Maqola

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

Lin LiDepartment of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USARoman BriskineDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USARobert SchaeferDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USAPatrick S. SchnableDepartment of Agronomy, Iowa State University, Ames, IA, 50011, USAChad L. MyersDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USALex FlagelDepartment of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USANathan M. SpringerDepartment of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USAGary J. MuehlbauerDepartment of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA. [email protected]

2016en

ABI

Annotatsiya

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.

Hali tarjima qilinmagan

Identifikatorlar

DOI: 10.1186/s12864-016-3194-0

Iqtiboslar va manbalar

2 ta iqtibos0 ta foydalanilgan manba

Koʻrsatkichlar — AkademScholar