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Novogene partners with the BiGTREE Training Programme for Biodiversity Genomics Research and Education

The BiGTREE training programme was established to provide funding opportunities for students from Colombia and Peru with an interest in evolutionary genetics, paleo-genomics, and biodiversity genomics to take advantage of the expertise and facilities available across three Norwegian institutes. The programme is a collaboration between the Norwegian University of Science and Technology (NTNU), the University of Bergen and the University of Oslo, each of which conducts state-of-the-art research at their respective natural history museums and has cutting edge genomics equipment at their disposal. The partners in Peru include the Universidad Nacional Mayor de San Marcos (UNMSM) and the Columbian partners include Universidad ICESI and Universidad del Rosario. There are also opportunities for Norwegian students to travel to the partner universities for masters and PhD exchanges.

Michael Martin is a Professor of evolutionary genomics at the Department of Natural History at NTNU and the project manager of the BiGTREE training programme. We recently spoke with Professor Martin about how the programme came to be and his hopes for it as it continues to develop.

How was the programme established and who is involved?

“The Norwegian Directorate for Higher Education puts out a call every four years to fund the establishment of training networks with partners in the Global South. It provides money to set up courses, fellowships for full-time masters programmes, and stipends for 3–6-month exchanges for masters and PhD students. I was already collaborating with my colleagues at the Universities of Bergen and Oslo for other projects, such as the Research School in Biosystematics project, which has been running for around 10 years now. This partnership now provides courses that prioritise the admission of Peruvian and Colombian students, and we are currently endeavouring to make these courses 100% online so they can be undertaken from anywhere.

“Because of these previous collaborations, the network for the BiGTREE project developed quite rapidly and organically towards the funding application deadline. I work with a Peruvian PhD student and a Spanish-speaking post-doctoral researcher named Dr. José Cerca, which made connecting with the Peruvian and Colombian universities much more straightforward. People they had previously worked with from the countries allowed within the grant parameters, who had an interest in biodiversity genomics, were contacted with an invitation. We got an excellent response, with really ambitious faculty members eager for some more international research experiences. We applied using this framework and some proposed collaborative teaching efforts and were delighted when we won the funding.”

Are you excited about any project in particular?

“All of them! We have such an excellent ancient DNA department here at NTNU so we are ready for the kind of samples that will be coming to us with these projects. There are archaeological sites in Peru that date back to pre-Incan times that have never had any genetic analysis applied, and there are so many interesting stories I’m sure are yet to be told. As an example, the Peruvian hairless dog is widely kept as a pet in Peru and there have been some ancient dog burials recently uncovered at the Tucumé archaeological site – it will be interesting to find out if these dogs are related to the modern breed and may give answers about domestication of animals as pets. There are a lot of interesting anthropological and botanical questions I believe can be answered from samples at this site. Another example is some of the featherworks that have been discovered there. The project to identify the parrot species these feathers came from is already underway. Interestingly, the feathers are not from birds that are native to the Peruvian coast, so they must have been traded from the Amazon regions. It will be fascinating to use this information to reconstruct how feather movement from the Amazon, over the Andes, to the coast, actually happened.”

Is there a particular significance to the Tucúme archaeological site you mentioned?

“It is one of the most productive pre-Incan and Incan archaeological sites in Peru, with lots of beautiful monumental architecture, and it’s the one that needs to be studied. The materials recovered from that site contain the answers to so many questions. We have other projects underway studying the abundant botanical samples found there, such as peppers, cucumbers, and peanuts, which are the domestic species still used today. Ancient DNA always adds a lot more interesting information beyond the physical presence of these samples, so there is a whole evolutionary history to their domestication that can be tracked using genomics.
“There is a plant called Nectandra that is sold in markets around Peru due to its medicinal properties for stomach ailments. Seeds have been recovered from the site in association with ritual killings, and our hypothesis is that the seeds of the plant were given to the people to be sacrificed to drug them and prepare them for the event. It will be interesting to see if we can match it to the modern species with genomics and whether it’s the same one being used for medicinal purposes today.”

Are all the projects based on specimens from the Tucúme site?

“Not at all, we’ve got a really diverse range of projects from across Peru and Colombia. We have one project looking at the underlying genetic mechanism of colour polymorphism in Gasteracantha cancriformis, a spider with a habitat that extends from the southern United States to northern Argentina. Another project is aiming to characterise the root fungal microbiome of the Espeletia plant, which is found in páramo habitats of Colombia. This plant is an example of adaptive radiation in plants where there was a rapid radiation of species from a common ancestor in response to an ecological niche that needed to be filled. It grows in high altitude planes of the Andes. We would like to find out if the root’s fungal microbiome is related to the function of the plant in its ecosystem or if it is unrelated.”

Are some of these projects underway already?

“Yes, we have a number of students from Peru and Colombia already here with us in Norway and their projects are full steam ahead. As a lot of the specimens we are analysing are from museum collections and sites in Peru and Colombia, one of the students had to carry over 500 specimens in his hand luggage! But we had all the paperwork organised well in advance, so it went smoothly. There was excellent work done in advance of his travels with a large team employed to sample and prepare the specimens in accordance to how they will be analysed, it was a great collaborative effort.”
If Norwegian, Peruvian, or Colombian students would like to get involved, what can they do?

“We have an “apply” section on our website where students can go if they would like to be considered for the programme. There are opportunities for Norwegian students to study in Peru and Colombia and for Peruvian and Colombian students to come to us. Under the “opportunities” tab of our website there is a synopsis of a range of projects available from our partner universities. Students can also apply with an idea of their own if they have a particular area of interest they would like to pursue.”

Novogene are the official sequencing partner for this project, what will we be doing for you?

“Yes, I have worked with Novogene in the past and find them very straightforward, flexible, and fast to work with. I’m delighted to be working with them again for such a big undertaking. Our next generation sequencing needs for the various projects will include RNA sequencing, de novo transcriptome assembly, metagenomic analysis, and whole genome sequencing.”

Novogene are delighted to be working on this project and are looking forward to lending our next generation sequencing expertise to the ground-breaking research being carried out by Professor Martin and his collaborators. We wish them every bit of luck and hope to keep up to date as the projects progress!