Ancestral segmental duplication in Solanaceae is responsible for the origin of CRCa-CRCb paralogues in the family.

Abstract

CRABS CLAW (CRC), a member of YABBY transcription factor family, has been previously reported to be principally involved in carpel development across angiosperms, and nectary development in core eudicots. Most of the studies suggest that CRC exists as a single copy gene, except in the Solanaceae where CRC occurs as paralogous pairs-CRCa-CRCb in Solanum lycopersicum, and CRC1-CRC2 in Petunia hybrida. In spite of their crucial role in carpel and nectary development, there is no information about the evolutionary history of the CRC paralogy in Solanaceae and whether the paralogy extends beyond Solanaceae. We analyzed homologues of CRC across angiosperms including genome sequence of fourteen species of Solanaceae available at Sol Genomics Network database, Phytozome and NCBI, to address the questions. Our phylogenetic reconstruction across angiosperms combined with comparative genomic, microsynteny and genome-fractionation analyses across the Solanaceae genomes revealed that (1) the CRCa-CRCb lineage is represented by a single copy in other flowering plants; (2) putative homologues of CRCa and CRCb are present in all the Solanaceae genomes studied; (3) the CRCa-CRCb paralogy in Solanaceae is associated with a large segmental duplication within Solanaceae (perhaps in its common ancestor), and (4) the duplicated segments have undergone different degrees of retention and loss of genes. Also, the CRC gene lineage expanded in Solanaceae following Solanaceae-α hexaploidy event and that two CRC duplicate copies were subsequently retained during the course of evolution. Besides the first detailed description of CRC evolution in Solanaceae, the study identifies potential candidate genes for future functional investigations.