title: The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage.
abstract: BACKGROUND
  Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway that catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. To date, PAL genes have been less extensively studied in gymnosperms than in angiosperms. Our interest in PAL genes stems from their potential role in the defense responses of Pinus taeda, especially with respect to lignification and production of low molecular weight phenolic compounds under various biotic and abiotic stimuli. In contrast to all angiosperms for which reference genome sequences are available, P. taeda has previously been characterized as having only a single PAL gene. Our objective was to re-evaluate this finding, assess the evolutionary history of PAL genes across major angiosperm and gymnosperm lineages, and characterize PAL gene expression patterns in Pinus taeda.
  
  
  METHODS
  We compiled a large set of PAL genes from the largest transcript dataset available for P. taeda and other conifers. The transcript assemblies for P. taeda were validated through sequencing of PCR products amplified using gene-specific primers based on the putative PAL gene assemblies. Verified PAL gene sequences were aligned and a gene tree was estimated. The resulting gene tree was reconciled with a known species tree and the time points for gene duplication events were inferred relative to the divergence of major plant lineages.
  
  
  RESULTS
  In contrast to angiosperms, gymnosperms have retained a diverse set of PAL genes distributed among three major clades that arose from gene duplication events predating the divergence of these two seed plant lineages. Whereas multiple PAL genes have been identified in sequenced angiosperm genomes, all characterized angiosperm PAL genes form a single clade in the gene PAL tree, suggesting they are derived from a single gene in an ancestral angiosperm genome. The five distinct PAL genes detected and verified in P. taeda were derived from a combination of duplication events predating and postdating the divergence of angiosperms and gymnosperms.
  
  
  CONCLUSIONS
  Gymnosperms have a more phylogenetically diverse set of PAL genes than angiosperms. This inference has contrasting implications for the evolution of PAL gene function in gymnosperms and angiosperms.
authors: Institute of Bioinformatics, The University of Georgia, Athens, GA 30602-7229, USA.
authors: Ujwal R
authors: UR
authors: Bagal
authors: James H
authors: JH
authors: Leebens-Mack
authors: W Walter
authors: WW
authors: Lorenz
authors: Jeffrey F D
authors: JF
authors: Dean
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D032462:Cycadopsida / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D020869:Gene Expression Profiling; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D019684:Magnoliopsida / Q000145:classification / Q000201:enzymology / Q000235:genetics; D008969:Molecular Sequence Data; D010650:Phenylalanine Ammonia-Lyase / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D041603:Pinus taeda / Q000201:enzymology / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D018547:Plant Stems / Q000201:enzymology / Q000235:genetics; D036226:Seedlings / Q000201:enzymology / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D010940:Plant Proteins; D010650:Phenylalanine Ammonia-Lyase