Mixing the DNA of different organisms for sequencing

Recently, there have been many molecular tools that allow us to both sequence a large part of the genome per individual, as well as to mix DNA from different individuals to sequence them in a single run.

In the laboratory, after extracting DNA from any organ of an individual, mainly muscle, we tag all the DNA fragments of each individual using short DNA sequences that we know and that are unique for each specimen. The DNA is then sequenced, and through bioinformatic tools, it is possible to identify all the sequences of the same organism within a large data set containing sequences from multiple organisms.

Lab procedure to tag the DNA of each individual. A plate with 96 holes with one organism per hole. Photo © Fausto Valenzuela

We made two pools with forty-eight individuals each. For one pool we obtained 262,387,764 raw sequences, and for the other pool we obtained 222,756,694. In both pools, we have few sequences containing ambiguity bases (0,01%) or low-quality (0.00%). This is the first quality control with bioinformatic tools after the sequencing run.

The pie chart indicates the percentage of clean sequences, sequences containing ambiguous bases, and low-quality sequences for the second pool.

Project

Six species of round stingray have been reported for the Mexican Pacific, but in the past they were incorrectly identified. This is a confusing group and scientists differ in their estimates of diversity for the Urotrygon genus (known as round stingrays). Ana will be combining traditional methods (looking at coloration, patterns and body measurements) with genetic research to help determine which round stingrays live where in the subtropical and tropical Mexican Pacific Ocean. Classified as either Near Threatened or Vulnerable on the IUCN Red List, all these species are an important food source for coastal communities with low economic means.

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