DOI: 10.5061/dryad.591sm73
title: Data from: Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates

description: Background: The ancestral dinoflagellate most likely established a
 peridinin-containing plastid, which have been inherited to the extant
 photosynthetic descendants. However, kareniacean dinoflagellates and
 Lepidodinium species were known to bear “non-canonical” plastids lacking
 peridinin, which were established through haptophyte and a green algal
 endosymbioses, respectively. For plastid function and maintenance, the
 aforementioned dinoflagellates were known to use nucleus-encoded proteins
 vertically inherited from the ancestral dinoflagellates (vertically
 inherited- or VI-type), and those acquired from non-dinoflagellate
 organisms (including the endosymbiont). These observations indicated that
 the proteomes of the non-canonical plastids derived from a haptophyte and
 a green alga were modified by “exogenous” genes acquired from
 non-dinoflagellate organisms. However, there was no systematic evaluation
 addressing how “exogenous” genes reshaped individual metabolic pathways
 localized in a non-canonical plastid. Results: In this study, we surveyed
 transcriptomic data from two kareniacean species (Karenia brevis and
 Karlodinium veneficum) and Lepidodinium chlorophorum, and identified
 proteins involved in three plastid metabolic pathways synthesizing
 chlorophyll a (Chl a), heme and isoprene. The origins of the individual
 proteins of our interest were investigated, and assessed how the three
 pathways were modified before and after the algal endosymbioses, which
 gave rise to the current non-canonical plastids. We observed a clear
 difference in the contribution of VI-type proteins across the three
 pathways. In both Karenia/Karlodinium and Lepidodinium, we observed a
 substantial contribution of VI-type proteins to the isoprene and heme
 biosynthesises. In sharp contrast, VI-type protein was barely detected in
 the Chl a biosynthesis in the three dinoflagellates. Discussion:
 Pioneering works hypothesized that the ancestral kareniacean species had
 lost the photosynthetic activity prior to haptophyte endosymbiosis. The
 absence of VI-type proteins in the Chl a biosynthetic pathway in Karenia
 or Karlodinium is in good agreement with the putative non-photosynthetic
 nature proposed for their ancestor. The dominance of proteins with
 haptophyte origin in the Karenia/Karlodinium pathway suggests that their
 ancestor rebuilt the particular pathway by genes acquired from the
 endosymbiont. Likewise, we here propose that the ancestral Lepidodinium
 likely experienced a non-photosynthetic period and discarded the entire
 Chl a biosynthetic pathway prior to the green algal endosymbiosis.
 Nevertheless, Lepidodinium rebuilt the pathway by genes transferred from
 phylogenetically diverse organisms, rather than the green algal
 endosymbiont. We explore the reasons why green algal genes were barely
 utilized to reconstruct the Lepidodinium pathway.
description: Matsuo_Inagaki_PeerJ2018_suppdata.tarWhen this tar.gz file is extracted, you will find three folders (“ML_Bayesian_trees,” “Lepdodinium_RNA-seq” and “alignment_heme_Chla_IPP”) and a compressed FASTA format file (Lepidodinium_RNA-seq.tar.gz). The details of the folders/files are described in README file.