Bioinformatic search for cellulose synthase genes in flax (Linum usitatissimum) and their phylogenetic analysis

Abstract

In silico search for the nucleotide sequences encoding cellulose synthases in the flax genome was carried out, together with the comparison of the identified sequences with the orthologous genes in dicotyledonous plants. The analysis resulted in the identification of 32 flax candidate genes, 16 of which encoded cellulose synthases with high possibility rate, while the remaining 16 encoded cellulose synthase-like proteins (Csl). The phylogenetic analysis of the protein products of the cellulose synthase genes allowed dividing them into six groups comprising cellulose synthases of different classes: CesA1/10, CesA3, CesA4, CesA5/6/2/9, CesA7, and CesA8. Paralogous sequences belonging to the classes CesA1/10 and CesA5/6/2/9, associated with the primary cell wall formation, were characterized by the higher intra-class similarity rate, than the orthologous sequences. At the same time, the genes that control cellulose biosynthesis for the secondary cell wall formation constituted distinct clades, CesA4, CesA7, and CesA8. The analysis of the 16 selected flax candidate cellulose synthase genes demonstrated that the flax genome contains at least 12 different variants of cellulose synthase genes, which belong to all six cellulose synthase clades. In such a way, at this stage, the cellulose synthase genes from all ten known CesA classes have been identified in the flax genome; however, their correct attribution to each of these classes requires some additional study.