Abstract
BackgroundProtein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes.ResultsOur analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications.ConclusionsOur data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing the notion that plant genomes have undergone dynamic evolution.
Highlights
Protein domains are the structural, functional and evolutionary units of the protein
We report in this study an investigation of protein domain architecture in the context of the various plant lineages, with a specific focus on the dynamics of domain architecture content and the effect of whole genome duplications
Together with fact that ~10% of the domain architecture diversity is species-specific (Table 1), this further demonstrates that domain architecture diversity has been maintained beyond the core components of domain architectures
Summary
Protein domains are the structural, functional and evolutionary units of the protein. The evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineagebased protein domain architecture content in 14 completed green plant genomes. Usually segments of continuous amino acids within a protein, are the structural, functional and evolutionary units of the protein. Protein domain architecture is a pattern of linear, sequential domain(s) in a given protein. Fong et al (2007) reported that in multi-domain architectures, domain fusion and domain fission are the most parsimonious domain recombination events with domain fusion events occurring much more frequently compared to domain fission events [4]
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