Comprehensive analysis of patched domain-containing genes reveals a unique evolutionary pattern

Patched domain-containing genes are members of a small family originally identified in Drosophila. A common feature of transmembrane patched domain-containing proteins is their function in the transport of sterols, sterol-modified proteins, and lipids. Recently, an expansion phenomenon of patched domain-containing genes was found in Caenorhabditis elegans; the major contributor to this higher number was patched-related (PTR) type genes. However, little is known about their expansion pattern and evolutionary origin. We performed a systematic genome-wide survey of patched domain-containing genes in species ranging from protozoa to vertebrates, as well as some plants. We found that patched domain-containing genes are conserved in plant and animal genomes and their expansion likely occurred in the early stages of nematode speciation. Based on analysis of phylogenetic and reconciled trees and calculation of synonymous substitutions, we discovered that the PTR genes appear to have experienced two expansions within a relatively short period after the speciation of nematodes. We also found that some patched domain-containing genes possessing a relatively recent evolutionary origin, such as PTR and PTCHD1, had fewer exons and shorter nucleotide coding sequence lengths compared with the older ones. It appears that the different types of patched domain-containing genes have different evolutionary patterns in different species.