Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis

Abstract

Comparisons within expanding sequence databases have revealed a dynamic interplay among genomic and epigenomic forces in driving plant evolution. Such forces are especially obvious within the F-Box (FBX) superfamily, one of the largest and most polymorphic gene families in land plants, where its frequent lineagespecific expansions and contractions provide an excellent model to assess how genetic variation impacted gene function before and after speciation. Previous phylogenetic comparisons based on orthology, diversity, and expression patterns identified three plant FBX groups-Common, Lineage-Specific, and Pseudo(genized)-whose emergences are consistent with genomic drift evolution. Here, we examined this variance within Arabidopsis thaliana by evaluating SNPs for all 877 FBX loci from 432 naturally occurring accessions and their relationships to variations in natural selection, expression, and DNA/histone methylation. In line with their phenotypic importance, Common FBX loci have low polymorphism but high deleterious mutation rates indicative of stringent functional constraints. In contrast, the Lineage-Specific and Pseudo groups are enriched in genes with basal expression and higher SNP density and more correlated with methylation marks (RNA-directed DNA methylation and histone H3K27 trimethylation) that promote transcriptional silencing. Taken together, we propose that reversible epigenomic modifications helped shape FBX gene evolution by transcriptionally suppressing the adverse effects of gene dosage imbalance and harmful FBX alleles that arise during genomic drift, while simultaneously allowing innovations to emerge through epigenomic reprogramming.ubiquitylation | population genomics | gene birth-and-death

Disentangling Interactions in the Microbiome: A Network Perspective

“…Markov clustering algorithm (MCL) tries to simulate a stochastic flow within the network structure, strengthening the flow where nodes are highly interconnected and weakening it in other regions until the flow process stabilizes [74]. MCL has found great popularity in network biology and has been used to characterize protein families within protein networks [75], detect orthologous and homologous groups [76], predict protein complexes from protein interaction networks [77], find gene clusters base on expression profiles [78], and to find clusters of putative pathogens and growth-promoting bacteria in phyllosphere microbiome [23].…”

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

“…Tandemly duplicated genes arising from unequal crossover can also exhibit substantial epigenetic diversity. The large family of F-box proteins in Arabidopsis provides evidence for diversity of chromatin states within complex loci containing these genes (Hua et al, 2013).…”

Closing Target Trimming: a Perl Package for Discovering Hidden Superfamily Loci in Genomes

“…Newly synthesized members in a family have been commonly recognized to experience either pseudogenization or fixation in a genome through four processes: 1) conservation if gene dosage is beneficial [1], 2) neofunctionalization if a novel function is acquired in one copy [1], 3) subfunctionalization if daughter copies split the function of the ancestral copy [7], or 4) specialization if all daughter copies perform new functions differing from their ancient copy [8]. Previous studies have suggested that dosage-balance constraints guarded duplicated copies against loss by determining the stoichiometry of duplicated products [9,10]. Interestingly, families involving different cellular functions have various birth over death ratios.…”

“…15 many biological laboratories are not yet able to take full advantage of the power of wholegenome sequencing because of the lack of the bioinformatic tools and/or skills.While many state-of-the-art bioinformatic tools have been developed to annotate genomes u, our studies have shown that superfamily members were often missing in various accomplished genome projects [5,6] (Tables 3 and 4). Studying gene duplications of a family across genomes can shed light on the evolutionary and functional mechanisms of intracellular regulatory pathways [4,6,10]. Yet, a biased conclusion could be made if a comprehensive understanding of the members of a gene family in genomes is not achieved.…”