Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees

Abstract

Wood formation was present in early angiosperms, but has been highly modified through evolution to generate the anatomical diversity seen in extant angiosperm lineages. In this project, we modeled changes in gene coexpression relationships associated with the evolution of wood formation in a phylogenetic survey of 13 angiosperm tree species. Gravitropic stimulation was used as an experimental treatment to alter wood formation and also perturb gene expression. Gene transcript abundances were determined using RNA sequencing of developing wood tissues from upright trees, and from the top (tension wood) and bottom (opposite wood) tissues of gravistimulated trees. A network-based approach was employed to align gene coexpression networks across species based on orthologous relationships. A large-scale, multilayer network was modeled that identified both lineage-specific gene coexpression modules and modules conserved across multiple species. Functional annotation and analysis of modules identified specific regulatory processes associated with conserved modules, including regulation of hormones, protein phosphorylation, meristem development and epigenetic processes. Our results provide novel insights into the evolution and development of wood formation, and demonstrate the ability to identify biological processes and genes important for the evolution of a foundational trait in nonmodel, undomesticated forest trees.

Expression Quantitative Trait Locus of Wood Formation-Related Genes in Salix suchowensis

“…DEGs were identified using DESeq2 v1.32.2 [ 95 ] with a threshold of q-value < 0.05 and |log 2 (fold change)| > 1. In addition, RNA-Seq data for S. suchowensis at different developmental stages were downloaded from NCBI [ 96 , 97 ], and analyzed using the same pipeline.…”

Applying molecular and genetic methods to trees and their fungal communities

“…Applicable in non-model species, cost-effective Potentially missing low-abundance transcripts Weber (2015); Harper et al (2016); Holliday et al (2019); Wu et al (2019); Zinkgraf et al (2020) functional and ecological attributes (e.g., Adnan et al 2022;Genre et al 2020;Holliday et al 2019;Isabel et al 2020;Lind et al 2018;Nilsson et al 2019;Plomion et al 2016).…”

“…Another attractive approach is the identification of gene expression networks that are conserved among species. This was done by Zinkgraf et al ( 2020 ) for the trait “wood formation”. The authors used RNA-seq to investigate gene expression related to wood formation in 13 different tree species and identified orthologous genes whose co-expression relationships were maintained across species (Zinkgraf et al 2020 ).…”

Evolution of two gene networks underlying adaptation to drought stress in the wild tomatoSolanum chilense

“…Moreover, phylogenetic and developmental studies have demonstrated that many physiological, structural, and regulatory innovations to cope drought stress have arisen throughout the history of plants, many of them even predating the emergence of land plants (Jill Harrison 2017; de Vries et al 2018; de Vries and Archibald 2018; Mustafin et al 2019; Wang et al 2020; Bowles et al 2021). Several conserved GCNs can be observed in fundamental biological processes such as protein metabolism, cell cycle, and photosynthesis and well as key traits such wood formation (Stuart et al 2003; Ficklin and Feltus 2011; Zinkgraf et al 2020).…”