Visitors   Views   Downloads

Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates.

View preprint
18 days ago
Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates. https://t.co/buOD2N2hc5
RT @Xenpaper: Trends in reconstruction of three nucleus-encoded, plastid-localized pathways for the heme, chlorophyll a and isopentenyl dip…
203 days ago
Trends in reconstruction of three nucleus-encoded, plastid-localized pathways for the heme, chlorophyll a and isopentenyl diphosphate biosynthesises in two separate dinoflagellate lineages bearing non-canonical plastids https://t.co/9TRIYUbVF2
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Supplemental Information

Fig S1. ML phylogenies of 8 proteins involved in C5 pathway for the heme biosynthesis (with full sequence names)

We provide the maximum-likelihood bootstrap values (MLBPs), which are equal or greater than 50%. Color-coding for subtrees/branches are same as described in Fig. 2. Page 1, glutamyl-tRNA reductase (GTR). Page 2, glutamate-1-semialdehyde 2,1-aminomutase (GSAT). Page 3, delta-aminolevulinic acid dehydratase (ALAD). Page 4, porphobilinogen deaminase (PBGD). Page 5, Uroporphyrinogen III synthase (UROS). Page 6, uroporphyrinogen decarboxylase (UROD). Page 7, coproporphyrinogen oxidase (CPOX). Page 8, protoporphyrinogen IX oxidase (PPOX). Page 9, ferrochelatase (FeCH).

DOI: 10.7287/peerj.preprints.3488v2/supp-1

Fig S2. ML phylogenies of 7 proteins involved in the Chl a biosynthetic pathway (with full sequence names)

The details of this figure are same as those of Fig. S1. Page 1, ChlD, one of the two nucleus-encoded subunits of Mg-chelatase (MgCH). Page 2, ChlH, the other nucleus-encoded subunit of MgCH. Page 3, S-adenosylmethionine:Mg-protoporphyrin O-methyltransferase (MgPMT). Page 4, divinyl chlorophyllide a 8-vinyl-reductase using ferredoxin for electron donor (F-DVR). Page 5, divinyl chlorophyllide a 8-vinyl-reductase using NADPH for electron donor (N-DVR). Page 6, light-dependent protochlorophyllide reductase (POR). Page 7, chlorophyll synthase (CS).

DOI: 10.7287/peerj.preprints.3488v2/supp-2

Fig S3. ML phylogenies of 7 proteins involved in the non-mevalonate pathway for IPP biosynthesis (with full sequence name)

The details of this figure are same as those of Fig. S1. Page 1, 1-deoxy-D-xylulose-5-phosphate (DXP) synthase (DXS). Page 2, DXP reductoisomerase (IspC/DXR). Page 3, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD). Page 4, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE). Page 5, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF). Page 6, 1-hydroxy-2-methyl-2-butenyl 4-diphosphate (HMB-PP) synthase (IspG). Page 7, HMB-PP reductase (IspH).

DOI: 10.7287/peerj.preprints.3488v2/supp-3

Accession numbers of the queries used for gene survey conducted in this study

DOI: 10.7287/peerj.preprints.3488v2/supp-4

Nucleotide sequences identified in this study

DOI: 10.7287/peerj.preprints.3488v2/supp-5

Accession numbers of the sequences included in the phylogenetic alignments

DOI: 10.7287/peerj.preprints.3488v2/supp-6

Summary of the phylogenetic alignments

DOI: 10.7287/peerj.preprints.3488v2/supp-7

The N-terminal extensions of the proteins examined in this study

DOI: 10.7287/peerj.preprints.3488v2/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Eriko Matsuo conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, conducted phylogenetic analyses.

Yuji Inagaki conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The RNA-seq data obtained from a dioflagellate Lepidodoinium chlorophorum was deposited in GenBank database (DRA accession number DRA006544).

Data Deposition

The following information was supplied regarding data availability:

The supplementary data were deposited at an online repository (https://drive.google.com/drive/folders/1X_CsF15twTbr-ziKENyADEVDidSJBOB_?usp=sharing).

Funding

E. M. was supported by a research fellowship from the Japanese Society for Promotion of Sciences (JSPS) for Young Scientists (no. 15J00821). This work was supported by grants from the JSPS awarded to Y. I. (23117006, 16H04826 and 17H03723). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies