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Photo: UC Davis

A trio of UC Davis researchers, including Professor of Animal Genetics Juan F. Medrano, teamed up to sequence the genome of Coffea Arabica, the species responsible for more than 70 percent of global coffee production. Released earlier this year, the sequenced genome provides vital information for developing high-quality, disease-resistant coffee varieties, which will prove highly beneficial to sustaining the future of the industry.

Medrano spoke with Laboratory Equipment’s Managing Editor Lauren Scrudato to elaborate on the significance of this project and how emerging genome sequencing technologies enabled the progress of his team’s work.

LS: What was the inspiration behind focusing on the C. Arabica strain for sequencing?
JM:
There are a number of issues happening with coffee. In 2013, there was a large coffee roast epidemic in Central America – 55 percent of the crop was lost and about 374,000 people lost their jobs. You think back and think, ‘Well, what is being done about this? Can we use new technologies to look into this?’

LS: How did the genome sequencing technology from Pacific Biosciences contribute to the success of this project?
JM:
One of the cases in developing a genome sequence is the structure of the genome, because characteristically they have a lot of repeats. Repeats are difficult to identify using short-read sequences. The advantage of Pacific Biosciences is that you can sequence very large fragments, from 20 to 40 kb, and that allows you to cover all the repeats, so you can do a much more continuous assembly. It’s a significant advantage when the objective is to develop a complete genome sequence.

LS: What were some of the challenges you faced when sequencing the complex genome?
JM:
When you’re doing a genome sequence, there’s always challenges. Sequencing is perhaps the easiest part, but then the issue becomes developing the assembly, and the bioinformatics involved, putting all this together and trying to make sense of all the sequences. I think that is the key component of developing a genome sequence, so that was a bit challenging. But the new technology developed by Pacific Biosciences facilitated this work, as well as new technology from Dovetail Genomics was really valuable in helping us with the scaffolding of the assembly.

Juan Medrano, Professor of Animal Genetics
Photo: UC David

LS: How can having the sequenced genome enhance the development of coffee crops that can cope with threats like changing climate, disease, etc.?
JM:
Developing a genome sequence is basically the beginning of the story. The next step is to annotate the DNA you have – ‘what genes are present, how many copies of these genes are there’ –  and then identify the function of these genes. Once you begin doing that, then you start to see a picture in which this information can become useful in identifying genes related to traits that may be of economic value to coffee, like disease-resistance, quality and climate adaptations.

LS: California is the first state in the continental U.S. to grow coffee plants – do you envision this discovery will prompt other parts of the world to grow as well?
JM:
We hope that the knowledge we have developed will contribute to the improved production of coffee in California. California is unique in terms of coffee production because it is far away from the tropics. But a farmer in Gardena, CA has been able to implement technologies and scientific understanding of agriculture to adapt the crop to this given environment. It’s a complete learning process – ‘how do you irrigate coffee, how do you fertilize coffee, what are the changes in timing in flowering and harvesting of coffee’ – so I think it’s been an interesting process to develop coffee production in California and we hope that with our understanding of the genome, we contribute to coffee production here and in similar areas.

LS: How does collaboration with other researchers help progress research projects like this?
JM:
That’s the fun part of doing research, when you find very good collaborators who are also good friends. The three of us that participated in this project work in genomics in different areas – Allen Van Deynze is a plant breeder and worked with peppers, spinach and number of other crops. Dario Cantu is a plant pathologist working mainly with grapes, and I’m an animal geneticist so I’ve worked with genomics of cattle. The multi-disciplinary approach gives you a better vision to the individual problems you have in regards to the sequencing, and moving forward with the project. That’s the strength of UC Davis, there’s such diversity and opportunities here to collaborate, making it a unique environment.

LS: How do you envision genome sequencing technologies progressing into the future?
JM:
I think the technology has progressed significantly. Every time we look at it there’s some new advancement. The opportunity to use the specific Pacific Bioscience technology was tremendous in terms of allowing you to do a total sequence. And what’s happening lately, is that the cost is going down. The throughput that can be put through machines has increased significantly so I think it’ll become a lot easier in the future and much more affordable to be able to sequence genomes and assemble them correctly, quickly. Also, not only the sequencing, but the bioinformatics component that puts all this together and makes sense of the sequences and does the annotation quickly. We’ll be able to characterize many genomes in the future that have not been done up to this point, which will be very valuable.

LS: How can having the sequenced genome enhance the development of coffee crops that can cope with threats like changing climate, disease, etc.?
JM:
Developing a genome sequence is basically the beginning of the story. The next step is to annotate the DNA you have – ‘what genes are present, how many copies of these genes are there’ –  and then identify the function of these genes. Once you begin doing that, then you start to see a picture in which this information can become useful in identifying genes related to traits that may be of economic value to coffee, like disease-resistance, quality and climate adaptations.

LS: California is the first state in the continental U.S. to grow coffee plants – do you envision this discovery will prompt other parts of the world to grow as well?
JM:
We hope that the knowledge we have developed will contribute to the improved production of coffee in California. California is unique in terms of coffee production because it is far away from the tropics. But a farmer in Gardena, CA has been able to implement technologies and scientific understanding of agriculture to adapt the crop to this given environment. It’s a complete learning process – ‘how do you irrigate coffee, how do you fertilize coffee, what are the changes in timing in flowering and harvesting of coffee’ – so I think it’s been an interesting process to develop coffee production in California and we hope that with our understanding of the genome, we contribute to coffee production here and in similar areas.

LS: How does collaboration with other researchers help progress research projects like this?
JM:
That’s the fun part of doing research, when you find very good collaborators who are also good friends. The three of us that participated in this project work in genomics in different areas – Allen Van Deynze is a plant breeder and worked with peppers, spinach and number of other crops. Dario Cantu is a plant pathologist working mainly with grapes, and I’m an animal geneticist so I’ve worked with genomics of cattle. The multi-disciplinary approach gives you a better vision to the individual problems you have in regards to the sequencing, and moving forward with the project. That’s the strength of UC Davis, there’s such diversity and opportunities here to collaborate, making it a unique environment.

LS: How do you envision genome sequencing technologies progressing into the future?
JM:
I think the technology has progressed significantly. Every time we look at it there’s some new advancement. The opportunity to use the specific Pacific Bioscience technology was tremendous in terms of allowing you to do a total sequence. And what’s happening lately, is that the cost is going down. The throughput that can be put through machines has increased significantly so I think it’ll become a lot easier in the future and much more affordable to be able to sequence genomes and assemble them correctly, quickly. Also, not only the sequencing, but the bioinformatics component that puts all this together and makes sense of the sequences and does the annotation quickly. We’ll be able to characterize many genomes in the future that have not been done up to this point, which will be very valuable.

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