Molecular Evolution and Regulatory Innovation in Plants: Gene Family Diversification and Small RNA Networks

Plant molecular evolution offers key insights into how coding and regulatory changes shape the diversity of form and function across the plant kingdom. The diversification of gene families through tandem, segmental, and whole-genome duplications has long been recognized as a major driver of plant innovation, creating the raw material for new developmental functions, biochemical capacities, and adaptive responses. In parallel, small RNA-based pathways, including those mediated by microRNAs, small interfering RNAs, and phasiRNAs, have emerged as powerful regulators of gene expression central to plant growth, reproduction, stress tolerance, and environmental adaptation. Recent advances in comparative genomics, transcriptomics, and functional biology have highlighted that these two evolutionary dimensions—gene family diversification and small RNA regulation—are not only closely associated but also mechanistically linked in many plant systems. Many small RNA-related proteins themselves belong to expanding gene families, while duplicated genes may gain, lose, or diversify small RNA-mediated regulation across lineages. Despite major progress, key questions remain about how these interacting layers of molecular change contribute to phenotypic innovation, lineage-specific adaptation, and regulatory diversity across the plant kingdom.This Research Topic aims to elucidate the evolutionary and mechanistic relationships linking plant gene family diversification and small RNA-based regulatory systems. It encourages investigations into how new gene functions emerge following duplication events, how small RNA networks originate and diversify, and how these processes together reshape gene regulation, developmental programs, and adaptive traits. Key goals include identifying the genetic and molecular principles underlying regulatory rewiring, the emergence of novel functions through subfunctionalization or neofunctionalization, and the integration of small RNA pathways with evolving developmental, physiological, and metabolic networks. At the same time, to maintain a broad and inclusive scope, we also welcome studies that provide strong evolutionary, mechanistic, or functional insight into either gene family diversification or small RNA pathways, even when the connection between the two is indirect rather than explicit. This initiative seeks to move the field beyond description toward mechanistic and evolutionary explanation, incorporating structural, biochemical, comparative, and experimental approaches to define how sequence change, expression divergence, and regulatory innovation shape plant biology.This Research Topic encompasses studies exploring the molecular evolution, functional diversification, and regulatory innovation of plant gene families and small RNA systems across model and non-model taxa. To gather further insights in this integrative field, we welcome articles addressing, but not limited to, the following themes: o evolutionary dynamics of gene family expansion, contraction, and diversification; o mechanisms and outcomes of gene duplication, including tandem, segmental, and whole-genome events; o origin and diversification of miRNA, siRNA, and phasiRNA pathways across plant lineages; o cross-talk between coding-gene evolution and small RNA-mediated regulation; functional and structural evolution of small RNA biogenesis and effector proteins; o comparative genomics linking sequence evolution with regulatory innovation; o the roles of gene family and small RNA evolution in plant stress adaptation, reproduction, and developmental innovation; o experimental studies integrating genomic, genetic, and biochemical evidence for evolutionary change. We welcome original research articles, reviews, mini reviews, perspectives, and methods papers. Topic editors: Ting Lan, Guiliang Tang Source: https://www.frontiersin.org/research-topics/81206/molecular-evolution-and-regulatory-innovation-in-plants-gene-family-diversification-and-small-rna-networks