Diagram showing the arrangement of genes in the mitochondrial genome of Drosophila yakuba. This is the typical arrangement for insects.
Mitochondria are organelles in the cell that provide energy-carrying molecules that are used in other cell functions. They do this in a manner somewhat analogous to a hydroelectric power station by creating an electrochemical gradient across a membrane, then using this gradient to power a turbine that produces the molecules. It's a place where a lot of activity is happening, and it needs a repair crew immediately on hand to keep it running. For this reason, there is a small amount of DNA inside the mitochondrion that contains the vital proteins and RNA units that are required for optimal performance.
Because there are a lot of mitochondria in each cell, mitochondrial DNA tends to be easily amplified from a range of organisms, making mitochondrial genes the regions of choice for phylogenetic analyses. One gene in particular,
cytochrome c oxidase subunit 1 (COI), has been earmarked as being the gene of choice for specimen identification or
DNA barcoding as it is otherwise known. For both these reasons, I am keen to use this gene in my analyses of
Irenimus relationships. However, I'm finding that this is more easily said than done. It seems that entimine weevils have a lot of variation in these genes, which makes them hard to amplify. One idea that I will be trying involves trying to amplify the 5000 base pair region between the 12S gene (which is often less variable between species) and COI. A schematic is shown above.
To assist in planning this endeavour, I am able to make use of the resources available on
Genbank. Genbank is a repository for DNA sequence data collected by scientists around the world.
One can use this data to get an idea of where might be good places to position
PCR primers, which provide the starting points for amplification. Unfortunately, there are only two complete weevil mitochondrial genomes available on Genbank—For
Naupactus xanthographus and an unidentified
Sphenophorus species. In addition, there are partial genomes available for
26 other species. However, these partial genomes cover everything but the region that I'm wanting to use, so are rather uninformative for my purposes. It looks like my plan going forward is just going to have to involve going in blind.
Read:
Mazur MA. 2012. First record of the tribe Eugnomini Lacordaire 1863 (Coleoptera: Curculionidae) from Fiji, with description of Pactola fiji sp. n.Zootaxa 3517: 63–70
Psalms 130–131
Websites:
Renaming files in Linux
Inkscape Manual—Patterns along paths
Wikipedia—The Planets
Half of all wetlands destroyed since 1900
It was a short week, thanks to Labour Day on Monday. While it was nice to have a day off, it did make the rest of the week rather hectic. The frentic pace was not helped by my plans to be in the field all of next week. The trickiest part of the week was sorting out meetings with a number of different people. Figuring out a time that suited without interfering with plans to get some actual work done was a difficult task. However, I think I (largely) managed to do it, and had the privilege of having good talks with people on a range of subjects including website design, collecting localities in Central Otago, the need for students to understand data management, what to get a student to do over summer, and how my PhD is going.They haven't been as significant as the conference pictured above (The 1st Solvay Conference), but they've each been helpful and enjoyable in their own way.
