As previously mentioned Beth Shapiro and her team at the UCSC Paleogenomics Lab have been performing the initial sample analysis for our attempt to sequence the moa genome. Unfortunately the news is not good for our first batch of samples. Here’s Beth’s report.
We extracted only one sample (and one blank) as a first pass. We sequenced about 4 million reads, of which 99.8% were unique (which means the library was very complex, or that a lot of different DNA sequences were present in the extract). Unfortunately, only 0.04% of these mapped to the Tinamou genome, which is approximately the same proportion that mapped to human. We also attempted to map the reads to the Anomalopteryx didiformis mitochondrial genome, and recovered only a few reads (0.014X coverage). A comparison to all data available online using the software MEGAN indicated that 84% of the recovered reads mapped to bacteria.
In summary, this specimen appears to have a very high bacterial component. It is not really possible to tell at this coverage whether there is also lots of moa DNA, but the enormous complexity of bacterial sequences means that ~99% of the recovered data will have to be thrown away.
If you want us to repeat the process or to sequence the sample more deeply (to see if we can learn whether there are lots of molecules of moa DNA present) we will. However, it might be better to attempt this with a better preserved bone at this point — one where the proportion of moa DNA to bacterial DNA is skewed more in favor of moa.
So unfortunately the first batch of samples appear to contain very little endogenous DNA. Therefore we will be resuming the hunt for better samples and will be repeating the process with the UCSC Paleogenomics Lab.
This result although disappointing was not particularly surprising. Obtaining a sample rich in endogenous DNA is very difficult, and it’s often necessary to process many samples before one of sufficient quality can be found. We will obtain a new batch of samples and repeat the process with the hope of more favorable results in the next round of analysis.