Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns  

Abstract

The evolution of a species involves changes in its genome and its transcriptome. Divergence in expression patterns may be more important than divergence in sequences for determining phenotypic changes, particularly among closely related species. We examined the relationships between organ evolution, sequence evolution, and expression evolution in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). We found correlated divergence of gene sequences and expression patterns, with distinct divergence rates that depend on the organ types in which a gene is expressed. For instance, genes specifically expressed in reproductive organs (i.e., stamen) evolve more quickly than those specifically expressed in vegetative organs (e.g., root). The different rates in organ evolution may be due to different degrees of functional constraint associated with the different physiological functions of plant organs. Additionally, the evolutionary rate of a gene sequence is correlated with the breadth of its expression in terms of the number of tissues, the number of coregulation modules, and the number of species in which the gene is expressed, as well as the number of genes with which it may interact. This linkage supports the hypothesis that constitutively expressed genes may experience higher levels of functional constraint accumulated from multiple tissues than do tissue-specific genes.

Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa)

“…The great expression variation of the lowly conserved miRNAs is largely coupled with their high level of sequence polymorphism among cultivated rice (Liu et al 2013), suggesting they are under weak selection pressures. Such a coupling of expression variation and sequence polymorphism of rice miRNAs is compatible with the correlated divergences between gene sequences and expression patterns during organ evolution in angiosperms (Yang and Wang 2013). The negligible overall correlation between expression changes of the lowly conserved miRNAs, also the lowly expressed miRNAs, and their targets further indicates that these miRNAs exert very modest, if any, repression on target genes.…”

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures

“…This modular organization showed the expressional diversity of gene profiles in a given tissue. Tissue preferential expression has been used to classify genes, and to carry out functional studies and evolutionary investigations of tissue differentiation (Ma et al, 2005;Pavy et al, 2008;Yang & Wang, 2013;Duval et al, 2014). We analysed xylem and phelloderm preferential genes conserved in three spruce species and found that they were distributed among all coexpression groups as well as being differentially represented in many of them (Fig.…”

Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory

“…The biosynthesis of these phenolic derivatives, with potential roles in pollen coat composition and establishment of fertilization barriers, has been linked to rapid metabolic gene evolution through retroposition and neofunctionalization (42). In a cross-species study on transcriptome evolutionary divergence, the fastest rates of gene expression divergence and signatures of transcriptome specialization were detected in anthers, whereas the lowest rates of evolution were detected in roots (43). Our metabolomics study therefore suggests that transcriptome and metabolome specialization may be coupled patterns in anthers, likely as a result of strong reproduction-related selection pressures exerted at this tissue level.…”