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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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Wang Y, Chen Y, Wei Q, Chen X, Wan H, Sun C. Characterization of repetitive sequences in Dendrobium officinale and comparative chromosomal structures in Dendrobium species using FISH. Gene 2022; 846:146869. [PMID: 36075328 DOI: 10.1016/j.gene.2022.146869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Tandem repeats are one of the most conserved features in the eukaryote genomes. Dendrobium is the third largest genus in family Orchidaceae compromising over 1,200 species. However, the organization of repetitive sequences in Dendrobium species remains unclear. In this study, we performed the identification and characterization of the tandem repeats in D. officinale genome using graph-based clustering and Fluorescence in situ hybridization (FISH). Six major clusters including five satellite DNAs (DofSat1-5) and one 5S rDNA repeat (Dof5S) were identified as tandem repeats. The tandem organization of DofSat5 was verified by PCR amplification and southern blotting. The chromosomal locations of the repetitive DNAs in D. officinale were investigated by FISH using the tandem repeats and oligos probes. The results showed that each of the DofSat5, 5S and 45S rDNA had one pair of strong signals on D. officinale chromosomes. The distribution of repetitive DNAs along chromosomes was also investigated based on genomic in situ hybridization (GISH) among four Dendrobium species. The results suggested complex chromosomal fusion/segmentation and rearrangements during the evolution of Dendrobium species. In conclusion, the present study provides new landmarks for unequival differentiation of the Dendrobium chromosomes and facilitate the understanding the chromosome evolution in Dendrobium speceis.
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Affiliation(s)
- Yunzhu Wang
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yue Chen
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Qingzhen Wei
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaoyang Chen
- Seed Management Terminal of Zhejiang, Hangzhou 310021, China.
| | - Hongjian Wan
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Chongbo Sun
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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First genome survey and repeatome analysis of Chrysopogon zizanioides based on next-generation sequencing. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00517-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Su D, Chen L, Sun J, Zhang L, Gao R, Li Q, Han Y, Li Z. Comparative Chromosomal Localization of 45S and 5S rDNA Sites in 76 Purple-Fleshed Sweet Potato Cultivars. PLANTS 2020; 9:plants9070865. [PMID: 32650507 PMCID: PMC7412053 DOI: 10.3390/plants9070865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022]
Abstract
In recent years, the purple-fleshed sweet potato has attracted more attention because of its high nutritional value. The cytogenetics of this crop is relatively unexplored, limiting our knowledge on its genetic diversity. Therefore, we conducted cytogenetic analysis of 76 purple-fleshed sweet potato cultivars to analyze the chromosome structure and distribution of 45S and 5S rDNA. We noted that only 62 cultivars had 90 chromosomes, and the others were aneuploid with 88, 89, 91, or 92 chromosomes. The number of 45S rDNA in the 76 cultivars varied from 16 to 21; these sites showed different signal sizes and intensities and were localized at the chromosomal termini or satellite. The number of 5S rDNA was relatively stable; 74 cultivars showed six sites located at the chromosomal sub-terminal or near the centromere. Only the ‘Quanzishu 96’ and ‘Yuzixiang 10’ showed seven and five 5S rDNA sites, respectively. Additionally, both parent cultivars of ‘Quanzishu 96’ showed 18 45S and six 5S rDNA sites. Overall, our results indicate a moderate diversity in the distribution pattern of rDNAs. Our findings provide comprehensive cytogenetic information for the identification of sweet potato chromosomes, which can be useful for developing a high-quality germplasm resource.
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Affiliation(s)
- Dan Su
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Lei Chen
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Jianying Sun
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Luyue Zhang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Runfei Gao
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou 221100, China; (R.G.); (Q.L.)
| | - Qiang Li
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou 221100, China; (R.G.); (Q.L.)
| | - Yonghua Han
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
- Correspondence: (Y.H.); (Z.L.); Tel.: +86-0516-8350-0083 (Y.H. & Z.L.)
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
- Correspondence: (Y.H.); (Z.L.); Tel.: +86-0516-8350-0083 (Y.H. & Z.L.)
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Abdel-Salam EM, Faisal M, Alatar AA, Saquib Q, Alwathnani HA. Comparative Analysis between Wild and Cultivated Cucumbers Reveals Transcriptional Changes during Domestication Process. PLANTS (BASEL, SWITZERLAND) 2020; 9:E63. [PMID: 31947725 PMCID: PMC7020419 DOI: 10.3390/plants9010063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/29/2019] [Accepted: 12/30/2019] [Indexed: 12/01/2022]
Abstract
The cultivated cucumber (Cucumis sativus L.) was reported to have been developed from a wild cucumber (Cucumis hystrix Chakrav.), nevertheless, these two organisms exhibit noteworthy differences. For example, the wild cucumber is known for its high resistance to different biotic and abiotic stresses. Moreover, the leaves and fruits of the wild cucumber have a bitter taste compared to the cultivated cucumber. These differences could be attributed mainly to the differences in gene expression levels. In the present investigation, we analyzed the RNA-sequencing data to show the differentially expressed genes (DEGs) between the wild and cultivated cucumbers. The identified DEGs were further utilized for Gene Ontology (GO) and pathway enrichment analysis and for identification of transcription factors and regulators. In the results, several enriched GO terms in the biological process, cellular component, and molecular functions categories were identified and various enriched pathways, especially the biosynthesis pathways of secondary products were recognized. Plant-specific transcription factor families were differentially expressed between the wild and cultivated cucumbers. The results obtained provide preliminary evidence for the transcriptional differences between the wild and cultivated cucumbers which developed during the domestication process as a result of natural and/or artificial selection, and they formulate the basis for future genetic research and improvement of the cultivated cucumber.
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Affiliation(s)
- Eslam M. Abdel-Salam
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
| | - Mohammad Faisal
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
| | - Abdulrahman A. Alatar
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
| | - Quaiser Saquib
- Zoology Department, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia;
| | - Hend A. Alwathnani
- Department of Botany & Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia; (E.M.A.-S.); (A.A.A.); (H.A.A.)
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Jiang J. Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res 2019; 27:153-165. [PMID: 30852707 DOI: 10.1007/s10577-019-09607-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 01/20/2023]
Abstract
Fluorescence in situ hybridization (FISH) was developed more than 30 years ago and has been the most paradigm-changing technique in cytogenetic research. FISH has been used to answer questions related to structure, mutation, and evolution of not only individual chromosomes but also entire genomes. FISH has served as an important tool for chromosome identification in many plant species. This review intends to summarize and discuss key technical development and applications of FISH in plants since 2006. The most significant recent advance of FISH is the development and application of probes based on synthetic oligonucleotides (oligos). Oligos specific to a repetitive DNA sequence, to a specific chromosomal region, or to an entire chromosome can be computationally identified, synthesized in parallel, and fluorescently labeled. Oligo probes designed from conserved DNA sequences from one species can be used among genetically related species, allowing comparative cytogenetic mapping of these species. The advances with synthetic oligo probes will significantly expand the applications of FISH especially in non-model plant species. Recent achievements and future applications of FISH and oligo-FISH are discussed.
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Affiliation(s)
- Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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Kroupin P, Kuznetsova V, Romanov D, Kocheshkova A, Karlov G, Dang TX, Khuat TML, Kirov I, Alexandrov O, Polkhovskiy A, Razumova O, Divashuk M. Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species. Genes (Basel) 2019; 10:E113. [PMID: 30717300 PMCID: PMC6409974 DOI: 10.3390/genes10020113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 11/19/2022] Open
Abstract
Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.
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Affiliation(s)
- Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Victoria Kuznetsova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Dmitry Romanov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Alina Kocheshkova
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Thi Xuan Dang
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Thi Mai L Khuat
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Oleg Alexandrov
- Laboratory of Plant Cell Engineering, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Alexander Polkhovskiy
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
| | - Olga Razumova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
| | - Mikhail Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia.
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Mlinarec J, Skuhala A, Jurković A, Malenica N, McCann J, Weiss-Schneeweiss H, Bohanec B, Besendorfer V. The Repetitive DNA Composition in the Natural Pesticide Producer Tanacetum cinerariifolium: Interindividual Variation of Subtelomeric Tandem Repeats. FRONTIERS IN PLANT SCIENCE 2019; 10:613. [PMID: 31156676 PMCID: PMC6532368 DOI: 10.3389/fpls.2019.00613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/25/2019] [Indexed: 05/02/2023]
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.), a plant species endemic to the east Adriatic coast, is used worldwide for production of the organic insecticide, pyrethrin. Most studies concerning Dalmatian pyrethrum have focused on its morphological and biochemical traits relevant for breeding. However, little is known about the chromosomal evolution and genome organization of this species. Our study aims are to identify, classify, and characterize repetitive DNA in the T. cinerariifolium genome using clustering analysis of a low coverage genomic dataset. Repetitive DNA represents about 71.63% of the genome. T. cinerariifolium exhibits linked 5S and 35S rDNA configuration (L-type). FISH reveals amplification of interstitial telomeric repeats (ITRs) in T. cinerariifolium. Of the three newly identified satellite DNA families, TcSAT1 and TcSAT2 are located subterminally on most of T. cinerariifolium chromosomes, while TcSAT3 family is located intercalary within the longer arm of two chromosome pairs. FISH reveals high levels of polymorphism of the TcSAT1 and TcSAT2 sites by comparative screening of 28 individuals. TcSAT2 is more variable than TcSAT1 regarding the number and position of FISH signals. Altogether, our data highlights the dynamic nature of DNA sequences associated with subtelomeres in T. cinerariifolium and suggests that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
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Affiliation(s)
- Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | - Ana Skuhala
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Jamie McCann
- Institute of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | | | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
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