• The idea for this project came out of recent research the RNA editing capabilities housed within the genome of cephalopods.
  • Found that RNA (instead of DNA) is highly edited in Octopus sp.
    • Occurs mostly in neurological tissue, but can also occur in other peripheral tissues.
  • Cuttlefish have not been studied.
  • In preparing for RNA transcriptome analysis, we realized that we did not have a reference sequence to compare our transcriptome analysis to, so we decided to sequence the genome as well.

Sepia bandensis

  • Mollusca (phylum) —> Cephalopoda (class)
  • Found off the coast of Philippines, Papua New Guinea and Indonesia in shallow water (water of 78-80F)
  • Babies are about 0.5in, adults are up to 2-3 inches.
  • 8 arms, with two rows of suckers along each arm, and two feeding tentacles with at least two rows of suckers along each
  • Cephalopods have three hearts, a ring shaped brain, blue, copper based blood, and have a lifespan between 6 months and 3 years (Sepia bandensis lives about a year)
  • Chromatophores and skin shaping used to hide from predators/hunt

  • The cephalopod genome is roughly 2.7GB.

    • There is no completed sequencing data on Cuttlefish (S. officianalis is being analyzed by Kim Worley’s group out of Baylor).
    • We do not know the size of S. bandensis’ genome.
    • We also don’t know how many chromosomes the organism has. S. pharaonic has 48 chromosomes (2N)
  • A recent paper showed that RNA editing occurs at greater levels in colder water. Will be interesting to highlight RNA editing in warm water fish

RNA Editing

  • A biological process in which an organism increases its adaptability by editing mRNA transcripts
  • Can be paired with gene splicing (i.e. in humans)
  • A to I RNA editing occurs when the adenosine is edited to an Inosine via deamination.
    • The resultant nucleotide substitution is a Guanine/Guanosine

Why is this Important?

  • RNA editing allows for the expression of functionally diverse proteins from a single gene (i.e. multiple transcripts from one gene) = enhanced adaptability
    • I.e. in an environment where the surrounding temperature changes it is useful to have functional variants of a protein that allows for an increase in ion permeability through the membrane (i.e. increased action potential)
  • Studying RNA editing in an organism allows us to answer questions about how the organism adapts to its environment.

Proposed Work

  • Karyotype the organism (how many chromosomes does it have).
  • Perform NGS of S. bandensis gDNA.
    • Annotate the genome of S. bandensis (using S. officianalis genomic data as a scaffolding reference).
  • Perform RNA Transcriptome analysis of all tissues.
    • Assess frequency of A to G substitutions within the transcriptome.
    • Determine which genes are edited

What needs to be done?

Cuttle Wranglin’

  • Setting up a salt water reef tank
  • Maintaining the fish until adulthood Tissue Processing
  • Karyotyping
  • Isolating neurological tissue and peripheral tissue
  • Prepping gDNA, sending frozen tissues off for RNA library production Data analysis
  • Genome assembly
  • Transcriptome analysis

Wikipedia page

Cuttlefish project google group.

Hanlon Lab – Overview

Faculty - Jeff Rogers and Kim Worley


PBS video - KINGS OF Camouflage HD

Science Friday

Images from Daniel Pon

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