Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

BMC Genomics

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

【 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

【 图 表 】

12864_2017_3605_Article_IEq7.gif

12864_2017_3645_Article_IEq5.gif

12864_2016_3194_Article_IEq3.gif

12864_2017_3487_Article_IEq32.gif

12864_2017_4030_Article_IEq26.gif