Wednesday, October 13, 2010

Genome diversity



The human genome project began in 1990 and completed in 2003. It took a mere 13 years to sequence ourselves, and determine that we have about 3 billion base pairs (DNA is made up of base pairs. Bases, called G, A, T, C are paired up and organized to make codes for proteins).Of that 22 000, only 1-2% are protein coding, generally proteins are what we hold responsible for traits, phenotypes whatever you call what you can discern as functions (like eye colour, hair, motor abilities). The rest have other functions..or none at all, "junk" DNA. (this used to include microRNAs, that actually control 30% of gene expression).

Just recently, a rare Japanese wild flower was fully sequenced. (the report is in Science). It has a whopping 150 billion base pairs, 50x the size of the human genome. Model plant Arabidopsis has 30 000  protein coding genes, 8 000 more than humans. If you wanted to be snarky, you would say it's about quality, not quantity. And it's probably true. As stated in the article, plants with larger genomes take longer to replicate those genes (considering there's so much more of it) and thus longer to reproduce.

It's one thing to sequence out the codes, that consist of only 4 "letters" (this in itself requires mammoth effort and time). It's another to figure out what it all means. Just by comparing genome sizes (150 billion base pair plant vs 3 billion base pair human), and then looking at the creatures they came from, you begin to wonder how all those genes fit together, or interact. And the interactions are sometimes never simple. Sometimes they are, and when you knock out or remove one gene, you see one specific loss of function (like fruit flies with black eyes instead of red). Sometimes, even after knocking down 13 genes reported to be associated with a trait, you still discern nothing. It's like Forrest Gump said, "life is like a box of chocolates, you never know what you gonna get". Until you go ahead and pick one, of course it's never haphazard. We have bioinformatics (computers) that can predict what some genes do, if they can do anything at all.

One of many uses of having fully sequenced genomes from many organisms, is that you can compare the similiarities of the genes. 75% of human genes associated with disease can be matched up with genes in Drosophila, the much studied fruit fly (factoid from wikipedia). Numbers schmumbers, we're still made up of a lot of the same codes.

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