当前位置： SCI文献检索 > BMC GENOMICS期刊下所有文献 > Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

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

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.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Li L,Briskine R,Schaefer R,Schnable PS,Myers CL,Flagel LE,Springer NM,Muehlbauer GJ

doi

10.1186/s12864-016-3194-0

subject

Has Abstract

pub_date

2016-11-04 00:00:00

pages

875

issue

issn

1471-2164

pii

10.1186/s12864-016-3194-0

journal_volume

pub_type

杂志文章

在线工具

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