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Huang Y, Yu F, Li X, Luo L, Wu J, Yang Y, Deng Z, Chen R, Zhang M. Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species. PLoS One 2017; 12:e0183447. [PMID: 28817651 PMCID: PMC5560572 DOI: 10.1371/journal.pone.0183447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 08/06/2017] [Indexed: 12/12/2022] Open
Abstract
The 45S ribosomal DNA (rDNA) units are separated by an intergenic spacer (IGS) containing the signals for transcription and processing of rRNAs. For the first time, we sequenced and analyzed the entire IGS region from three original species within the genus Saccharum, including S. spontaneum, S. robustum, and S. officinarum in this study. We have compared the IGS organization within three original species of the genus Saccharum. The IGS of these three original species showed similar overall organizations comprised of putative functional elements needed for rRNA gene activity as well as a non-transcribed spacer (NTS), a promoter region, and an external transcribed spacer (ETS). The variability in length of the IGS sequences was assessed at the individual, intraspecies, and interspecies levels of the genus Saccharum, including S. spontaneum, S. robustum, and S. officinarum. The ETS had greater similarity than the NTS across species, but nevertheless exhibited variation in length. Within the IGS of the Saccharum species, base substitutions and copy number variation of sub-repeat were causes of the divergence in IGS sequences. We also identified a significant number of methylation sites. Furthermore, fluorescent in situ hybridization (FISH) co-localization of IGS and pTa71 probes was detected on all representative species of the genus Saccharum tested. Taken together, the results of this study provide a better insight into the structure and organization of the IGS in the genus Saccharum.
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Affiliation(s)
- Yongji Huang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fan Yu
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueting Li
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ling Luo
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayun Wu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou, China
- Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Yongqing Yang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zuhu Deng
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
- * E-mail:
| | - Rukai Chen
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
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Chang KD, Fang SA, Chang FC, Chung MC. Chromosomal conservation and sequence diversity of ribosomal RNA genes of two distant Oryza species. Genomics 2010; 96:181-90. [PMID: 20580815 DOI: 10.1016/j.ygeno.2010.05.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Revised: 04/30/2010] [Accepted: 05/18/2010] [Indexed: 01/31/2023]
Abstract
Contrary to the chromosomal polymorphism of 45S ribosomal genes (45S rDNA) loci in other Oryza species, each of Oryza australiensis and Oryza brachyantha has only one 45S rDNA locus at the most conserved position of 45S rDNAs in Oryza. O. australiensis and O. brachyantha are known phylogenetically distant and have extremely different genome sizes among diploid Oryza species. This study reveals that the sequences and organizations of intergenic spacer (IGS) for 45S rDNA of both O. australiensis and O. brachyantha are different from other Oryza species. The IGS of O. australiensis contains 13 tandem repeats and only one transcriptional initiation site, while there are four tandem repeats and three transcriptional initiation sites in the IGS of O. brachyantha. Our results suggest different evolution processes of orthologous rDNA loci in the genus Oryza. Here we also demonstrate an efficient strategy to study locus-specific IGS before whole genome sequences data are available.
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Affiliation(s)
- Kwei-Duan Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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