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Expectations.md

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Genes/pathways we expect to change

Fatty acid desaturase

This is one of the genes most upregulated in all resting stages, and is consistent with previous findings

Mechanisms for uptake of nitrate and ammonium

  • DiAMT1/DiNRT2?

Mechanisms for anaerobic fermentation?

Upregulation of DNRA?

  • Nitrate reductase - 1.7.5.1/1.9.6.1
  • Nitrite reductase - 1.7.2.1/1.7.2.2
  • Nitrite oxide reductase - 1.7.5.2/1.7.2.5
  • Nitrous oxide reductase - 1.7.2.4

None of the above EC numbers are present in the v1.1.2 eggnog mapper file

Sm_t00011895-RA labelled as 'nitrate reductase activity'

  • This is downregulated in the vegetative cells?? Sm_t00006755-RA seems to be a nitrate reductase but may be assimilatory
  • Seems to be upregulated in resting stages

Nitrate/nitrite reductases - Nap/Nrf and Nar/Nir?

Any significant downregulation signal?

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Abscisic acid (ABA)?

Important in resting stages of dinoflagellates and higher plants

  • Looking at NCBI, some diatom sequences are present for genes in this pathway
  • Coscinodiscus granii? (Kentzer and Mazur, 1991)

Pathway genes (noted for dinoflagellate, as starting point; see Deng et al., 2017)

  • Zeaxanthin epoxidase (ZEP); present in T. pseudonana

    • Sm_g00013199? (Sm_000038F) - Downregulated in later resting stages?
    • Sm_g00012687? (Sm_000029F) - Downregulated in all resting stages?
    • Sm_g00005941? (Sm_000011F) - Downregulated in all resting stages?
    • In S. trochoidea, ZEP is UPREGULATED in cysts...

  • 9-cis-epoxycarotenoid dioxygenases (NCED)

    • Sm_g00012791? (Sm_000027F) - Upregulated quite significantly in all resting stages
      • Best BLAST hit to the NCED sequence of P. tricornutum
    • Possibly Sm_g00003413? (Sm_000003F) - Downregulated in later resting stages
    • In S. trochoidea, NCED is highest in immature cysts

  • Abscisic-aldehyde oxidase (AAO)

    • Sm_g00005740 (Sm_000007F) - Weird signal: downregulated in all resting stages except 189d, and upregulated between resting stages as time goes on
      • Best BLAST hit to the AAO sequence of (dinoflagellate) Scrippsiella trochoidea
      • Strong domain hits to xanthine dehydrogenase/aldehyde oxidase
    • In S. trochoidea, no significant difference between stages

  • ABA-8'-hydroxylase (ABAH) [CYP707A family genes]

    • Sm_g00014680? (Sm_000034F) - Weird signal: upregulated in 49d, but downregulated between 49d and later resting stages
      • BLASTs to cytochrome P450
        • ABA-8'-hydroxylase IS a cytochrome P450 protein
    • Sm_g00000943? (Sm_000000F) - downregulated quite significantly among resting stages
    • Many other decent-length hits
    • In S. trochoidea, highest in vegetative cells and immature cysts

Other phytohormones and their pathways?