BP: Could you tell us about the “Cat Genome Project” ?
Mike: Well we decided to sequence a domestic cat genome in 2007 here. The genome was finished and
made available in 2011. This is from a cat, name Cinnamon. The genome was an improvement on
a previous draft assembly. Once we had the genome available, we were able to discover where the genes are located within the genome, and then we did some comparative analysis with genomes from other carnivores and non carnivores. We looked at dog, and we looked at Tiger also human and the cow. When we analyzed the genes from each of these organisms, we saw differences in the cat genome that made them distinct from these other carnivores and non carnivores. That was the first part of the study.
The second part was looking at the Wildcat genes compared to the cat genes to see what differences where in the cat genes that made them perhaps different from the Wildcat.
The third part of the study was looking at specific breed to determine what gene was likely involved in pigmentation pattern. The way the coat color of this breed, called the Birman breed was different from other cat breeds.
Those are the three components that we put together for the article.
BP: What does make cats different from other carnivores?
Mike: We noticed several genes that showed higher rates of evolution or quicker rates of change compared to the other genes in these other carnivores. These genes are typically associated with sensory systems.
Cats have very specialized hearing and vision. Some of the genes that were different from the other mammals that we looked at were involved with sight and hearing. We know this because when we see mutations in human genes that are similar, this results in things like blindness or deafness or loss of night vision. So we focused in the paper on these genes at that have something to do with the sensory system of the cats that allowed them to hunt and also to process a diet high in meat .Cats are carnivorous, they rely solely on meet and so we looked at to the genes that are involved in lipid metabolism. We find differences in these genes that make them distinct from other animals that we included.
BP: Cats’ processing speed between the time they see/hear something and act ,is very fast. Is this related to their intelligence?
Mike: We know that cats can sense sound waves that are different frequency from other carnivores. They have a wider range of sound waves that they can detect. I don’t know if I would call that intelligence but it’s an adaptation to be able to hear very quiet sounds, most likely in their natural habitat. Most cats are solitary hunters, so would help an animal that hunts to be able to hear very low frequency or very high frequency sounds that our ears wouldn’t be able to detect. The same goes with dogs, even the cow that doesn’t have as broad a range of hearing. These are the genes that we focused on because they’re involved in those processes that allow cats to adapt to the environment to be successful hunters.
BP: What about Cinnamon?
Mike: Cinnamon was housed at Missouri and she passed away several years ago, but we have a cell line and so we continue to use the DNA from Cinnamon and she passed naturally, she was an older cat when she passed. We are continuing to improve the genome and just because we published doesn’t mean that we’ve stopped trying to improve the reference so we’re planning on doing more work with her cells to improve the cat genome.
BP: In your research, do animals get hurt?
Mike: No. We took all the samples that we collected, were from small bits of tissue or you know cats have regular checkups in these facilities so maybe we draw blood and but none of the animals were harmed in any way to generate the data for this study.
BP: How will this project continue?
Mike: When our paper became available, the third draft of the cat genome was also made available. You can download the latest reference. This is a reference that we haven’t analyzed yet. It’s a new draft of the the genome and we’re already planning on a fourth draft of the genome to be made available possibly next year, 2016. This will be a high a highly improved cat genome again using the same DNA source, using Cinnamon’s cells. So, part of the plan for our next steps involve using some new technologies to improve the quality of the genome.
The second thing we’d like to do is to increase the number of cats that we look at. We will include more breeds and will include more Wildcats. This’ will give us a better idea of the process of domestication of cats and how Wildcats contributed to domestic cats,including different genes that are involved but the domestication process.
BP: Is genome analysis process probabilistic?
Mike: We had to take a step at a time ,so we have made available the reference genome that I analyzed in 2011, four years ago almost. With each release of the draft assembly, we have to do some analysis to see what we have. And each time that we improve genome, we expect to have better predictions for the genes and a more complete picture of what the genetics might be saying when we do different analyses. So, it’s possible that we could have different answers from different cats or different genome improvements.
That’s one of the goals to continue doing these types of analyses to see if the signals that we saw in my paper also hold up when we do it again with different cats and with an improved reference.
BP: You are an anthropologist, right?
Mike: Yes, I studied primates at graduate school.
BP: How do you participate to this study? What was interesting for you?
Mike: I’m mostly interested in genomics and learning about how to look at genomic data. So,
I can apply it to primate studies or humans or cats or flies,fish, birds .I mean the number of projects that I can be involved in is not less, because every biological organism has DNA. Being able to analyze DNA allows me to do these different kinds of projects.
BP: What about biostatistics? how does big data effect your research?
Mike: As you saw in our paper, we use a lot of different sequences from many different animals, many different cat breeds. So, we need powerful computers to perform the statistics that we are doing. We need to rely on computer programming and storing the data and visualizing the data. So, that’s also the new way of doing science compared to when I was doing my studies where with the monkeys and in South America the data that I was using wasn’t very big at all. So this is a new experience for me, doing a whole genome analysis.
BP: Are there any outside organizations participating in this project?
Mike: Some outside organizations funded the project. Morris Animal Foundation, Nestle Purina, Hills and other organizations veterinarians, pet food companies are some of them.