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Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome

Inverted duplicates (IDs) are pervasive in genomes and have been reported to play functional roles in various biological processes. However, the general underlying evolutionary forces that maintain IDs in genomes remain largely elusive. Through a systematic screening of the Drosophila melanogaster g...

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Autores principales: Chen, Zhen-Xia, Zhang, Yong E., Vibranovski, Maria, Luo, Jingchu, Gao, Ge, Long, Manyuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176832/
https://www.ncbi.nlm.nih.gov/pubmed/21546357
http://dx.doi.org/10.1093/molbev/msr101
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author Chen, Zhen-Xia
Zhang, Yong E.
Vibranovski, Maria
Luo, Jingchu
Gao, Ge
Long, Manyuan
author_facet Chen, Zhen-Xia
Zhang, Yong E.
Vibranovski, Maria
Luo, Jingchu
Gao, Ge
Long, Manyuan
author_sort Chen, Zhen-Xia
collection PubMed
description Inverted duplicates (IDs) are pervasive in genomes and have been reported to play functional roles in various biological processes. However, the general underlying evolutionary forces that maintain IDs in genomes remain largely elusive. Through a systematic screening of the Drosophila melanogaster genome, 20,223 IDs were detected in nonrepetitive intergenic regions, far more than expectation under the neutrality model. 3,846 of these IDs were identified to have stable hairpin structure (i.e., the structural IDs). Based on whole-genome transcriptome profiling data, we found 628 unannotated expressed structural IDs, which had significantly different genomic distributions and structural properties from the unexpressed IDs. Among the expressed structural IDs, 130 exhibited higher expression in males than in females (i.e., male-biased expression). Compared with sex-unbiased ones, these male-biased IDs were significantly underrepresented on the X chromosome, similar to previously reported pattern of male-biased protein-coding genes. These analyses suggest that a selection-driven process, rather than a purely neutral mutation-driven mechanism, contributes to the maintenance of IDs in the Drosophila genome.
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spelling pubmed-31768322011-09-21 Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome Chen, Zhen-Xia Zhang, Yong E. Vibranovski, Maria Luo, Jingchu Gao, Ge Long, Manyuan Mol Biol Evol Research Articles Inverted duplicates (IDs) are pervasive in genomes and have been reported to play functional roles in various biological processes. However, the general underlying evolutionary forces that maintain IDs in genomes remain largely elusive. Through a systematic screening of the Drosophila melanogaster genome, 20,223 IDs were detected in nonrepetitive intergenic regions, far more than expectation under the neutrality model. 3,846 of these IDs were identified to have stable hairpin structure (i.e., the structural IDs). Based on whole-genome transcriptome profiling data, we found 628 unannotated expressed structural IDs, which had significantly different genomic distributions and structural properties from the unexpressed IDs. Among the expressed structural IDs, 130 exhibited higher expression in males than in females (i.e., male-biased expression). Compared with sex-unbiased ones, these male-biased IDs were significantly underrepresented on the X chromosome, similar to previously reported pattern of male-biased protein-coding genes. These analyses suggest that a selection-driven process, rather than a purely neutral mutation-driven mechanism, contributes to the maintenance of IDs in the Drosophila genome. Oxford University Press 2011-10 2011-05-05 /pmc/articles/PMC3176832/ /pubmed/21546357 http://dx.doi.org/10.1093/molbev/msr101 Text en © The Author(s) 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Chen, Zhen-Xia
Zhang, Yong E.
Vibranovski, Maria
Luo, Jingchu
Gao, Ge
Long, Manyuan
Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome
title Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome
title_full Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome
title_fullStr Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome
title_full_unstemmed Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome
title_short Deficiency of X-Linked Inverted Duplicates with Male-Biased Expression and the Underlying Evolutionary Mechanisms in the Drosophila Genome
title_sort deficiency of x-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the drosophila genome
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176832/
https://www.ncbi.nlm.nih.gov/pubmed/21546357
http://dx.doi.org/10.1093/molbev/msr101
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