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Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species

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. rob...

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Autores principales: Huang, Yongji, Yu, Fan, Li, Xueting, Luo, Ling, Wu, Jiayun, Yang, Yongqing, Deng, Zuhu, Chen, Rukai, Zhang, Muqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560572/
https://www.ncbi.nlm.nih.gov/pubmed/28817651
http://dx.doi.org/10.1371/journal.pone.0183447
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author Huang, Yongji
Yu, Fan
Li, Xueting
Luo, Ling
Wu, Jiayun
Yang, Yongqing
Deng, Zuhu
Chen, Rukai
Zhang, Muqing
author_facet Huang, Yongji
Yu, Fan
Li, Xueting
Luo, Ling
Wu, Jiayun
Yang, Yongqing
Deng, Zuhu
Chen, Rukai
Zhang, Muqing
author_sort Huang, Yongji
collection PubMed
description 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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spelling pubmed-55605722017-08-25 Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species Huang, Yongji Yu, Fan Li, Xueting Luo, Ling Wu, Jiayun Yang, Yongqing Deng, Zuhu Chen, Rukai Zhang, Muqing PLoS One Research Article 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. Public Library of Science 2017-08-17 /pmc/articles/PMC5560572/ /pubmed/28817651 http://dx.doi.org/10.1371/journal.pone.0183447 Text en © 2017 Huang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Huang, Yongji
Yu, Fan
Li, Xueting
Luo, Ling
Wu, Jiayun
Yang, Yongqing
Deng, Zuhu
Chen, Rukai
Zhang, Muqing
Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species
title Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species
title_full Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species
title_fullStr Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species
title_full_unstemmed Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species
title_short Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species
title_sort comparative genetic analysis of the 45s rdna intergenic spacers from three saccharum species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560572/
https://www.ncbi.nlm.nih.gov/pubmed/28817651
http://dx.doi.org/10.1371/journal.pone.0183447
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