Genome-wide identification and transcriptional expression analysis of chalcone synthase in flax (Linum usitatissimum L.)

• We identified nine CHS genes from the flax genome.
• LuCHSs were classified into two classes, CHS-like (CHSL) gene group and CHS group.
• LuCHSs in the CHS gene group were strongly up-regulated by stress-related stimuli.

Chalcone synthase (CHS, E.C. 2.3.1.74) is a key enzyme in the biosynthetic pathway leading to production of flavonoids. Although CHS has been systematically investigated in several plant species including maize, rice, and Arabidopsis, no systematic analysis has been conducted in industrial crop Linum usitatissimum L. In this study, we identified nine CHS genes from the flax genome by analyzing multiple alignment, phylogenetic relationship, and protein motif. The phylogenetic analysis revealed that flax CHS (LuCHS) 1, 2, 8, and 9 were clustered with CHS-like (CHSL) gene group, whereas the CHS group contained the remaining LuCHS proteins. To establish detailed expression data of the LuCHS gene family, flax-cultured cells were treated with salicylic acid, methyl jasmonic acid, chitosan, and pectin. LuCHSs in the CHS gene group were strongly up-regulated by stress-related stimuli, whereas other genes clustered in the CHSL group were slightly up-regulated or down-regulated, indicating a divergence in the function of LuCHSs. Taken together, our comparative and expression analysis of CHS genes and encoded proteins in flax provide the first step towards the functional dissection of the CHS gene family in response to different stimuli.