期刊论文详细信息
BMC Genomics
Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias
Research Article
Gary J. Muehlbauer1  Lin Li2  Patrick S. Schnable3  Chad L. Myers4  Roman Briskine4  Robert Schaefer4  Nathan M. Springer5  Lex E. Flagel6 
[1] Department of Agronomy and Plant Genetics, University of Minnesota, 55108, Saint Paul, MN, USA;Department of Plant and Microbial Biology, University of Minnesota, 55108, Saint Paul, MN, USA;Department of Agronomy and Plant Genetics, University of Minnesota, 55108, Saint Paul, MN, USA;National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China;Department of Agronomy, Iowa State University, 50011, Ames, IA, USA;Department of Computer Science and Engineering, University of Minnesota, 55455, Minneapolis, MN, USA;Department of Plant and Microbial Biology, University of Minnesota, 55108, Saint Paul, MN, USA;Monsanto Company, 63017, Chesterfield, MO, USA;Department of Plant and Microbial Biology, University of Minnesota, 55108, Saint Paul, MN, USA;
关键词: Gene duplication;    Gene expression;    Co-expression network;    Regulatory divergence;    Zea mays;   
DOI  :  10.1186/s12864-016-3194-0
 received in 2016-06-15, accepted in 2016-10-22,  发布年份 2016
来源: Springer
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【 摘 要 】

BackgroundGene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized.ResultsTo address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks – maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize.ConclusionsOur work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types, duplication ages and co-expression consequences.

【 授权许可】

CC BY   
© The Author(s). 2016

【 预 览 】
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