DOI: 10.5061/dryad.3ss6p
title: Data from: Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

description: Background: Two non-homologous, isofunctional enzymes catalyze the
 penultimate step of chlorophyll a synthesis in oxygenic photosynthetic
 organisms such as cyanobacteria, eukaryotic algae and land plants: the
 light-independent (LIPOR) and light-dependent (POR) protochlorophyllide
 oxidoreductases. Whereas the distribution of these enzymes in
 cyanobacteria and land plants is well understood, the presence, loss,
 duplication, and replacement of these genes have not been surveyed in the
 polyphyletic and remarkably diverse eukaryotic algal lineages. Results: A
 phylogenetic reconstruction of the history of the POR enzyme (encoded by
 the por gene in nuclei) in eukaryotic algae reveals replacement and
 supplementation of ancestral por genes in several taxa with horizontally
 transferred por genes from other eukaryotic algae. For example,
 stramenopiles and haptophytes share por gene duplicates of prasinophytic
 origin, although their plastid ancestry predicts a rhodophytic por signal.
 Phylogenetically, stramenopile pors appear ancestral to those found in
 haptophytes, suggesting transfer from stramenopiles to haptophytes by
 either horizontal or endosymbiotic gene transfer. In dinoflagellates whose
 plastids have been replaced by those of a haptophyte or diatom, the
 ancestral por genes seem to have been lost whereas those of the new
 symbiotic partner are present. Furthermore, many chlorarachniophytes and
 peridinin-containing dinoflagellates possess por gene duplicates.In
 contrast to the retention, gain, and frequent duplication of algal por
 genes, the LIPOR gene complement (chloroplast-encoded chlL, chlN, and chlB
 genes) is often absent. LIPOR genes have been lost from haptophytes and
 potentially from the euglenid and chlorarachniophyte lineages. Within the
 chlorophytes, rhodophytes, cryptophytes, heterokonts, and chromerids, some
 taxa possess both POR and LIPOR genes while others lack LIPOR. The gradual
 process of LIPOR gene loss is evidenced in taxa possessing pseudogenes or
 partial LIPOR gene compliments. No horizontal gene transfer of LIPOR genes
 was detected.ConclusionsWe document a pattern of por gene acquisition and
 expansion as well as loss of LIPOR genes from many algal taxa, paralleling
 the presence of multiple por genes and lack of LIPOR genes in the
 angiosperms. These studies present an opportunity to compare the
 regulation and function of por gene families that have been acquired and
 expanded in patterns unique to each of various algal taxa.
description: AdditionalFile1_Alignment_NexusFormatNexus formatted alignment of all protein sequences used for POR phylogeny inference.AdditionalFile2_BayesianTree_NexusFormat4FigTreeBayesian POR phylogeny in Nexus format, readable in the program FigTree.AdditionalFile3_MaximumLikelihoodTree_NewickFormatMaximum-likelihood POR phylogeny in Newick format.AdditionalFile4_PorSpeciesTableExcel spreadsheet of identifying information (e.g., accessions) for all sequences used in the POR phylogeny.AdditionalFile5_PrimerTableTable of degenerate and species-specific primers used to amplify por gene sequences from stramenopile algae.