The Evolution of Protein Families

Most proteins belong to evolutionary lineages commonly referred to as protein families, although this fundamental feature is often overlooked in everyday research. For instance, Arabidopsis thaliana contains multiple functional actin homologues, yet this diversity is frequently taken for granted. Although protein evolution is continuous, it proceeds hierarchically under functional constraints. As a result, many protein families form complex superfamilies composed of nested clades that reflect successive layers of functional diversification. Two major classes of genomic events drive the evolution of these families: gene duplication and recombination. Duplication, often described as "birth", generates functional redundancy that can permit sequence divergence and, ultimately, the emergence of novel functions or, alternatively, the loss of redundant paralogues, or "death". Recombination, in turn, contributes to the mosaic domain architectures that characterize many multidomain families. Together, these processes generate the remarkable structural and functional diversity observed across plant protein superfamilies.Although protein family evolution can be studied experimentally, most current insights derive, at least in part, from computational approaches, a trend further accelerated by the rise of phylogenomics. In recent years, methodological advances have greatly expanded the tools available to researchers. However, many of these approaches remain underused or insufficiently familiar within the plant science community. Important challenges persist, particularly for families with heterogeneous domain architectures, for which standard analytical pipelines often perform poorly. Evolutionary complexity adds another layer of difficulty, as the interplay among redundancy, divergence, and selection frequently produces intricate phylogenetic patterns in which functional relationships remain difficult to resolve. This is especially apparent in protein families associated with specialized plant metabolism, where diversification is shaped not only by redundancy but also by broad substrate permissiveness. In parallel, the growing recognition of lineage-specific metabolic subnetworks across multiple plant families and orders has increased interest in pangenomics as a framework for understanding functional diversification. Taken together, these observations highlight the need for greater attention to the many dimensions of protein family evolution in plants.This Research Topic aims to bring together studies that advance our understanding of how protein families and superfamilies have evolved across the plant kingdom. Although the general principles of protein family evolution extend beyond taxonomic boundaries, plants offer a particularly compelling system because their evolutionary history has been profoundly shaped by repeated whole-genome duplications, which have promoted diversification, adaptation, and innovation. To gather further insights in plant protein family evolution, we welcome articles addressing, but not limited to, the following themes:• Mechanisms and consequences of gene duplication and recombination in plants• Evolutionary processes shaping multidomain and mosaic protein architectures• Comparative genomics and phylogenomics of plant protein families and superfamilies• Functional characterization of novel and diversified paralogs• Evolution of protein families involved in specialized metabolism and metabolic networks• Impact of pangenomics on understanding lineage-specific diversification• Integration of computational, structural, and experimental approaches in evolutionary studies• Co-evolutionary analyses, including host–pathogen and protein–protein interaction networks Topic editors: Arjen Ten Have, Christin Naumann Source: https://www.frontiersin.org/research-topics/80247/the-evolution-of-protein-families