally resides as a highly repetitive and dynamic structure, making it difficult to study. Here, a synthetic rDNA array on chromosome III in budding yeast was constructed to serve as the sole source of rRNA. Utilizing the loxPsym site within each rDNA repeat and the Cre recombinase, we were able to reduce the copy number to as few as eight copies. Additionally, we constructed strains with two or three rDNA arrays and found that the presence of multiple arrays did not affect the formation of a single nucleolus. Although alteration of the position and number of rDNA arrays did impact the three-dimensional genome structure, the additional rDNA arrays had no deleterious influence on cell growth or transcriptomes. Overall, this study sheds light on the high plasticity of rDNA organization and opens up opportunities for future rDNA engineering.
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Affiliation(s)
- Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Zelin Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wang
- BGI Research, BGI, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Cheng Zeng
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiaying Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
| | - Wenfei Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenghao Su
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shijun Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, BGI, Shenzhen 518083, China
| | - Yue Shen
- BGI Research, BGI, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Road, Shenzhen 518055, China.
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Liu J, Lin X, Wang X, Feng L, Zhu S, Tian R, Fang J, Tao A, Fang P, Qi J, Zhang L, Huang Y, Xu J. Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus). BMC PLANT BIOLOGY 2024; 24:71. [PMID: 38267860 PMCID: PMC10809672 DOI: 10.1186/s12870-024-04739-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.
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Affiliation(s)
- Jiarui Liu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinyi Lin
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaojie Wang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Shixin Zhu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Runmeng Tian
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Aifen Tao
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pingping Fang
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianmin Qi
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwu Zhang
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongji Huang
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Jiantang Xu
- Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Mann L, Balasch K, Schmidt N, Heitkam T. High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly. BMC Genomics 2024; 25:109. [PMID: 38267856 PMCID: PMC10809544 DOI: 10.1186/s12864-023-09948-4] [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: 10/26/2023] [Accepted: 12/28/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative repeat consensuses be derived from unassembled genomes? RESULTS Here, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplification setups, and (3) specific repeat-centred questions, such as the linked vs. unlinked arrangement of ribosomal genes. In all our use cases, the derived consensuses are robust and representative. To evaluate overall performance, we compare our high-fidelity repeat consensuses to RepeatExplorer2-derived contigs and check, if they represent real transposable elements as found in long reads. Our results demonstrate that it is possible to generate useful, reliable and trustworthy consensuses from short reads by a combination from read cluster and genome assembly methods in an automatable way. CONCLUSION We anticipate that our workflow opens the way towards more efficient and less manual repeat characterization and annotation, benefitting all genome studies, but especially those of non-model organisms.
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Affiliation(s)
- Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Kristin Balasch
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany.
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, Graz, A-8010, Austria.
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10
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Islam-Faridi N, Hodnett GL, Zhebentyayeva T, Georgi LL, Sisco PH, Hebard FV, Nelson CD. Cyto-molecular characterization of rDNA and chromatin composition in the NOR-associated satellite in Chestnut (Castanea spp.). Sci Rep 2024; 14:980. [PMID: 38225361 PMCID: PMC10789788 DOI: 10.1038/s41598-023-45879-6] [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: 10/11/2022] [Accepted: 10/25/2023] [Indexed: 01/17/2024] Open
Abstract
The American chestnut (Castanea dentata, 2n = 2x = 24), once known as the "King of the Appalachian Forest", was decimated by chestnut blight during the first half of the twentieth century by an invasive fungus (Cryphonectria parasitica). The Chinese chestnut (C. mollissima, 2n = 2x = 24), in contrast to American chestnut, is resistant to this blight. Efforts are being made to transfer this resistance to American chestnut through backcross breeding and genetic engineering. Both chestnut genomes have been genetically mapped and recently sequenced to facilitate gene discovery efforts aimed at assisting molecular breeding and genetic engineering. To complement and extend this genomic work, we analyzed the distribution and organization of their ribosomal DNAs (35S and 5S rDNA), and the chromatin composition of the nucleolus organizing region (NOR)-associated satellites. Using fluorescent in situ hybridization (FISH), we have identified two 35S (one major and one minor) and one 5S rDNA sites. The major 35S rDNA sites are terminal and sub-terminal in American and Chinese chestnuts, respectively, originating at the end of the short arm of the chromosome, extending through the secondary constriction and into the satellites. An additional 5S locus was identified in certain Chinese chestnut accessions, and it was linked distally to the major 35S site. The NOR-associated satellite in Chinese chestnut was found to comprise a proximal region packed with 35S rDNA and a distinct distal heterochromatic region. In contrast, the American chestnut satellite was relatively small and devoid of the distal heterochromatic region.
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Affiliation(s)
- Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, Southern Institute of Forest Genetics, USDA Forest Service, Southern Research Station, Texas A&M University, College Station, TX, 77843, USA.
| | - George L Hodnett
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, 40546, USA
| | - Laura L Georgi
- Meadowview Research Farms, The American Chestnut Foundation, 29010 Hawthorne Drive, Meadowview, VA, 24361, USA
| | - Paul H Sisco
- The American Chestnut Foundation, 50 North Merrimon Ave., Suite 115, Asheville, NC, 28804, USA
| | - Frederick V Hebard
- Meadowview Research Farms, The American Chestnut Foundation, 29010 Hawthorne Drive, Meadowview, VA, 24361, USA
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Forest Health Research and Education Center, Lexington, KY, 40546, USA
- USDA Forest Service, Southern Institute of Forest Genetics, Harrison Experimental Forest, 23332 Success Road, Saucier, MS, 39574, USA
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11
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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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12
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Wang W, Zhang X, Garcia S, Leitch AR, Kovařík A. Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity (Edinb) 2023; 131:179-188. [PMID: 37402824 PMCID: PMC10462631 DOI: 10.1038/s41437-023-00634-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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Affiliation(s)
- Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | - Andrew R Leitch
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61200, Czech Republic.
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Dalíková M, Provazníková I, Provazník J, Grof-Tisza P, Pepi A, Nguyen P. The Role of Repetitive Sequences in Repatterning of Major Ribosomal DNA Clusters in Lepidoptera. Genome Biol Evol 2023; 15:evad090. [PMID: 37226278 PMCID: PMC10257491 DOI: 10.1093/gbe/evad090] [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: 05/31/2022] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Genes for major ribosomal RNAs (rDNA) are present in multiple copies mainly organized in tandem arrays. The number and position of rDNA loci can change dynamically and their repatterning is presumably driven by other repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second- and third-generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses among the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA into terminal regions of lepidopteran chromosomes as efficiency of ectopic recombination depends on the proximity of homologous sequences to telomeres.
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Affiliation(s)
- Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Provazník
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patrick Grof-Tisza
- Institute of Biology, Laboratory of Evolutionary Entomology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Adam Pepi
- Department of Biology, Tufts University
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
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14
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Ding X, Chen J, Dai C, Shi P, Pan H, Lin Y, Chen Y, Gong L, Chen L, Wu W, Qiu X, Xu J, Huang Z, Liao B. Developing population identification tool based on polymorphism of rDNA for traditional Chinese medicine: Artemisia annua L. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154882. [PMID: 37210961 DOI: 10.1016/j.phymed.2023.154882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Artemisia annua, a well-known traditional Chinese medicine, is the main source for production of artemisinin, an anti-malaria drug. A. annua is distributed globally, with great diversity of morphological characteristics and artemisinin contents. Diverse traits among A. annua populations impeded the stable production of artemisinin, which needs an efficient tool to identify strains and assess population genetic homogeneity. PURPOSE In this study, ribosomal DNA (rDNA), were characterized for A. annua for strains identification and population genetic homogeneity assessment. METHODS The ribosomal RNA (rRNA) genes were identified using cmscan and assembled using rDNA unit of LQ-9 as a reference. rDNA among Asteraceae species were compared performing with 45S rDNA. The rDNA copy number was calculated based on sequencing depth. The polymorphisms of rDNA sequences were identified with bam-readcount, and confirmed by Sanger sequencing and restriction enzyme experiment. The ITS2 amplicon sequencing was used to verify the stability of ITS2 haplotype analysis. RESULTS Different from other Asteraceae species, 45S and 5S linked-type rDNA was only found in Artemisia genus. Rich polymorphisms of copy number and sequence of rDNA were identified in A. annua population. The haplotype composition of internal transcribed spacer 2 (ITS2) region which had moderate sequence polymorphism and relative short size was significantly different among A. annua strains. A population discrimination method was developed based on ITS2 haplotype analysis with high-throughput sequencing. CONCLUSION This study provides comprehensive characteristics of rDNA and suggests that ITS2 haplotype analysis is ideal tool for A. annua strain identification and population genetic homogeneity assessment.
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Affiliation(s)
- Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jieting Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Chunyan Dai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Peiqi Shi
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hengyu Pan
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yanqi Lin
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yikang Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Lu Gong
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Linming Chen
- Guangzhou Huibiao Testing Technology Center, Guangzhou 510700, China
| | - Wenguang Wu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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15
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Dyomin A, Galkina S, Ilina A, Gaginskaya E. Single Copies of the 5S rRNA Inserted into 45S rDNA Intergenic Spacers in the Genomes of Nototheniidae (Perciformes, Actinopterygii). Int J Mol Sci 2023; 24:ijms24087376. [PMID: 37108537 PMCID: PMC10138776 DOI: 10.3390/ijms24087376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
In the vast majority of Animalia genomes, the 5S rRNA gene repeats are located on chromosomes outside of the 45S rDNA arrays of the nucleolar organiser (NOR). We analysed the genomic databases available and found that a 5S rDNA sequence is inserted into the intergenic spacer (IGS) between the 45S rDNA repeats in ten species of the family Nototheniidae (Perciformes, Actinopterigii). We call this sequence the NOR-5S rRNA gene. Along with Testudines and Crocodilia, this is the second case of a close association between four rRNA genes within one repetitive unit in deuterostomes. In both cases, NOR-5S is oriented opposite the 45S rDNA. None of the three nucleotide substitutions compared to the canonical 5S rRNA gene influenced the 5S rRNA secondary structure. In transcriptomes of the Patagonian toothfish, we only found NOR-5S rRNA reads in ovaries and early embryos, but not in testis or somatic tissues of adults. Thus, we consider the NOR-5S gene to be a maternal-type 5S rRNA template. The colocalization of the 5S and 45S ribosomal genes appears to be essential for the equimolar production of all four rRNAs in the species that show rDNA amplification during oogenesis. Most likely, the integration of 5S and NOR rRNA genes occurred prior to Nototheniidae lineage diversification.
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Affiliation(s)
- Alexander Dyomin
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
| | - Svetlana Galkina
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
| | - Arina Ilina
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
| | - Elena Gaginskaya
- Biological Faculty, St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia
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Almeida B, Malcher S, Costa M, Martins J, Procópio R, Noronha R, Nagamachi C, Pieczarka J. High Chromosomal Reorganization and Presence of Microchromosomes in Chactidae Scorpions from the Brazilian Amazon. BIOLOGY 2023; 12:biology12040563. [PMID: 37106763 PMCID: PMC10135684 DOI: 10.3390/biology12040563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 04/29/2023]
Abstract
Scorpions are of particular interest in cytogenomic studies, as they can present a high incidence of chromosomal rearrangements heterozygous in natural populations. In this study, we cytogenetically analyzed four species of Chactidae. In Brotheas, 2n = 40 was observed in Brotheas silvestris, 2n = 48 in Brotheas paraensis, and 2n = 50 (cytotype A) or 2n = 52 (cytotype B) among populations of Brotheas amazonicus. Our results showed a bimodal karyotype in Neochactas parvulus, 2n = 54, with microchromosomes and a concentration of constitutive heterochromatin in macrochromosomes. The 45S rDNA is located in only one pair of the karyotype, with different heteromorphisms of clusters of this rDNA in the cytotype B of B. amazonicus, with NOR-bearing chromosomes involved in multi-chromosomal associations during meiosis I. The U2 snDNA was mapped in the interstitial region of distinct karyotype pairs of three Chactidae species. Our results indicate the possible formation of cryptic species in B. amazonicus; the different 45S rDNA configurations in the genome of this species may result from amplification and degeneration. We suggest that the bimodal karyotype in N. parvulus results from fusion/fission events and that the unequal distribution of repetitive DNAs between macro and microchromosomes contributes to the maintenance of its asymmetry.
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Affiliation(s)
- Bruno Almeida
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Av. Perimetral da Ciência, km 01, Guamá, Belém 66075-750, PA, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Pará-Campus Itaituba, R. Universitário, s/n, Maria Magdalena, Itaituba 68183-300, PA, Brazil
| | - Stella Malcher
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Av. Perimetral da Ciência, km 01, Guamá, Belém 66075-750, PA, Brazil
| | - Marlyson Costa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Av. Perimetral da Ciência, km 01, Guamá, Belém 66075-750, PA, Brazil
| | - Jonas Martins
- Instituto Nacional de Pesquisas da Amazonia, Av. André Araújo, 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Rudi Procópio
- Medical School, Universidade do Estado do Amazonas, Av. Carvalho Leal, 1777, Cachoeirinha, Manaus 69065-170, AM, Brazil
| | - Renata Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Av. Perimetral da Ciência, km 01, Guamá, Belém 66075-750, PA, Brazil
| | - Cleusa Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Av. Perimetral da Ciência, km 01, Guamá, Belém 66075-750, PA, Brazil
| | - Julio Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Av. Perimetral da Ciência, km 01, Guamá, Belém 66075-750, PA, Brazil
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17
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Yao TL, Nazre M, McKey D, Jalonen R, Duminil J. The origin of cultivated mangosteen ( Garcinia mangostana L. var. mangostana): Critical assessments and an evolutionary-ecological perspective. Ecol Evol 2023; 13:e9792. [PMID: 36937066 PMCID: PMC10020034 DOI: 10.1002/ece3.9792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 03/18/2023] Open
Abstract
Mangosteen (Garcinia mangostana var. mangostana) is a popular tropical fruit, yet many aspects of its biology and evolutionary history are little known. Its origin remains contentious, although recent findings suggest G. mangostana L. var. malaccensis (Hook. f.) Nazre (synonym: G. malaccensis Hook. f.) as the sole progenitor. We review hypotheses on the origin of mangosteen and clarify points that have been affected by errors of fact and interpretation. The narrow focus and lack of detail in published results make their interpretation difficult. When possible, we support our interpretations with field observations and examination of herbarium specimens. We outline the main biological traits (e.g., dioecy, facultative apomixis, and polyploidy) of mangosteen and its wild relatives to infer traits that might have evolved during domestication of mangosteen. We find no clear indication that apomixis and polyploidy evolved during domestication. Polyploidy is known in the wild relatives, but apomixis has not yet been demonstrated. Also, we propose a testable new evolutionary-ecological framework that we call "Forest-Dusun Interface" to infer processes in the origin of mangosteen. Dusun (Malay) refers to subsistence orchards in this context. Lastly, we propose future studies to address identified knowledge gaps.
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Affiliation(s)
- T. L. Yao
- DIADEUniversity of Montpellier, IRD, CIRADMontpellierFrance
- Faculty of Forestry and EnvironmentUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Forestry and Environment DivisionForest Research Institute MalaysiaKepongSelangorMalaysia
| | - M. Nazre
- Faculty of Forestry and EnvironmentUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - D. McKey
- CEFE, University of Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - R. Jalonen
- Alliance of Bioversity International and CIATAsia – Malaysia Office, c/o WorldFish HeadquartersPenangMalaysia
| | - J. Duminil
- DIADEUniversity of Montpellier, IRD, CIRADMontpellierFrance
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18
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Joshi P, Ansari H, Dickson R, Ellison NW, Skema C, Tate JA. Polyploidy on islands - concerted evolution and gene loss amid chromosomal stasis. ANNALS OF BOTANY 2023; 131:33-44. [PMID: 35390127 PMCID: PMC9904340 DOI: 10.1093/aob/mcac051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/04/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Polyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand. METHODS We determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1, was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy. KEY RESULTS The chromosome number for all species investigated was 2n = 42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius, had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1, indicated that some lineages maintained three copies of the locus, while others have lost one or two copies. CONCLUSIONS Although island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing.
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Affiliation(s)
- Prashant Joshi
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Helal Ansari
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Rowan Dickson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Cynthia Skema
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Morris Arboretum of the University of Pennsylvania, Philadelphia, PA, USA
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Rodríguez-González R, Gutiérrez ML, Fuentes I, Gálvez-Prada F, Sochorová J, Kovařík A, Garcia S. Release 4.0 of the Plant rDNA Database: A Database on Plant Ribosomal DNA Loci Number, Their Position, and Organization: An Information Source for Comparative Cytogenetics. Methods Mol Biol 2023; 2703:237-245. [PMID: 37646950 DOI: 10.1007/978-1-0716-3389-2_18] [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: 09/01/2023]
Abstract
This paper presents the latest update to the Plant rDNA database (Release 4.0), a valuable resource for researchers in the field of plant cytogenetics. The database provides information on the number, position, and arrangement of ribosomal DNA loci in plants, including angiosperms, gymnosperms, bryophytes, and pteridophytes. The new release includes new data for 820 species coming from additional 173 papers. In the updated version of the Plant rDNA database, 4948 entries comprising 2760 organisms can be found. A brief guide on how to navigate the database and obtain the desired information is also provided. The regular updating of the database is important for ensuring the information it contains is accurate, up-to-date, and useful for the research community. The Plant rDNA database continues to be beneficial for phylogenetic and cytogenetic studies in a wide range of taxa including angiosperms, gymnosperms, and early diverging groups, such as bryophytes and lycophytes.
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Affiliation(s)
- Roi Rodríguez-González
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - María Luisa Gutiérrez
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Inés Fuentes
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
- Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Catalonia, Spain
| | | | - Jana Sochorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
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20
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Garcia S, Pascual-Díaz JP, Krumpolcová A, Kovarík A. Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol. Methods Mol Biol 2023; 2672:501-512. [PMID: 37335496 DOI: 10.1007/978-1-0716-3226-0_30] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The ribosomal RNA genes (rDNA) are universal genome components with a housekeeping function, given the crucial role of ribosomal RNA in the synthesis of ribosomes and thus for life-on-Earth. Therefore, their genomic organization is of considerable interest for biologists, in general. Ribosomal RNA genes have also been largely used to establish phylogenetic relationships, and to identify allopolyploid or homoploid hybridization.Here, we demonstrate how high-throughput sequencing data, through graph clustering implemented in RepeatExplorer2 pipeline ( https://repeatexplorer-elixir.cerit-sc.cz/galaxy/ ), can be helpful to decipher the genomic organization of 5S rRNA genes. We show that the linear shapes of cluster graphs are reminiscent to the linked organization of 5S and 35S rDNA (L-type arrangement) while the circular graphs correspond to their separate arrangement (S-type). We further present a simplified protocol based on the paper by (Garcia et al., Front Plant Sci 11:41, 2020) about the use of graph clustering of 5S rDNA homoeologs (S-type) to identify hybridization events in the species history. We found that the graph complexity (i.e., graph circularity in this case) is related to ploidy and genome complexity, with diploids typically showing circular-shaped graphs while allopolyploids and other interspecific hybrids display more complex graphs, with usually two or more interconnected loops representing intergenic spacers. When a three-genomic comparative clustering analysis from a given hybrid (homoploid/allopolyploid) and its putative progenitor species (diploids) is performed, it is possible to identify the corresponding homoeologous 5S rRNA gene families, and to elucidate the contribution of each putative parental genome to the 5S rDNA pool of the hybrid. Thus, the analysis of 5S rDNA cluster graphs by RepeatExplorer, together with information coming from other sources (e.g., morphology, cytogenetics) is a complementary approach for the determination of allopolyploid or homoploid hybridization and even ancient introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alice Krumpolcová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ales Kovarík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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21
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Yücel G, Senderowicz M, Kolano B. The Use of Ribosomal DNA for Comparative Cytogenetics. Methods Mol Biol 2023; 2672:265-284. [PMID: 37335483 DOI: 10.1007/978-1-0716-3226-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) sequences provides excellent chromosome markers for comparative cytogenetic analyses, especially in non-model plant species. The tandem repeat nature of a sequence and the presence of a highly conserved genic region make rDNA sequences relatively easy to isolate and clone. In this chapter, we describe the use of rDNA as markers for comparative cytogenetics studies. Traditionally, cloned probes labeled with Nick-translation have been used to detect rDNA loci. Recently, pre-labeled oligonucleotides are also employed quite frequently to detect both 35S and 5S rDNA loci. Ribosomal DNA sequences, together with other DNA probes in FISH/GISH or with fluorochromes such as CMA3 banding or silver staining, are very useful tools in comparative analyses of plant karyotypes.
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Affiliation(s)
- Gülru Yücel
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
| | - Magdalena Senderowicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bożena Kolano
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
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22
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Belyakov EA, Mikhaylova YV, Machs EM, Zhurbenko PM, Rodionov AV. Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing. Sci Rep 2022; 12:21610. [PMID: 36517537 PMCID: PMC9750990 DOI: 10.1038/s41598-022-25954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Sparganium is an emergent aquatic macrophyte widely spread in temperate and subtropical zones. Taxa of this genus feature high phenotypic plasticity and can produce interspecific hybrids. By means of high-throughput sequencing of the internal transcribed spacer (ITS1) of 35S rDNA, the status of 15 Eurasian Sparganium species and subspecies was clarified and the role of hybridization events in the recent evolution of the genus was investigated. It has been shown that a number of species such as S. angustifolium, S. fallax and S. subglobosum have homogenized rDNA represented by one major ribotype. The rDNA of other taxa is represented by two or more major ribotypes. Species with high rDNA heterogeneity are apparently of hybrid origin. Based on the differences in rDNA patterns, intraspecific diversity was identified in S. probatovae and S. emersum. Thus, we have concluded that Sparganium has extensive interspecific hybridization at the subgenus level, and there may also be occasional hybridization between species from different subgenera.
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Affiliation(s)
- Evgeny A. Belyakov
- grid.464570.40000 0001 1092 3616Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl Region, Nekouz District, 109, Borok, Russia 152742 ,grid.446199.70000 0000 8543 3323Cherepovets State University, Lunacharsky Ave., 5, Cherepovets, Russia 162600
| | - Yulia V. Mikhaylova
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Eduard M. Machs
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Peter M. Zhurbenko
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
| | - Aleksandr V. Rodionov
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
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23
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Samatadze TE, Yurkevich OY, Khazieva FM, Basalaeva IV, Konyaeva EA, Burova AE, Zoshchuk SA, Morozov AI, Amosova AV, Muravenko OV. Agro-Morphological and Cytogenetic Characterization of Colchicine-Induced Tetraploid Plants of Polemonium caeruleum L. (Polemoniaceae). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192585. [PMID: 36235449 PMCID: PMC9570621 DOI: 10.3390/plants11192585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 06/12/2023]
Abstract
Polemonium caeruleum L. (Polemoniaceae) is a valuable medicinal herb with a wide spectrum of biological activities. Under natural conditions, the productivity of this species is rather low. In this study, colchicine-induced tetraploid plants (2n = 4x = 36) of P. caeruleum were obtained, and for the first time, their morphological and cytogenetic characterization was performed. In the tetraploid plants, raw material productivity and also the content of triterpene saponins were significantly higher than in the control diploids. The analysis of chromosome behavior at meiosis and FISH chromosome mapping of 45S and 5S rDNA generally demonstrated stability of both genomes in the tetraploid plants. Based on chromosome morphology and distribution patterns of the studied molecular cytogenetic markers, all chromosome pairs in karyotypes were identified, and chromosome karyograms and idiograms of P. caeruleum were constructed. The revealed specific microdiagnostic characteristics of P. caeruleum (strongly sinuous cells and anomocytic stomata of the leaf epidermis, and also glandular hairs along the veins) could be useful for raw material identification. In the obtained tetraploids, the predominance of large stomata on the lower leaf epidermis was determined. The studied tetraploids can be used in various breeding programs to obtain high-quality pharmaceutical raw materials of P. caeruleum.
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Affiliation(s)
- Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Firdaus M. Khazieva
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Irina V. Basalaeva
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Elena A. Konyaeva
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Alla E. Burova
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Alexander I. Morozov
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
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24
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Karyotype Analysis, Genomic and Fluorescence In Situ Hybridization (GISH and FISH) Reveal the Ploidy and Parental Origin of Chromosomes in Paeonia Itoh Hybrids. Int J Mol Sci 2022; 23:ijms231911406. [PMID: 36232706 PMCID: PMC9570356 DOI: 10.3390/ijms231911406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Itoh hybrids are intersectional hybrids in Paeonia L. with sect. Moutan and sect. Paeonia as paternal and maternal parents, respectively. Therefore, these hybrids have herbaceous stems with improved ornamental value introduced by the paternal parent. Although both of their parents are diploids, Itoh hybrids are triploids. Moreover, the parental origin of their chromosomes has not been extensively studied. This study systematically analyzed the genome size, ploidy, and karyotype of Itoh hybrids and compared them with their parental taxa. Although the monoploid genome size of Itoh hybrids was different, it was not significantly different from that of the parents. However, the size of varieties in the two parental taxa was significantly different from the wild species, probably due to genome rearrangements caused by artificial selection. Further karyotype analysis, correlation analysis, and hierarchical clustering could not identify the parental origin of chromosomes in Itoh hybrids. Verification through genomic and fluorescence in situ hybridization (GISH and FISH) suggested that for the three sets of chromosomes in Itoh hybrids, two were from the paternal parent, and one was from the maternal parent. One of the first two sets was from wild species, and the other from a cultivated variety. GISH could not label the chromosomes of cultivated peonies from the sect. Moutan, probably due to the huge and complex genomes compared with the wild species. Meanwhile, 5S rDNA-based FISH was first applied in Paeonia, which may be used for ploidy assessment. This work may give insights into the utilization of Itoh hybrid resources.
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Yucel G, Betekhtin A, Cabi E, Tuna M, Hasterok R, Kolano B. The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae). Int J Mol Sci 2022; 23:ijms231911033. [PMID: 36232345 PMCID: PMC9570107 DOI: 10.3390/ijms231911033] [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: 09/05/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 02/02/2023] Open
Abstract
The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.
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Affiliation(s)
- Gulru Yucel
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55200, Turkey
- Department of Biology, Institute of Natural and Applied Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Evren Cabi
- Department of Biology, Faculty of Arts and Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Metin Tuna
- Department of Field Crops, Faculty of Agriculture, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Bozena Kolano
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
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26
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Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species ( Iris Series Chinenses, Iridaceae). Int J Mol Sci 2022; 23:ijms231810929. [PMID: 36142840 PMCID: PMC9504294 DOI: 10.3390/ijms231810929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 12/16/2022] Open
Abstract
The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.
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Mlinarec J, Boštjančić LL, Malenica N, Jurković A, Boland T, Yakovlev SS, Besendorfer V. Structure and Methylation of 35S rDNA in Allopolyploids Anemone multifida (2 n = 4 x = 32, BBDD) and Anemone baldensis (2 n = 6 x = 48, AABBDD) and Their Parental Species Show Evidence of Nucleolar Dominance. FRONTIERS IN PLANT SCIENCE 2022; 13:908218. [PMID: 35874014 PMCID: PMC9296772 DOI: 10.3389/fpls.2022.908218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/07/2022] [Indexed: 05/26/2023]
Abstract
Transcriptional silencing of 35S rDNA loci inherited from one parental species is occurring relatively frequently in allopolyploids. However, molecular mechanisms by which it is selected for transcriptional silencing remain unclear. We applied NGS, silver staining and bisulfite sequencing to study the structure, expression and methylation landscape of 35S rDNA in two allopolyploids of common origin, allotetraploid Anemone multifida (2n = 4x = 32, genome composition BBDD) and allohexaploid A. baldensis (2n = 6x = 48, AABBDD), and their genome donors, A. sylvestris (2n = 16, AA), A. cylindrica (2n = 16, BB) and A. parviflora (2n = 16, DD). The size of the recovered 35S rDNA units varied from 10,489 bp in A. cylindrica to 12,084 bp in A. sylvestris. Anemone showed an organization typical of most ribosomal 35S rDNA composed of NTS, ETS, rRNA genes, TTS and TIS with structural features of plant IGS sequences and all functional elements needed for rRNA gene activity. The NTS was more variable than the ETS and consisted of SRs which are highly variable among Anemone. Five to six CpG-rich islands were found within the ETS. CpG island located adjacent to the transcription initiation site (TIS) was highly variable regarding the sequence size and methylation level and exhibited in most of the species lower levels of methylation than CpG islands located adjacent to the 18S rRNA gene. Our results uncover hypomethylation of A. sylvestris- and A. parviflora-derived 35S rDNA units in allopolyploids A. multifida and A. baldensis. Hypomethylation of A. parviflora-derived 35S rDNA was more prominent in A. baldensis than in A. multifida. We showed that A. baldensis underwent coupled A. sylvestris-derived 35S rDNA array expansion and A. parviflora-derived 35S rDNA copy number decrease that was accompanied by lower methylation level of A. sylvestris-derived 35S rDNA units in comparison to A. parviflora-derived 35S rDNA units. These observations suggest that in A. baldensis nucleolar dominance is directed toward A. sylvestris-derived chromosomes. This work broadens our current knowledge of the 35S rDNA organization in Anemone and provides evidence of the progenitor-specific 35S rDNA methylation in nucleolar dominance.
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Affiliation(s)
| | - Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
- Department of Computer Science, ICube, UMR 7357, CNRS, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, Strasbourg, France
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Todd Boland
- Memorial University of Newfoundland’s Botanical Gardens, St. John’s, NL, Canada
| | - Sonja Siljak Yakovlev
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
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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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He J, Zhao Y, Zhang S, He Y, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Wang Z, Chen F, Wang H. Uneven Levels of 5S and 45S rDNA Site Number and Loci Variations across Wild Chrysanthemum Accessions. Genes (Basel) 2022; 13:genes13050894. [PMID: 35627279 PMCID: PMC9141308 DOI: 10.3390/genes13050894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/30/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosomal DNA (rDNA) is an excellent cytogenetic marker owing to its tandem arrangement and high copy numbers. However, comparative studies have focused more on the number of rDNA site variations within the Chrysanthemum genus, and studies on the types of rDNA sites with the same experimental procedures at the species levels are lacking. To further explore the number and types of rDNA site variations, we combined related data to draw ideograms of the rDNA sites of Chrysanthemum accessions using oligonucleotide fluorescence in situ hybridization (Oligo-FISH). Latent variations (such as polymorphisms of 45S rDNA sites and co-localized 5S-45S rDNA) also occurred among the investigated accessions. Meanwhile, a significant correlation was observed between the number of 5S rDNA sites and chromosome number. Additionally, the clumped and concentrated geographical distribution of different ploidy Chrysanthemum accessions may significantly promote the karyotype evolution. Based on the results above, we identified the formation mechanism of rDNA variations. Furthermore, these findings may provide a reliable method to examine the sites and number of rDNA variations among Chrysanthemum and its related accessions and allow researchers to further understand the evolutionary and phylogenetic relationships of the Chrysanthemum genus.
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Gnutikov AA, Nosov NN, Loskutov IG, Blinova EV, Shneyer VS, Probatova NS, Rodionov AV. New Insights into the Genomic Structure of Avena L.: Comparison of the Divergence of A-Genome and One C-Genome Oat Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:1103. [PMID: 35567104 PMCID: PMC9102028 DOI: 10.3390/plants11091103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome Avena species. We used 4−49 accessions per species that represented the As genome (A. atlantica, A. hirtula, and wiestii), Ac genome (A. canariensis), Ad genome (A. damascena), Al genome (A. longiglumis), and Ap genome (A. prostrata). We also took into our analysis one C-genome species, A. clauda, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in A. longiglumis to four in A. wiestii. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for A. damascena, A. hirtula, and A. wiestii, and the second for A. longiglumis, A. atlantica, and A. wiestii), and a third ribotype shared between A. atlantica and A. wiestii. A characteristic feature of the A. clauda ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that A. clauda can be a hybrid between As- and C-genome oats.
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Affiliation(s)
- Alexander A. Gnutikov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Nikolai N. Nosov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Igor G. Loskutov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Elena V. Blinova
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Viktoria S. Shneyer
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Nina S. Probatova
- Laboratory of Botany, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
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Ding Q, Li R, Ren X, Chan LY, Ho VWS, Xie D, Ye P, Zhao Z. Genomic architecture of 5S rDNA cluster and its variations within and between species. BMC Genomics 2022; 23:238. [PMID: 35346033 PMCID: PMC8961926 DOI: 10.1186/s12864-022-08476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ribosomal DNAs (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosomes during generation of genome assembly. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. RESULTS Here we generate ultra-long Oxford Nanopore Technologies (ONT) and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains of C. elegans and C. briggsae. We classify the individual rDNA's repeating units into 25 types based on the unique sequence variations in each unit of C. elegans (N2). We next perform assembly of the cluster by taking advantage of the long reads that carry these units, which led to an assembly of 5S rDNA cluster consisting of up to 167 consecutive 5S rDNA units in the N2 strain. The ordering and copy number of various rDNA units are consistent with the separation time between strains. Surprisingly, we observed a drastically reduced level of variation in the unit composition in the 5S rDNA cluster in the C. elegans CB4856 and C. briggsae AF16 strains than in the C. elegans N2 strain, suggesting that N2, a widely used reference strain, is likely to be defective in maintaining the 5S rDNA cluster stability compared with other wild isolates of C. elegans or C. briggsae. CONCLUSIONS The results demonstrate that Nanopore DNA sequencing reads are capable of generating assembly of highly repetitive sequences, and rDNA units are highly dynamic both within and between population(s) of the same species in terms of sequence and copy number. The detailed structure and variation of the 5S rDNA units within the rDNA cluster pave the way for functional and evolutionary studies.
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Affiliation(s)
- Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong SAR, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Vincy W S Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China.
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China.
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Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato. Int J Mol Sci 2022; 23:ijms23073643. [PMID: 35409003 PMCID: PMC8998684 DOI: 10.3390/ijms23073643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
Although Crepis was the first model plant group in which chromosomal changes were considered to play an important role in speciation, their chromosome structure and evolution have been barely investigated using molecular cytogenetic methods. The aim of the study was to provide a better understanding of the patterns and directions of Crepis chromosome evolution, using comparative analyses of rDNA loci number and localisation. The chromosome base number and chromosomal organisation of 5S and 35S rDNA loci were analysed in the phylogenetic background for 39 species of Crepis, which represent the evolutionary lineages of Crepis sensu stricto and Lagoseris, including Lapsana communis. The phylogenetic relationships among all the species were inferred from nrITS and newly obtained 5S rDNA NTS sequences. Despite high variations in rDNA loci chromosomal organisation, most species had a chromosome with both rDNA loci within the same (usually short) chromosomal arm. The comparative analyses revealed several independent rDNA loci number gains and loci repositioning that accompanied diversification and speciation in Crepis. Some of the changes in rDNA loci patterns were reconstructed for the same evolutionary lineages as descending dysploidy.
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Ansari HA, Ellison N, Stewart AV, Williams WM. Distribution patterns of rDNA loci in the Schedonorus- Lolium complex (Poaceae). COMPARATIVE CYTOGENETICS 2022; 16:39-54. [PMID: 35437460 PMCID: PMC8971122 DOI: 10.3897/compcytogen.v16.i1.79056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The Schedonorus-Lolium complex of the subtribe Loliinae (Poaceae) includes several economically important forage and turf grasses. This complex encompasses Lolium Linnaeus, 1753, Festuca Linnaeus, 1753 subgenus Schedonorus (P. Beauvois, 1824) Petermann, 1849 and Micropyropsis Romero Zarco et Cabezudo, 1983. New FISH results of 5S and 18S-26S rDNA sequences are presented for three species and the results are interpreted in a review of distribution patterns of 5S and 18S-26S rDNA sequences among other species in the complex. Micropyropsistuberosa Romero Zarco et Cabezudo, 1983 (2n = 2x = 14) displayed a distribution pattern of rDNA sequences identical to that of F.pratensis Hudson, 1762, supporting a close phylogenetic relationship at the bottom of the phylogenetic tree. "Loliummultiflorum" Lamarck, 1779 accessions sourced from Morocco showed a different pattern from European L.multiflorum and could be a unique and previously uncharacterised taxon. North African Festucasimensis Hochstetter ex A. Richard, 1851 had a marker pattern consistent with allotetraploidy and uniparental loss of one 18S-26S rDNA locus. This allotetraploid has previously been suggested to have originated from a hybrid with Festucaglaucescens (Festucaarundinaceavar.glaucescens Boissier, 1844). However, the distribution patterns of the two rDNA sequences in this allotetraploid do not align with F.glaucescens, suggesting that its origin from this species is unlikely. Furthermore, comparisons with other higher alloploids in the complex indicate that F.simensis was a potential donor of two sub-genomes of allohexaploid Festucagigantea (Linnaeus) Villars, 1787. In the overall complex, the proximal locations of both rDNA markers were conserved among the diploid species. Two types of synteny of the two markers could, to a considerable extent, distinguish allo- and autogamous Lolium species. The ancestral parentage of the three Festuca allotetraploids has not yet been determined, but all three appear to have been sub-genome donors to the higher allopolypoids of sub-genus Schedonorus. Terminal locations of both the markers were absent from the diploids but were very frequently observed in the polyploids.
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Affiliation(s)
- Helal Ahmad Ansari
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Nicholas Ellison
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Alan Vincent Stewart
- PGG Wrightson Seeds, Kimihia Research Centre, 1375 Springs Road, RD4, Lincoln 7674, New ZealandKimihia Research CentreLincolnNew Zealand
| | - Warren Mervyn Williams
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
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Stepanenko A, Chen G, Hoang PTN, Fuchs J, Schubert I, Borisjuk N. The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units. FRONTIERS IN PLANT SCIENCE 2022; 13:819750. [PMID: 35310643 PMCID: PMC8928438 DOI: 10.3389/fpls.2022.819750] [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: 11/22/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
The freshwater plant water lettuce (Pistia stratiotes L.) grows in warm climatic zones and is used for phytoremediation and biomass production. P. stratiotes belongs to the Araceae, an ecologically and structurally diverse early monocot family, but the phylogenetic relationships among Araceae members are poorly understood. Ribosomal DNAs (rDNAs), including the 35S and 5S rDNA, encode the RNA components of ribosomes and are widely used in phylogenetic and evolutionary studies of various plant taxa. Here, we comprehensively characterized the chromosomal locations and molecular organization of 35S and 5S rDNA genes in water lettuce using karyological and molecular methods. Fluorescence in situ hybridization revealed a single location for the 35S and 5S rDNA loci, each on a different pair of the species' 28 chromosomes. Molecular cloning and nucleotide sequencing of 35S rDNA of P. stratiotes, the first representative Araceae sensu stricto in which such a study was performed, displayed typical structural characteristics. The full-length repeat showed high sequence conservation of the regions producing the 18S, 5.8S, and 25S rRNAs and divergence of the internal transcribed spacers ITS1 and ITS2 as well as the large intergenic spacer (IGS). Alignments of the deduced sequence of 18S rDNA with the sequences available for other Araceae and representatives of other clades were used for phylogenetic analysis. Examination of 11 IGS sequences revealed significant intra-genomic length variability due to variation in subrepeat number, with four types of units detected within the 35S rDNA locus of the P. stratiotes genome (estimated size 407 Mb/1C). Similarly, the 5S rDNA locus harbors gene units comprising a conserved 119-bp sequence encoding 5S rRNA and two types of non-transcribed spacer (NTS) sequences. Type I was classified into four subtypes, which apparently originated via progressive loss of subrepeats within the duplicated NTS region containing the 3' part of the 5S rRNA gene. The minor Type II NTS is shorter than Type I and differs in nucleotide composition. Some DNA clones containing two or three consecutive 5S rDNA repeats harbored 5S rDNA genes with different types of NTSs, confirming the mosaic composition of the 5S rDNA locus.
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Affiliation(s)
- Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Phuong T. N. Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Faculty of Biology, Dalat University, Đà Lạt, Vietnam
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
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Hall AN, Morton E, Queitsch C. First discovered, long out of sight, finally visible: ribosomal DNA. Trends Genet 2022; 38:587-597. [PMID: 35272860 PMCID: PMC10132741 DOI: 10.1016/j.tig.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 10/18/2022]
Abstract
With the advent of long-read sequencing, previously unresolvable genomic elements are being revisited in an effort to generate fully complete reference genomes. One such element is ribosomal DNA (rDNA), the highly conserved genomic region that encodes rRNAs. Genomic structure and content of the rDNA are variable in both prokarya and eukarya, posing interesting questions about the biology of rDNA. Here, we consider the types of variation observed in rDNA - including locus structure and number, copy number, and sequence variation - and their known phenotypic consequences. With recent advances in long-read sequencing technology, incorporating the full rDNA sequence into reference genomes is within reach. This knowledge will have important implications for understanding rDNA biology within the context of cell physiology and whole-organism phenotypes.
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Lee SH, Kim J, Park HS, Koo H, Waminal NE, Pellerin RJ, Shim H, Lee HO, Kim E, Park JY, Yu HS, Kim HH, Lee J, Yang TJ. Genome structure and diversity among Cynanchum wilfordii accessions. BMC PLANT BIOLOGY 2022; 22:4. [PMID: 34979940 PMCID: PMC8722063 DOI: 10.1186/s12870-021-03390-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/06/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Cynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information. RESULTS We collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events. CONCLUSIONS Cw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.
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Affiliation(s)
- Sae Hyun Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiseok Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - HyunJin Koo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Remnyl Joyce Pellerin
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun-Oh Lee
- Phyzen Genomics Institute, Seongnam, 13558, Republic of Korea
| | - Eunbi Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hong Seob Yu
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Jeonghoon Lee
- National Institute of Horticultural and Herbal Science, RDA, Eumseong, 27709, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Rosselló JA, Maravilla AJ, Rosato M. The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:788911. [PMID: 35283933 PMCID: PMC8908318 DOI: 10.3389/fpls.2022.788911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/27/2022] [Indexed: 05/04/2023]
Abstract
The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.
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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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Hemleben V, Grierson D, Borisjuk N, Volkov RA, Kovarik A. Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:797348. [PMID: 34992624 PMCID: PMC8724763 DOI: 10.3389/fpls.2021.797348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss - from a personal view - the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on "Molecular organization, evolution, and function of ribosomal DNA."
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Affiliation(s)
- Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Donald Grierson
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nikolai Borisjuk
- School of Life Sciences, Huaiyin Normal University, Huai'an, China
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Ales Kovarik
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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Davidian AG, Dyomin AG, Galkina SA, Makarova NE, Dmitriev SE, Gaginskaya ER. 45S rDNA Repeats of Turtles and Crocodiles Harbor a Functional 5S rRNA Gene Specifically Expressed in Oocytes. Mol Biol Evol 2021; 39:6432055. [PMID: 34905062 PMCID: PMC8789306 DOI: 10.1093/molbev/msab324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In most eukaryotic genomes, tandemly repeated copies of 5S rRNA genes are clustered outside the nucleolus organizer region (NOR), which normally encodes three other major rRNAs: 18S, 5.8S, and 28S. Our analysis of turtle rDNA sequences has revealed a 5S rDNA insertion into the NOR intergenic spacer in antisense orientation. The insertion (hereafter called NOR-5S rRNA gene) has a length of 119 bp and coexists with the canonical 5S rDNA clusters outside the NOR. Despite the ∼20% nucleotide difference between the two 5S gene sequences, their internal control regions for RNA polymerase III are similar. Using the turtle Trachemys scripta as a model species, we showed the NOR-5S rDNA specific expression in oocytes. This expression is concurrent with the NOR rDNA amplification during oocyte growth. We show that in vitellogenic oocytes, the NOR-5S rRNA prevails over the canonical 5S rRNA in the ribosomes, suggesting a role of modified ribosomes in oocyte-specific translation. The orders Testudines and Crocodilia seem to be the only taxa of vertebrates with such a peculiar rDNA organization. We speculate that the amplification of the 5S rRNA genes as a part of the NOR DNA during oogenesis provides a dosage balance between transcription of all the four ribosomal RNAs while producing a maternal pool of extra ribosomes. We further hypothesize that the NOR-5S rDNA insertion appeared in the Archelosauria clade during the Permian period and was lost later in the ancestors of Aves.
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Affiliation(s)
- Asya G Davidian
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander G Dyomin
- Laboratory of Cell Technologies, Saratov State Medical University, Saratov, Russia
| | - Svetlana A Galkina
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
| | - Nadezhda E Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Elena R Gaginskaya
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
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Analyses of the Updated "Animal rDNA Loci Database" with an Emphasis on Its New Features. Int J Mol Sci 2021; 22:ijms222111403. [PMID: 34768834 PMCID: PMC8584138 DOI: 10.3390/ijms222111403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists.
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Roshka NM, Cherevatov OV, Volkov RA. Molecular Organization and Polymorphism of 5S rDNA in Carpathian Bees. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721050108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Variation in Ribosomal DNA in the Genus Trifolium (Fabaceae). PLANTS 2021; 10:plants10091771. [PMID: 34579303 PMCID: PMC8465422 DOI: 10.3390/plants10091771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023]
Abstract
The genus Trifolium L. is characterized by basic chromosome numbers 8, 7, 6, and 5. We conducted a genus-wide study of ribosomal DNA (rDNA) structure variability in diploids and polyploids to gain insight into evolutionary history. We used fluorescent in situ hybridization to newly investigate rDNA variation by number and position in 30 Trifolium species. Evolutionary history among species was examined using 85 available sequences of internal transcribed spacer 1 (ITS1) of 35S rDNA. In diploid species with ancestral basic chromosome number (x = 8), one pair of 5S and 26S rDNA in separate or adjacent positions on a pair of chromosomes was prevalent. Genomes of species with reduced basic chromosome numbers were characterized by increased number of signals determined on one pair of chromosomes or all chromosomes. Increased number of signals was observed also in diploids Trifolium alpestre and Trifolium microcephalum and in polyploids. Sequence alignment revealed ITS1 sequences with mostly single nucleotide polymorphisms, and ITS1 diversity was greater in diploids with reduced basic chromosome numbers compared to diploids with ancestral basic chromosome number (x = 8) and polyploids. Our results suggest the presence of one 5S rDNA site and one 26S rDNA site as an ancestral state.
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Menezes RST, Cabral-de-Mello DC, Milani D, Bardella VB, Almeida EAB. The relevance of chromosome fissions for major ribosomal DNA dispersion in hymenopteran insects. J Evol Biol 2021; 34:1466-1476. [PMID: 34331340 DOI: 10.1111/jeb.13909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/04/2021] [Accepted: 07/28/2021] [Indexed: 01/20/2023]
Abstract
Ribosomal DNA (rDNA) loci are essential for cellular metabolism due to their participation in ribosome biogenesis. Although these genes have been widely cytogenetically mapped, the evolutionary mechanisms behind their variability in number and chromosomal location remain elusive, even in well-known biological groups, such as ants, bees and wasps (Insecta: Hymenoptera). To address this question in Hymenoptera and therefore advance the understanding of rDNA evolution in insects in general, we integrated molecular cytogenetic data, a phylogenomic framework, model-based predictions and genome sequencing. Hence, we assessed the main evolutionary trends shaping the chromosomal distribution of rDNA loci in Hymenoptera. We noticed the conservation of one site of rDNA per haploid genome, suggesting that a single 45S rDNA locus is the putative ancestral pattern for aculeate Hymenoptera. Moreover, our results highlighted a nonrandom distribution of rDNA in Hymenoptera karyotypes, as well as a lineage-specific preferential location. The proximal location of rDNA is favoured in species with multiple loci and in the two families of Hymenoptera that show the highest range of chromosome numbers: Formicidae and Vespidae. We propose that chromosome fissions have played a crucial role in the distribution pattern of rDNA loci through the evolutionary diversification of Hymenoptera. Moreover, our genomic analysis of two species, one with a single locus of rDNA and one with multiple loci, supported that loci multiplication is followed by sequence divergence. Our results provide detailed information about the number and chromosomal position of rDNA in Hymenoptera and, therefore, broaden our knowledge regarding rDNA evolutionary dynamics in insects.
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Affiliation(s)
- Rodolpho S T Menezes
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
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Ince AG, Karaca M. Tissue and/or developmental stage specific methylation of nrDNA in Capsicum annuum. JOURNAL OF PLANT RESEARCH 2021; 134:841-855. [PMID: 33886005 DOI: 10.1007/s10265-021-01287-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
The nuclear ribosomal DNA (nrDNA) sequences are often used for phylogenetic analysis among organisms. Because DNA cytosine methylation and nucleolar dominancy are two common epigenetic mechanisms of nrDNA, we hypothesized that internal transcribed spacer 1 (ITS1), 5.8S rRNA and ITS2 of nrDNA sequences could be used as epigenetic biomarkers. Thus, this research was undertaken to study level and pattern of site-specific cytosine methylation of ITS1, 5.8S and ITS2 in nine tissues and/or developmental stage of pepper Capsicum annuum L. cultivar Demre Sivrisi. Tissues studied consisted of young and old roots at 30 and 90 days after sowing (das), mature dry seeds and seeds at 26 days of post anthesis (dpa), flowering buds at 1 day before flowering, pericarps at 3, 15 and 65 dpa. Levels and patterns of DNA cytosine methylation were identified at single base resolution using bisulfite conversion sequencing. Results of this study revealed that DNA cytosine level and pattern of ITS1, 5.8S and ITS2 were different in most tissues and/or developmental stages studied. In addition, methylation levels of CG, CHG and CHH contexts were also significantly different among the regions. Based on the findings of this study, it was concluded that high level of methylation of nrDNA sequences was relatively higher as observed in transposable element and promoter. On the other hand, its tissue-specific gene expression was effective as that of gene body and promoter methylation. Overall findings revealed that methylation levels of nrDNA could be used as biomarkers for tissue identification or age estimation in plants.
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Affiliation(s)
- Ayse Gul Ince
- Vocational School of Technical Sciences, Akdeniz University, 07059, Antalya, Turkey.
| | - Mehmet Karaca
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07059, Antalya, Turkey
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Qu M, Zhang L, Li K, Sun J, Li Z, Han Y. Karyotypic stability of Fragaria (strawberry) species revealed by cross-species chromosome painting. Chromosome Res 2021; 29:285-300. [PMID: 34152515 DOI: 10.1007/s10577-021-09666-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
Chromosome karyotyping analysis is particularly useful in determining species relationships and the origin of polyploid species. Identification of individual chromosomes is the foundation for karyotype development. For Fragaria (strawberry) species, definitive identification of the individual chromosomes is extremely difficult because of their small size and similar shape. Here, we identified all chromosomes for 11 representative Fragaria species with different ploidy using a set of oligonucleotide-based probes developed in Fragaria vesca. Comprehensive molecular cytogenetic karyotypes were established based on the individually identified chromosomes. In addition, we used oligo probes to assign the 5S and 45S rDNA loci to specific chromosomes in 16 Fragaria species. We found that these Fragaria species maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements at the cytological level were observed in any of the chromosomes among these species. Despite karyotypic stability and similarity, variations in the signal intensity of oligo probes were observed among the homologous chromosomes in several polyploid species. Moreover, most Fragaria species also showed differences in the distribution patterns of 45S and 5S rDNA. These data provide new insights into the origins of several polyploid Fragaria species.
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Affiliation(s)
- Manman Qu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Luyue Zhang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Kunpeng Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jianying Sun
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
| | - Yonghua Han
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
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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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Ribeiro T, Nascimento J, Santos A, Félix LP, Guerra M. Origin and evolution of highly polymorphic rDNA sites in Alstroemeria longistaminea (Alstroemeriaceae) and related species. Genome 2021; 64:833-845. [PMID: 33852822 DOI: 10.1139/gen-2020-0159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Alstroemeria (Alstroemeriaceae) displays a conserved and highly asymmetric karyotype, where most rDNA sites can be properly recognized by the size and morphology of the chromosomes. We analyzed the intraspecific variation of rDNA sites in A. longistaminea and compared with their distribution in other species (A. caryophyllaea and A. piauhyensis) and a representative of a sister genus, Bomarea edulis. All three species of Alstroemeria presented 2n = 16, and one to six B chromosomes were found in some individuals of A. longistaminea. There was a set of 12 conserved rDNA sites (four 5S and eight 35S) and up to 11 variable sites. B chromosomes were almost entirely covered by 35S signals, coupled with tiny 5S sites. Noteworthy, most rDNA sites found in A. caryophyllaea and A. piauhyensis were localized in chromosome positions similar to those in A. longistaminea, suggesting the existence of conserved hotspots for rDNA accumulation. Some of these hotspots were absent in Chilean Alstromeria as well in B. edulis. We propose that insertions of rDNA sequences on chromosomes do not occur randomly but rather on preferential sites or hotspots for insertions. The maintenance of these arrays, however, may be favored/constrained by different factors, resulting in stable or polymorphic sites.
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Affiliation(s)
- Tiago Ribeiro
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Jéssica Nascimento
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Amanda Santos
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Leonardo P Félix
- Universidade Federal da Paraíba, Departamento de Biociências, Campus II, Areia, Paraíba, Brasil
| | - Marcelo Guerra
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
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Vozárová R, Herklotz V, Kovařík A, Tynkevich YO, Volkov RA, Ritz CM, Lunerová J. Ancient Origin of Two 5S rDNA Families Dominating in the Genus Rosa and Their Behavior in the Canina-Type Meiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:643548. [PMID: 33763100 PMCID: PMC7984461 DOI: 10.3389/fpls.2021.643548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/15/2021] [Indexed: 05/02/2023]
Abstract
The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.
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Affiliation(s)
- Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Yuri O. Tynkevich
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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Goffová I, Fajkus J. The rDNA Loci-Intersections of Replication, Transcription, and Repair Pathways. Int J Mol Sci 2021; 22:1302. [PMID: 33525595 PMCID: PMC7865372 DOI: 10.3390/ijms22031302] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/28/2022] Open
Abstract
Genes encoding ribosomal RNA (rDNA) are essential for cell survival and are particularly sensitive to factors leading to genomic instability. Their repetitive character makes them prone to inappropriate recombinational events arising from collision of transcriptional and replication machineries, resulting in unstable rDNA copy numbers. In this review, we summarize current knowledge on the structure and organization of rDNA, its role in sensing changes in the genome, and its linkage to aging. We also review recent findings on the main factors involved in chromatin assembly and DNA repair in the maintenance of rDNA stability in the model plants Arabidopsis thaliana and the moss Physcomitrella patens, providing a view across the plant evolutionary tree.
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Affiliation(s)
- Ivana Goffová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic;
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic;
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
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