Molecular analysis and barcoding Ryuji Machida, Rob Jennings.

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Presentation transcript:

Molecular analysis and barcoding Ryuji Machida, Rob Jennings

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

Re-visit CMarZ goals Integrated morphological and molecular taxonomic analysis. DNA barcoding of all zooplankton species.

Our progress to date

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. Identify challenges and make plans to overcome them

Comparison of genes Genes Organelle Good point Bad point 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. 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.

Sampling site Site; Off Pohnpei Mouth opening; 2m 2 Mesh size; 0.69mm Depth range; 0-721m

Pairwise Distance (p) Frequency Frequency of pairwise distance between each sequences 828 colonies have been sequenced. Sequences distance is less than 0.09 = same species more than 0.09 = different species Minimum value was observed in 0.09