The putative phytocyanin genes in Chinese cabbage (Brassica rapa L.): genome-wide identification, classification and expression analysis

Phytocyanins (PCs) are a plant-specific family of small copper-containing electron transfer proteins. PCs may bind with a single copper atom to function as electron transporters in various biological systems, such as copper trafficking and plant photosynthesis. Evidence indicates that PCs may also be involved in plant developmental processes and stress responses. Many PCs possess arabinogalactan protein-like regions and are therefore termed chimeric arabinogalactan proteins (CAGPs). Previously, 38 and 62 PC genes have been identified in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), respectively. The recent release of the Chinese cabbage genome (B. rapa ssp. Pekinensis line Chiifu-401-42) enabled us to perform a genome-wide identification and analysis. In this study we identified 84 putative PC genes in the B. rapa genome. All of the Brassica rapa phytocyanins (BrPCs) described here could be divided, based on motif constitution, into the following three main subclasses: 52 early nodulin-like proteins (ENODLs), 16 uclacyanin-like proteins (UCLs), and 11 stellacyanin-like proteins (SCLs). A structural analysis predicted that 71 BrPCs contained N-terminal secretion signals and 45 BrPCs may be glycosylphosphatidylinositol-anchored to the plasma membrane. Glycosylation prediction revealed that 48 BrPCs were CAGPs with putative arabinogalactan glycomodules, and 57 BrPCs had N-glycosylation sites. Additionally, gene duplication analysis demonstrated that almost all of the duplicated BrPC genes shared the same conserved collinear blocks and that segmental duplications play an important role in the diversification of this gene family. Surprisingly, all BrUCL genes were duplicated except for BrUCL16. Expression analyses indicated that BrENODL22/27 and BrSCL8/9 were highly expressed in reproductive organs; BrUCL6/16 was strongly expressed in roots and even more strongly expressed in stems. The genome-wide identification, classification and expression analysis of BrPCs will provide a fundamental basis for the evolution and modification of the gene family after a polyploidy event and enable the functional study of PC genes in a polyploid crop species.