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Nyaku ST, Karapareddy S, Cebert E, Lawrence K, Eleblu JSY, Sharma GC, Sripathi VR. Two Intra-Individual ITS1 rDNA Sequence Variants Identified in the Female and Male Rotylenchulus reniformis Populations of Alabama. PLANTS (BASEL, SWITZERLAND) 2023; 13:5. [PMID: 38202313 PMCID: PMC10780758 DOI: 10.3390/plants13010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
Around 300 different plant species are infected by the plant-parasitic reniform nematode (Rotylenchulus reniformis), including cotton. This is a devasting nematode with a preference for cotton; it is commonly found in Alabama farms and causes severe reduction in yields. Its first internal transcribed spacer (ITS1) region can be sequenced, and potential mutations can be found in order to study the population dynamics of the reniform nematode. The goal of our study was to sequence the ITS1 rDNA region in male and female RNs that were collected from BelleMina, Hamilton, and Lamons locations in Alabama. After separating the single male and female RNs from the samples collected from the three selected listed sites above, the ITS1 region was amplified selectively using specific primers, and the resulting products were cloned and sequenced. Two distinct bands were observed after DNA amplification of male and female nematodes at 550 bp and 730 bp, respectively. The analysis of sequenced fragments among the three populations showed variation in average nucleotide frequencies of female and male RNs. Singletons within the female and male Hamilton populations ranged from 7.8% to 10%, and the variable sites ranged from 13.4% to 26%. However, female and male BelleMina populations had singletons ranging from 7.1% to 19.7% and variable regions in the range of 13.9% to 49.3%. The female and male Lamons populations had singletons ranging from 2.5% to 8.7% and variable regions in the range of 2.9% to 14.2%. Phylogenetic (neighbor-joining) analysis for the two ITS1 fragments (ITS-550 and ITS-730) showed relatively high intra-nematode variability. Different clone sequences from an individual nematode often had greater similarity with other nematodes than with their own sequences. RNA fold analysis of the ITS1 sequences revealed varied stem and loop structures, suggesting both conserved and variable regions in the variants identified from female and male RNs, thus underscoring the presence of significant intra- and inter-nematodal variation among RN populations in Alabama.
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Affiliation(s)
- Seloame T. Nyaku
- Department of Crop Science, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 44, Ghana;
| | - Sowndarya Karapareddy
- Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville, AL 35811, USA (G.C.S.)
| | - Ernst Cebert
- Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville, AL 35811, USA (G.C.S.)
| | - Kathy Lawrence
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA;
| | - John S. Y. Eleblu
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 30, Ghana
| | - Govind C. Sharma
- Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville, AL 35811, USA (G.C.S.)
| | - Venkateswara R. Sripathi
- Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville, AL 35811, USA (G.C.S.)
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Huang Y, Liu Y, Guo X, Fan C, Yi C, Shi Q, Su H, Liu C, Yuan J, Liu D, Yang W, Han F. New insights on the evolution of nucleolar dominance in newly resynthesized hexaploid wheat Triticum zhukovskyi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1298-1315. [PMID: 37246611 DOI: 10.1111/tpj.16320] [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: 01/11/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Nucleolar dominance (ND) is a widespread epigenetic phenomenon in hybridizations where nucleolus transcription fails at the nucleolus organizer region (NOR). However, the dynamics of NORs during the formation of Triticum zhukovskyi (GGAu Au Am Am ), another evolutionary branch of allohexaploid wheat, remains poorly understood. Here, we elucidated genetic and epigenetic changes occurring at the NOR loci within the Am , G, and D subgenomes during allopolyploidization by synthesizing hexaploid wheat GGAu Au Am Am and GGAu Au DD. In T. zhukovskyi, Au genome NORs from T. timopheevii (GGAu Au ) were lost, while the second incoming NORs from T. monococcum (Am Am ) were retained. Analysis of the synthesized T. zhukovskyi revealed that rRNA genes from the Am genome were silenced in F1 hybrids (GAu Am ) and remained inactive after genome doubling and subsequent self-pollinations. We observed increased DNA methylation accompanying the inactivation of NORs in the Am genome and found that silencing of NORs in the S1 generation could be reversed by a cytidine methylase inhibitor. Our findings provide insights into the ND process during the evolutionary period of T. zhukovskyi and highlight that inactive rDNA units may serve as a 'first reserve' in the form of R-loops, contributing to the successful evolution of T. zhukovskyi.
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Affiliation(s)
- Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaolan Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Congyang Yi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Handong Su
- Huazhong Agricultural University, Hubei, 430070, China
| | - Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Borowska-Zuchowska N, Mykhailyk S, Robaszkiewicz E, Matysiak N, Mielanczyk L, Wojnicz R, Kovarik A, Hasterok R. Switch them off or not: selective rRNA gene repression in grasses. TRENDS IN PLANT SCIENCE 2023; 28:661-672. [PMID: 36764871 DOI: 10.1016/j.tplants.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/31/2022] [Accepted: 01/11/2023] [Indexed: 05/13/2023]
Abstract
Nucleolar dominance (ND) is selective epigenetic silencing of 35-48S rDNA loci. In allopolyploids, it is frequently manifested at the cytogenetic level by the inactivation of nucleolar organiser region(s) (NORs) inherited from one or several evolutionary ancestors. Grasses are ecologically and economically one of the most important land plant groups, which have frequently evolved through hybridisation and polyploidisation events. Here we review common and unique features of ND phenomena in this monocot family from cytogenetic, molecular, and genomic perspectives. We highlight recent advances achieved by using an allotetraploid model grass, Brachypodium hybridum, where ND commonly occurs at a population level, and we cover modern genomic approaches that decipher structural features of core arrays of NORs.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland.
| | - Serhii Mykhailyk
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland
| | - Natalia Matysiak
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland
| | - Lukasz Mielanczyk
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland; Silesian Nanomicroscopy Centre in Zabrze, Silesia LabMed - Research and Implementation Centre, Medical University of Silesia, Katowice, Poland
| | - Romuald Wojnicz
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland; Silesian Nanomicroscopy Centre in Zabrze, Silesia LabMed - Research and Implementation Centre, Medical University of Silesia, Katowice, Poland
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, CZ-61200 Brno, Czech Republic
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland.
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