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

Lin Li, Roman Briskine, Robert Schaefer, Patrick S. Schnable, Chad L. Myers, Lex E. Flagel, Nathan M. Springer, Gary J. Muehlbauer

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish (US)
Article number875
JournalBMC Genomics
Volume17
Issue number1
DOIs
StatePublished - Nov 4 2016

Fingerprint

Duplicate Genes
Gene Duplication
Zea mays
Genome
Genes
Gene Regulatory Networks
RNA
Gene Expression

Keywords

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

Cite this

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias. / Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S.; Myers, Chad L.; Flagel, Lex E.; Springer, Nathan M.; Muehlbauer, Gary J.

In: BMC Genomics, Vol. 17, No. 1, 875, 04.11.2016.

Research output: Contribution to journalArticle

@article{a1a17ca3bd9b4c168dfe7e1417fddd0c,
title = "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.",
keywords = "Co-expression network, Gene duplication, Gene expression, Maize (Zea mays L.), Regulatory divergence",
author = "Lin Li and Roman Briskine and Robert Schaefer and Schnable, {Patrick S.} and Myers, {Chad L.} and Flagel, {Lex E.} and Springer, {Nathan M.} and Muehlbauer, {Gary J.}",
year = "2016",
month = "11",
day = "4",
doi = "10.1186/s12864-016-3194-0",
language = "English (US)",
volume = "17",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

AU - Li, Lin

AU - Briskine, Roman

AU - Schaefer, Robert

AU - Schnable, Patrick S.

AU - Myers, Chad L.

AU - Flagel, Lex E.

AU - Springer, Nathan M.

AU - Muehlbauer, Gary J.

PY - 2016/11/4

Y1 - 2016/11/4

N2 - 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.

AB - 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.

KW - Co-expression network

KW - Gene duplication

KW - Gene expression

KW - Maize (Zea mays L.)

KW - Regulatory divergence

UR - http://www.scopus.com/inward/record.url?scp=84994516347&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84994516347&partnerID=8YFLogxK

U2 - 10.1186/s12864-016-3194-0

DO - 10.1186/s12864-016-3194-0

M3 - Article

C2 - 27814670

AN - SCOPUS:84994516347

VL - 17

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 875

ER -