Molecular analysis and barcoding

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Molecular analysis and barcoding

• Ryuji Machida, Rob Jennings

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Molecular analysis and barcoding

1. Re-visit CMarZ goals
2. Review our progress to date
3. Identify challenges and make plans to overcome
   them

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Re-visit CMarZ goals

• Integrated morphological and molecular taxonomic
  analysis.
• DNA barcoding of all zooplankton species.

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Our progress to date
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Identify challenges and make plans to overcome
them

• Needs of database infrastructure.
• Regional differences in sequence submission, e.g.
  Indian Ocean.
• CMarZ own protocols. Preservation of the samples
  which lose morphological information in ethanol,
  extraction of DNA from small animals, extraction
  from jellies, needs of paratype sample, etc.
• Data and sample use policy
• Demand for another genes to be sequenced.

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Comparison of genes
Genes Organelle Good point Bad point
ITS Nuclear Can distinguish species in
Cnidarian. Universal primer is available, and
applicable to most of species. Easy to get
clear sequences. Need of cloning.
COI Mithocondria Can distinguish species,
generally. Universal primer is available, and
applicable to most of species. Can not
distinguish species in Cnidarian. Difficult to
get clear sequences.
12S srRNS Mithocondria Can
distinguish species, generally. Universal
primer is available, and applicable to most
of species. Easy to get clear sequences.
Can not distinguish species in Cnidarian.
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Sampling site
Site Off Pohnpei Mouth opening 2m2 Mesh
size 0.69mm Depth range 0-721m
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• 828 colonies have been sequenced.

Frequency of pairwise distance between each
sequences
Sequences distance is less than 0.09 same
species more
than 0.09 different species