Putting it in to perspective

As I read more papers covering DNA barcoding I had a few questions of my own. one of these questions was why does every paper focus on the cytochrome c oxidase gene. why is it the special one. the answer was pretty simple. According to ibol.org this gene is used because its short enough to be sequenced quickly and cheaply. My next question was does this gene work well for barcoding other living things such as plants. Plants are barcoded using two genes from the chloroplasts, matK and rbcL. This website also gives an overall descripition of the barcoding process.

Here is the link to the website for more information:

http://www.ibol.org/about-us/background/
http://www.ibol.org/about-us/what-is-dna-barcoding/

Problems with barcoding

Like any identification system there are do’s and don’ts. For DNA barcoding there are seven major don’ts or as the paper calls them “seven deadly sins”. The sins are as follows failure to test clear hypotheses, inadequate a priori identification of specimens, the use of the term ‘species identification, inappropriate use of neighbor-joining trees, inappropriate use of bootstrap resampling, inappropriate use of fixed distance thresholds, and the one that I will be discussing today incorrectly interpreting the barcoding gap. The paper states that incorrectly interpreting the barcoding gap has “two distinct scenarios”, the first being for specimen identification and the second being species discovery.

The first scenario just means that the organism is so close to another organism in its species that t is identified incorrectly as the other organism. The second scenario means that a new species could be incorrectly identified as a pre-existing species. I feel like all the sins listed above could be easily avoided just by being careful when examining the species. But I think instead of having a system that relies on the barcoding “sequence” of one gene, have a system that if questions or errors like this are possible add an extra position that is barcoded on that gene.

Here is the link to the article:

http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12046/full

DNA Barcoding

Today I will be discussing a paper that I found on DNA barcoding. For those that do not know, DNA barcoding is a way to identify a species using a genetic marker in the organisms DNA. The author of this project discusses how this “project was initially was conceived as a standard system for fast and accurate identification of animal species” but now is used to “assign” and “enhance the discovery of new species”(Frézal and Leblois). This paper discusses that it uses a region of “648 base pair (bp) of the cytochrome c oxidase gene”(Frézal and Leblois).  This region is used to identify all eukaryotic species. The author then states that they are also working on a way to use this system for identifying microscopic eukaryotic life. For this they are looking at a 600 bp region of a ribosomal subunit (Frézal and Leblois). This paper did a good job explaining the idea of DNA barcoding for eukaryotes, but can this idea be used to classify prokaryotes (using RNA instead of DNA)?

Here is the link to the paper as well as the citation.

http://www.sciencedirect.com/science/article/pii/S1567134808001238

Frézal, Lise, and Raphael Leblois. “Four Years of DNA Barcoding: Current Advances and Prospects.” Infection, Genetics and Evolution 8.5 (2008): 727–736. ScienceDirect. Web. 11 Sept. 2015.