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Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice

Segmental duplication is a major structural variation that occurs in chromosomes. Duplication leads to the production of gene copies with increased numbers of related repeat segments, causing the global genome to be in a state of imbalance. In addition, if the added segment contains a centromeric sp...

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Autores principales: Zhang, Rong, Xue, Chao, Liu, Guanqing, Liu, Xiaoyu, Zhang, Mingliang, Wang, Xiao, Zhang, Tao, Gong, Zhiyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5457480/
https://www.ncbi.nlm.nih.gov/pubmed/28577021
http://dx.doi.org/10.1038/s41598-017-02796-9
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author Zhang, Rong
Xue, Chao
Liu, Guanqing
Liu, Xiaoyu
Zhang, Mingliang
Wang, Xiao
Zhang, Tao
Gong, Zhiyun
author_facet Zhang, Rong
Xue, Chao
Liu, Guanqing
Liu, Xiaoyu
Zhang, Mingliang
Wang, Xiao
Zhang, Tao
Gong, Zhiyun
author_sort Zhang, Rong
collection PubMed
description Segmental duplication is a major structural variation that occurs in chromosomes. Duplication leads to the production of gene copies with increased numbers of related repeat segments, causing the global genome to be in a state of imbalance. In addition, if the added segment contains a centromeric specific DNA, the duplicated chromosome will have structural multiple centromeres. We identified a segmental duplication containing structurally tricentric regions derived from the short arm of chromosome 11 (11L∙ + 11L∙ + 11S∙11S∙11S∙11S, “∙” represents the centromeric DNA repeat loci), and analyzed its implications for cell division and genome-wide expression. In the variant, only the middle centromere of 11S∙11S∙11S∙11S is functionally active. As a result, the structurally tricentric chromosome was stable in mitosis, because it is actually a functional monocentric chromosome. However, the structurally tricentric chromosome, which usually formed a bivalent, was either arranged on the equatorial plane or was lagging, which affected its separation during meiosis. Furthermore, RNA-seq and RT-qPCR analysis showed that the segmental duplication affected genome-wide expression patterns. 34.60% of genes in repeat region showed positive dosage effect. Thus, the genes on chromosome arm 11S-2 didn’t exhibit obviously dosage compensation, as illustrated by no peak around a ratio of 1.00. However, the gene dosage effect will reduce after sexual reproduction of a generation.
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spelling pubmed-54574802017-06-06 Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice Zhang, Rong Xue, Chao Liu, Guanqing Liu, Xiaoyu Zhang, Mingliang Wang, Xiao Zhang, Tao Gong, Zhiyun Sci Rep Article Segmental duplication is a major structural variation that occurs in chromosomes. Duplication leads to the production of gene copies with increased numbers of related repeat segments, causing the global genome to be in a state of imbalance. In addition, if the added segment contains a centromeric specific DNA, the duplicated chromosome will have structural multiple centromeres. We identified a segmental duplication containing structurally tricentric regions derived from the short arm of chromosome 11 (11L∙ + 11L∙ + 11S∙11S∙11S∙11S, “∙” represents the centromeric DNA repeat loci), and analyzed its implications for cell division and genome-wide expression. In the variant, only the middle centromere of 11S∙11S∙11S∙11S is functionally active. As a result, the structurally tricentric chromosome was stable in mitosis, because it is actually a functional monocentric chromosome. However, the structurally tricentric chromosome, which usually formed a bivalent, was either arranged on the equatorial plane or was lagging, which affected its separation during meiosis. Furthermore, RNA-seq and RT-qPCR analysis showed that the segmental duplication affected genome-wide expression patterns. 34.60% of genes in repeat region showed positive dosage effect. Thus, the genes on chromosome arm 11S-2 didn’t exhibit obviously dosage compensation, as illustrated by no peak around a ratio of 1.00. However, the gene dosage effect will reduce after sexual reproduction of a generation. Nature Publishing Group UK 2017-06-02 /pmc/articles/PMC5457480/ /pubmed/28577021 http://dx.doi.org/10.1038/s41598-017-02796-9 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Zhang, Rong
Xue, Chao
Liu, Guanqing
Liu, Xiaoyu
Zhang, Mingliang
Wang, Xiao
Zhang, Tao
Gong, Zhiyun
Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice
title Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice
title_full Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice
title_fullStr Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice
title_full_unstemmed Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice
title_short Segmental Duplication of Chromosome 11 and its Implications for Cell Division and Genome-wide Expression in Rice
title_sort segmental duplication of chromosome 11 and its implications for cell division and genome-wide expression in rice
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5457480/
https://www.ncbi.nlm.nih.gov/pubmed/28577021
http://dx.doi.org/10.1038/s41598-017-02796-9
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