Characterization and Dynamics of Intracellular Gene Transfer in Plastid Genomes of (Violaceae) and Order Malpighiales.

Functional gene transfer from organelles to the nucleus, known as intracellular gene transfer (IGT), is an ongoing process in flowering plants. The complete plastid genomes (plastomes) of two Ulleung island endemic violets, and , were characterized, revealing a lack of the plastid-encoded , , and genes. In addition, functional replacement of the three plastid-encoded genes in the nucleus was confirmed within the genus and the order Malpighiales. Three strategies for the acquisition of a novel transit peptide for successful IGT were identified in the genus . Nuclear acquired a novel transit peptide with very low identity between these proteins, whereas the nuclear gene acquired an existing transit peptide fusion with the nuclear-encoded plastid-targeted gene (Cu-Zn superoxide dismutase superfamily) as one exon, and translated both proteins in the cytosol using alternative mRNA splicing. Nuclear contains an internal transit peptide without an N-terminal extension. Gene loss or pseudogenization of the plastid-borne and loci was inferred to occur in the common ancestor of the genus based on an infrageneric phylogenetic framework in Korea. Although was lost in the common ancestor of the order Malpighiales, the and genes were lost multiple times independently within the order. Our current study sheds additional light on plastid genome composition and IGT mechanisms in the violet genus and in the order Malpighiales.