Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks.

Planta
Fabricio Almeida-SilvaThiago M Venancio

Abstract

We report a soybean gene co-expression network built with data from 1284 RNA-Seq experiments, which was used to identify important regulators, modules and to elucidate the fates of gene duplicates. Soybean (Glycine max (L.) Merr.) is one of the most important crops worldwide, constituting a major source of protein and edible oil. Gene co-expression networks (GCN) have been extensively used to study transcriptional regulation and evolution of genes and genomes. Here, we report a soybean GCN using 1284 publicly available RNA-Seq samples from 15 distinct tissues. We found modules that are differentially regulated in specific tissues, comprising processes such as photosynthesis, gluconeogenesis, lignin metabolism, and response to biotic stress. We identified transcription factors among intramodular hubs, which probably integrate different pathways and shape the transcriptional landscape in different conditions. The top hubs for each module tend to encode proteins with critical roles, such as succinate dehydrogenase and RNA polymerase subunits. Importantly, gene essentiality was strongly correlated with degree centrality and essential hubs were enriched in genes involved in nucleic acids metabolism and regulation of cell replication...Continue Reading

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Citations

Nov 18, 2021·Functional & Integrative Genomics·Fabricio Almeida-Silva, Thiago M Venancio

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Methods Mentioned

BETA
RNA-seq
ubiquitination
transgenic

Software Mentioned

Perl script
fasta
R package WGCNA
R package bc3net
WGCNA
PhytoMine
get
R package igraph
MEME

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