In silico characterisation of PAL homologs and metabolomic profiling of shade response indicates potential presence of PTALs and Tyr as a probable precursor of lignin biosynthesis in conifers

Norway spruce and Scots pine show enhanced lignin synthesis under shade along with differential expression of defense-related genes that renders disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants and tyrosine (Tyr) forms an additional lignin precursor in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed a relatively higher amount of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggests potential presence of PTALs in conifers, which is novel. Exome sequence analysis revealed latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and PTAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.