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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

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RT @Xenpaper: Trends in reconstruction of three nucleus-encoded, plastid-localized pathways for the heme, chlorophyll a and isopentenyl dip…
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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
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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.3488v1/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.3488v1/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.3488v1/supp-3

Summary of the Karenia, Karlodinium and Lepidodinium transcripts encoding proteins involved in the heme biosynthesis

DOI: 10.7287/peerj.preprints.3488v1/supp-4

Summary of the Karenia, Karlodinium and Lepidodinium transcripts encoding proteins involved in the Chl a biosynthesis

DOI: 10.7287/peerj.preprints.3488v1/supp-5

Summary of the Karenia, Karlodinium and Lepidodinium transcripts encoding proteins involved in the IPP biosynthesis

DOI: 10.7287/peerj.preprints.3488v1/supp-6

Summary of the alignments analyzed in this study

DOI: 10.7287/peerj.preprints.3488v1/supp-7

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, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, conducted phylogenetic analyses.

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

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 (SRA no. NNNN).

Data Deposition

The following information was supplied regarding data availability:

The research in this article generated no data except the DNA sequence data deposited in GenBank

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 in part by grants from the JSPS awarded to Y. I. (23117006 and 16H04826). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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