Specialization and evolution of endogenous small RNA pathways

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Abstract
Eukaryotes have evolved small-RNA-guided regulatory systems for the control of RNA transcripts, chromatin, genome content and invasive agents. Specialized silencing systems evolved in eukaryotic lineages through proliferation and specialization of small-RNA biogenesis and effector factors. Genomes spawn new types of RNA silencing triggers through sequence duplications, bidirectional transcription and evolution of self-complementary foldbacks Amplification of endogenous silencing signals occurs by distinct secondary small interfering RNA (siRNA)-biogenesis mechanisms that involve RNA-dependent RNA polymerases in various lineages. Plant genomes can spawn new microRNA (miRNA)-generating loci de novo by inverted duplication of protein-coding sequences followed by accommodation by the specialized miRNA-biogenesis apparatus through sequence drift miRNA families expand through gene duplication, yielding sets of miRNAs with redundant, overlapping and specific functions. miRNA specialization within families can result from miRNA sequence differences and differential regulation of family members.