Format

Send to

Choose Destination
BMC Genomics. 2016 Nov 4;17(1):875.

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

Author information

1
Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
2
National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
3
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
4
Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
5
Monsanto Company, Chesterfield, MO, 63017, USA.
6
Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
7
Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA. Muehl003@umn.edu.
8
Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA. Muehl003@umn.edu.

Abstract

BACKGROUND:

Gene 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.

RESULTS:

To 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.

CONCLUSIONS:

Our 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.

KEYWORDS:

Co-expression network; Gene duplication; Gene expression; Maize (Zea mays L.); Regulatory divergence

PMID:
27814670
PMCID:
PMC5097351
DOI:
10.1186/s12864-016-3194-0
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center