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Barn Swallow Project Helps Introduce PacBio Long Read Technology to Italy

Monday, December 3, 2018

Its reliable return to the same spot year after year has made the barn swallow a beloved symbol of Spring and safe passage, for mariners and landlubbers alike. But our changing climate is altering the birds’ migratory behavior, and Italian ecologists are turning to genetics to figure out how.

As reported previously in this blog, scientists at the University of Milan joined forces with researchers from the University of Pavia and California State Polytechnic University to create the first high-quality reference genome for the European barn swallow (Hirundo rustica rustica), using SMRT Sequencing and newly available Bionano Genomics optical mapping at the Functional Genomics Center in Zurich.

To mark the publication of the work in the journal Gigascience, we spoke with Giulio Formenti, co-first author with Matteo Chiara, about their pioneering use of long-read sequencing in Italy and the technology’s potential to change the field of behavioral ecology.

 

Why the barn swallow?

The barn swallow is a very important species from a scientific and ecological perspective. It has been a model species in behavioral ecology, with around 1,600 studies published since 1985 about the birds’ migration, reproductive behavior and variability, but there have been very few genetic studies. 

In our lab (PI Prof. Nicola Saino), we have been studying this species for a very long time, but we were hindered by a lack of a reference genome. We had been relying on genomes such as that of the flycatcher to design probes, primers and other experiments. The flycatcher is a relatively closely related species, but it has often turned out not to be close enough. It was preventing us from designing probes correctly or, even worse, led us to design probes that seemed OK, but ended up not working, ruining experiments and causing people to waste a lot of time. This is a serious issue, and the reason why it is so important to have top quality reference genomes to work with.

 

Why did you choose PacBio sequencing?

One of my previous projects was concerning Huntington’s Disease, which is caused by expanded C-A-G repeats. It was very hard to study these repeats due to limitations of short-read technology, but a few years ago it became possible to do it with long-read technology. So I had already explored the realm of long-read technology and proposed it for this project because I knew it was much better in terms of results. I was also inspired by the preliminary results of genomes generated by the Vertebrate Genomes Project.

When we started drafting the proposal in November 2017, I knew very little about the technical aspects of long reads. But I went to the PacBio UGM (User Group Meeting) in Barcelona, met people from the Functional Genomics Center in Zurich, and started collaborating with them. By January, they had started the sequencing, which took a few months, then we spent a few more weeks assembling the reads. By July we had completed the assembly, aligned, annotated and analyzed the results, and submitted our paper. Now, almost exactly one year later, we have a publication; for this kind of project, I think it’s quite impressive in terms of speed.

“Long reads, and in particular PacBio reads, appear to be the key to 21st century genomics.”

 

Bionano optical mapping shows single DNA molecules that flow inside nanometer-sized channels on a silicone support. Fluorescent compounds that bind tightly to the DNA help visualize the molecules themselves (blue) and some specific sequences (light green).

What challenges did you face?

Long-read technologies are not so well-known in Italy. In fact, the very first PacBio Sequel machine in Italy was purchased just a few months ago by the Department of Biology at University of Florence. So we had to send our samples to Zurich, where we also had the opportunity to use the latest optical mapping technology, which had just been released by Bionano in February. This added a whole new element to the study, and resulted in very high level, near chromosome-level scaffolding.

 

What are the potential impacts of this research?

Barn swallows are famous for settling into a particular spot and returning there after migration for several years. Here in Italy, people wait for the barn swallow to appear as a sign that Spring has started.  But this is something that is changing as the climate changes. They are not coming back to the same place. They are now dispersing — partly to avoid inbreeding, but also because they seem to be sensing changes in the ecological conditions at their destination.

We had remarkable findings in a paper we recently published in Scientific Reports, which showed that the birds were able to predict the climate conditions of their destinations several weeks in advance, and that they were changing the timing or location of spring migration accordingly. It’s important to understand what’s going on here, and the availability of a high quality genome sequence will accelerate our efforts to learn how these adaptive processes could help populations respond to changing environmental conditions.

I hope that now that the paper is out, there will be many more people joining such efforts. We desperately need more people in the field who know how to use this technology. Most ecologists working with non-model species are still not incorporating genomics. They tend to look at phenotypes, and are not so familiar with changes at the genomic level. Studies of the effects of radiation from the Fukushima nuclear accident on butterflies, for example, have been based on phenotypic abnormalities, but no genetic evidence. This is one of the fastest developing fields in science, and we need to be able to understand genetic and bioinformatic data in order to deal with new challenges, and those that are already here. This is how modern biology is going to be.

 

What’s next?

European Barn Swallow

As a scientific community, we have started to realize since the Human Genome Project that we need many genomes in addition to reference genomes, to understand variation across populations. With this project we wanted to generate a resource that we and others could then build upon.

As soon as we got the sequence, we started new projects to study the genetic impacts of environmental changes in swallows from different parts of the world, such as radiation fall-out locations. We are also re-visiting our work on migration phenotypes to study their associations with variations in genes, such as those dealing with circadian rhythm.

 

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