Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3194-0) contains supplementary material, which is available to authorized users.
Highlights
Gene duplication is prevalent in many species and can result in coding and regulatory divergence
Significant co-expression relationships (Z score >2.5) were adopted to construct a co-expression network, which contained 189 moderatesize modules of 31,811 genes (Fig. 1b). This network was integrated into the COB database [40] and can be explored by selecting the shoot apical meristem- (SAM) dataset [46]
We examined the relationship between coexpression patterns and duplication age, which was estimated using synonymous mutations
Summary
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). Most higher plants have experienced at least one whole genome duplication (WGD) and tandem/segmental duplications are widely observed [2,3,4]. Large- and small-scale gene duplications contributed predominantly to the evolution and adaptive radiation of species [7]. Gene duplication followed by the diversity of genomic content and gene regulation is probably the major factor resulting in the speciation and adaptation in plants [8]. The additional copies of genes can introduce functional redundancy, which may promote evolutionary processes at either the coding or the regulatory level [9]. Duplicate copies may be affected by nonfunctionalization, where pseudogenization occurs, or neofunctionalization, where a novel gene function emerges, or subfunctionalization, where duplicate genes partition and share the ancestral gene function in different tissues and/or developmental stages [1, 6, 9,10,11,12]
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