In the second episode of Genomic Connections, Kasia and Christian are joined by Claudio Ciofi, Professor at the University of Florence (UNIFI) and founder of the Florence High-Throughput Sequencing Facility.
They ask Claudio about the many ways DNA information is empowering biodiversity research and improving conservation outcomes, the top methods and technologies for obtaining high-quality genomic data, his first-hand experiences working in the field to collect samples from fascinating species such as Komodo dragons and Galápagos tortoises, and, finally, his vision for the future of the rapidly evolving field of biodiversity genomics.
You can listen to Genomic Connections on Spotify and PocketCast. The RSS Feed is available here.
The episode’s full Transcript (AI-generated) is available below the credits.
Credits
“Genomic Connections” is a podcast about the science, stories, and people behind biodiversity genomics produced by ERGA and iBOL Europe within the Biodiversity Genomics Europe (BGE) project.
“Genomic Connections” is written and produced by Christian de Guttry, Kasia Fantoni, Luisa Marins and Chiara Bortoluzzi.
Graphic design by Luisa Marins.
Music (intro and outro): “Nostalgic Reflections” by Ant.Survila (c) copyright 2025 Licensed under a CC-BY-NC 4.0 license. Ft: airtone.
BGE is a Horizon Europe project funded by the European Commission, the Swiss Confederation and the United Kingdom.
The episode is licensed under a CC-BY 4.0 license.
You can listen to Genomic Connections on Spotify and PocketCast.
Episode #2 Transcript
0:01: A friend of mine convinced me to buy a DNA test kit, you know, , one of those where you spit and send the sample to the company.
0:11: Oh wow, so you’re going to learn the secrets of your ancestry at last, right?
0:16: Yeah, I’m tempted, but then I started wondering what’s actually going to happen with my sample once I mail it off and who is going to do the sequencing and keep the data.
0:29: Yeah, that’s a great point, but you know that sequencing isn’t just about ancestry kits.
0:33: In biodiversity genomics, we rely on professional sequencing centres where samples are processed and managed similar to a high-tech lab in a movie.
0:42: Yeah, exactly.
0:44: And that’s what we are exploring today.
0:46: Why these centres are so important, how they handle thousands of samples at a time, and what makes them special in our field.
0:53: So in other words, we’ll get the insight scoop on how a sequencing centre works.
0:59: I am Christian De Gutri, URA project manager, and I am Kasha Antoni, AO Europe Community Manager, and this is Genomic Connections, the podcast about biodiversity genomics.
1:14: For this episode we are joined by Claudio Shofi, professor of ecology and molecular ecology at the University of Florence in Italy.
1:23: Claudio has had a truly international career, including operating his PhD in the United Kingdom and two postdoctoral appointments in the United States.
1:33: Still today he keeps intense international collaborations.
1:36: Indeed, Claudio co-founded the European Reference Genome Atlas ERA.
1:41: And he is also part of the coordination committee of the Biodiversity Genomics Europe project.
1:47: Both of them are particularly dear to our podcast.
1:51: Also, Claudio holds special collaboration with Indonesia on reptile conservation biology and genetics.
1:59: At the University of Florence, Claudio set up a molecular genetics lab focused on wildlife conservation, and he also founded the Florence High Throughput sequencing Facility.
2:10: The university itself is one of Italy’s largest and most active public research institution.
2:16: It takes part in a lot of important research projects, both nationally and internationally, and it offers more than 140 degree programmes across all the main disciplines, making it especially appealing to students from abroad.
2:31: But after this huge advertisement, most importantly, who would not enjoy a visit to Tuscany?
2:37: But OK, let’s get started with the, with our questions.
2:45: Claudio, why it is so important to use DNA in biodiversity research, be it barcoding or reference genomes.
2:56: Well, Christian, this is, , that is a, , a perspective that I generally bring up to my, , students in, , conservation genetics and also molecular ecology classes.
3:09: , in fact, there are a number of, , , questions that cannot be answered or resolved or are very difficult to resolve, , using, , standard ecological, , methodology.
3:22: , for instance, how do you assess the level of biodiversity of an area or, , how do you assess the presence or, or the absence, , of a species, , being that species a rare one or an invasive species that, , say just arrived in a region.
3:40: You might want to go and use, , a classical ecological techniques in which you, you go and try to , capture a species in the field or you can go for noninvasive sampling, , so, , go into the field and collect, , , part of, of an animals had had been left in the territory.
4:07: And use these, , these non-invasive biological samples like for instance, a, a bunch of hair or a faecal samples, and classical non-invasive sample samples, and you extract DNA from these samples and From this DNA you can basically characterise a sequence of DNA, a barcoding sequence, OK, which is which is species specific, which tells you which species that samples belong to.
4:38: And this is a very, say very important aspect of, of barcoding.
4:45: So to identify a Particular species in a in a territory without seeing the animals at all and that’s that’s important again for species that are very cryptic or elusive or or invasive species that have only just one individual that just arrived in a particular area of interest.
5:04: With the same methodology which is, which is called generally meta barcoding and the world basically.
5:11: Is kind of self explanatory.
5:13: You can use environmental samples and so samples like of water or of soil you extract the DNA from these samples and then in this DNA you have all the genomic components of the of all the species that have been.
5:32: They have been or are living in that, in that area and that left a tiny particles of their body in the in, in, in the terrain or or in the water, OK?
5:45: And so we extracted NA from, from these from these environmental samples and you can then with the with novel, , 2nd and 3rd generation.
5:59: , sequencing techniques, , you can have an idea of how many species are in that area because, , you can identify the, these, , , species specific, , barcode, , DNA, , that belongs to the species that, , that live in the particular territory.
6:23: So with, with barcoding and meta barcoding, you can identify species and, and describe biodiversity in area, , most of the time much quicker than you can do with classical ecological techniques.
6:37: I mean, the methodologies are, , they complement each other.
6:41: It’s not that the, the one is, is better than the other.
6:45: But, , molecular genetic techniques basically have proven to be very useful to say improve the knowledge of the biodiversity of a certain territory, something that now is required by by the European Community, for instance, to the to the local authorities, particularly in Italy with genomics on the other hand, you go.
7:07: And assess in first say the the evolutionary history of the species, how a particular taxa say have colonised the territory and how it disperse in the territory.
7:18: So describing movements of individual is important, say to .
7:23: Assess for instance connection among populations and say see for instance whether ecological barrier exists and this is important for assessing whether restored, for instance, ecological corridors actually function, OK, in the restoration in restoration ecology.
7:44: Describing movements of individuals is very important.
7:47: Again, you can, you can do that by using classical ecological techniques like, , for instance, GPS tracking, OK, or capture marker capture in which you capture the animal, you mark the animals, and then you again, you try to recapture the animal to see where it go, where it went.
8:06: , but, , that has some limitation about, I mean, the, , the effort that you had to, , make to, , to trap the animals and, , see whether you are, you are trapping and you are, , , collecting, , you basically, you’re marking the right ones that make, that, that do move, , from one population to, to the other.
8:29: With genetic, with, , with the, with the genetic and particular genomic, , , genomic studies, you can have, you can have information on the average number of individuals that per generation they move from one population to the other.
8:46: Again, and this is quite important to assess both, both the success of ecological restoration programme.
8:57: But and also to identify in this case, , how distinct and how isolated populations are OK, , this is important as we all know that maintaining a high level of genetic diversity in the population is crucial to assess whether this population is viable and then determine whether.
9:22: , this population, , is, , is prone to extinction or not.
9:27: high, high level of genetic variability bring with itself, a good chance for the population of survival, a low genetic variability can basically lead to physiological, morphological, , , defects, you know, and, and then, , increase the risk of extinction.
9:48: So.
9:49: Maintenance of genetic diversity is important also to see as we know to respond to climate and therefore habitat changes and assess whether say dear mutations exist that may imperil again the survival of the species.
10:10: To make things a bit more tangible, , you know, people often want to know, , about real life, real world impact.
10:21: , do you have any success or intriguing story for both barcoding and genome that you can share?
10:29: I’ve been working and I’m working on, , on, on tropical species.
10:33: Yeah, I’ve been working on, , on giant Galapagos tortoises and, and, , and I.
10:38: Keep working on Komodo dragons in, in southeastern Indonesia and for both species which are of conservation concerns, one thing that genomic has served in particular.
10:56: Was the again the identification of of conservation of management units for conservation, OK, something that that both barcoding, so the characterization of, of single DNA sequences and a more comprehensive view of the genome have .
11:23: Have helped us to do in on in the Galapagos tortoise, for instance, , you know, the Galapagos tortoises are found on different volcanoes in Galapagos Island and there is.
11:37: A centre in Santa Cruz in the island of Santa Cruz where these animals are bred in captivity and these tortoises, some of these these tortoises come from from parents which origin was unknown comparing basically the the genomic signature of each young tortoise with the genomic signature of white population.
12:07: , the centre can basically, , choose, , which population is the most similar from a genetic point of view and therefore can basically translocate or reintroduce the particular individual to the population of origin and these assessment, the assessment of the different.
12:24: In among the national population has improved with genomics from single locals to multi-locals to genome wide say comparison of national population in a similar way we are working in in in Indonesia.
12:42: There is, , within the, the range of Komodo Dragon, , which is in, in the archipelago of Komodo National Park and the Island of Flores in the southeast, southeast Indonesia is about 500 kilometres east of Bali, , north, say, , a bit north of, , of Darwin in Australia.
13:03: , in this, , in this archipelago, , you basically have 6, different island population in one, in one island, , these species went extinct in the early 80s and because of because of pushing of its main prey, the Timor deer.
13:27: , since the establishment, basically of of Komodo National Park, the deer has been reintroduced, and the, , Indonesian government, , wanted to know whether these the predators, the Komodo dragons could be reintroduced as well in this island.
13:42: And again, knowing the genomic structure of the, , the, the, the extant populations, , it was very important to determine.
13:55: If we had to, we were to choose individuals from the from the national population which individual we had to choose to create a new population for introduction so that the genetic variability of this population is high enough to have a a high chance of survival in the generation to come and for these having a.
14:17: A comprehensive view of, of the genomics of natural population is very important for in this case, reintroduction purpose and in the case of Galapagos Island for demographic reinforcement, let’s say, purposes.
14:35: These are fantastic stories, Claudio.
14:37: So basically, if I understood correctly with barcoding, you go there, you identify the species, and then with the reference genomes or whole genome sequencing, you then can study on how to better protect them and in the meantime, studying their history.
14:54: And that’s fantastic.
14:56: So you mentioned that now genomics improved a lot, these practises, and we know that genomics is closely linked also in its definition to the technology.
15:07: We hear much about the new tech like Oxford Nanoor, Pack Bao and high C sequencing.
15:14: So while all of them are excellent tools to enhance biodiversity genomics, what’s the one that made you go, wow, Oxford Apo, , And specific bioscience, , technologies are complementary techniques.
15:31: Oxford Nanopole provide long, , very long stretches of information on very long stretches of DNA, , and, , see bioscience techniques provide information of long stretches of DNA a bit shorter than oxo nanopore but with a slightly higher quality, OK.
15:52: Then you have these methods on the, the high C metals which are metals basically to capture to understand chromosome conformation and and then characterise they say the number of interaction between genes that may be separated by many nucleotides in the, in the linear genome.
16:13: And, and this again a method that complement the long long re technologies to describe chromosome level genome.
16:24: , among these techniques, the first that we used and we, , have been very excited with, , was indeed the second one.
16:34: So the one, provided by, , by, , Pacific Bioscience.
16:39: I don’t want to make any advertising advertising here.
16:42: I’m just saying that.
16:44: Generally labs that are relatively young laboratories, OK, they and they they have no they have some limits budget wise they generally are forced to choose one techniques or the other at first they can they can’t afford to buy all platforms that are on the market so we focused on.
17:07: On the pack Bao, , mainly, , because of high quality of the, , sequences that this technique, , provide, we started from Sanger sequencing in our lab, , which provide very high quality of DNA sequences then we moved to the .
17:28: To the short rate sequencing which is basically the the lumina or sequencing by synthesis techniques, OK, which again has a very high quality of provide very high quality of DNA sequencing but characterising short rates of DNA.
17:46: And pack Bao basically gave us the opportunity to look at DNA with the same amount of accuracy or or or very similar to the amount of accuracy that you can that you can get with the lumina sequencing so with the with the sequencing by synthesis technique.
18:08: With all of this, it means like that there are samples which are stored, , preserved somewhere, and indeed we know that biobanking is essential to keep the samples fresh.
18:21: If the future scientists were to discover one of your stored samples 50 years from now, what do you hope or wish they could learn or do with it?
18:32: We, we do take advantage now, no, of the, of the reconstruction of genetic structure.
18:37: of extinct population using museum samples or biological remains.
18:43: , this has been done again same example with Galapagos tortoises where bones of, of dead tortoises have been found on islands where these species, .
18:58: , went extinct and from these bones, , DNA was extracted and, and, and with that we were able to basically to reconstruct the degenerative structure of an extinct populations.
19:10: And again, this is important for reintroduction, reintroduction purposes.
19:15: , so I, , something that, , the samples that we have now say in the, in the ultra freezer.
19:24: , again, can be used basically for similar purposes.
19:30: So to compare the genetic structure of current populations to the genetic genomic structure of the population will, which will have survived in 50 years from now.
19:43: The difference is in 50 years they will be able.
19:46: , for sure they will be able to to to make a much better prediction on population viability and survival potential that we are able to do now based on, on, on the, on this comparison.
19:59: So comparing the genetic structure of ancient population.
20:05: A population that 50 years ago with the genetic structure of current populations, one can make prediction knowing the difference in this genetic structure, , and genomic components make prediction on the viability and the, the, the chance of surviving on this population with The tools both genetic and bioinformatic tools that we will have a disposal in 50 years from now, I think that this prediction on population variability which will be much, much better and much, much improved respect to to to the present.
20:49: Thank you, Claudio, and let’s hope that the technology will give us other views of the DNA compared to what we have today in 15 years.
20:58: Maybe only one click or one picture would reveal the species’ DNA.
21:02: Who knows how things will go in the future.
21:06: , so now what regarding your lab, could you give us a sneak peek at what’s the next big thing in the horizon that you can’t wait to tackle?
21:16: Perhaps the possibility of analysing genomes with the same speed and ease with which we now analyse single or multi-locus part of the genomes.
21:34: , analyse genomes for say hundreds of individuals, , , , again with, , with the same, .
21:45: Economic and logistical and equipment possibility that, that we are using now to, to analyse to, to do multi-local assays or reduce representation or using reduced representation techniques.
22:00: , particularly for say subtleties of the genomes that make a small population surviving, , heart condition without say going extinct.
22:12: OK.
22:12: Now, , we can do this with pos with economic and, , facility, , possibilities, possibilities that we have, we, we, we can do this.
22:24: With tens of a few hundreds of individuals, but the, the, the, the vision here is to, is to enlarge this to, to make it easy to, to, to, to characterise the part of the genomes for hundreds of individuals much easier than we can do now basically.
22:44: And, , from the lab, I would move to the field and I ask you, what happened?
22:52: What’s the most unexpected experience you’ve ever had while sampling like some sort of Indiana Jones moment?
23:01: Well, I can’t say with cargos tortoise because they’re quite a timid animals.
23:06: , I will have to think, , something about Komodo dragons.
23:11: , and, , The, the, the, the, these, these animals are generally very shy and wary of human beings, OK.
23:21: Although tourists now that goes to to specific part of Komodo National Park, they are used to see these animals resting on the ground or basking, , , and they see not, not to be bothered by, by, by humans.
23:39: , they are.
23:40: Basically just used to the presence of humans, but these are just a very tiny proportion of the number of individuals that one can find in Komodo National Park.
23:49: And I remember in a, in a, in a, in one of the smallest islands on the southern very southern part of the part that overlook basically the south, OK, , Timor and then Antarctica basically, , , in these islands, these, these Komo dragons have never seen a human being.
24:10: , so we, we expected these animals to be very, , very difficult to find, very difficult to capture, , very difficult to see.
24:20: And while we were walking, , I remember on a trail that we were, , the, the, the, that, that we that we did, , , cut, , , across the, across the, across the tropical forest, we at a certain point, all of a sudden and basically we notice a, a, a relatively large dragon aiming for us running down the hill.
24:47: , aiming, , against us, and I basically stopped, , wondering what what is this guy doing, .
24:57: Don’t you see that we are humans, , we are not something to eat.
25:01: Probably he, he or she confused us, , for deer, , because the size basically of a Timor deer is the same size of a, , of a, of a person which is seen, , which, which is, , , seen from uphill, .
25:22: And, and in fact, after basically when, when this animal arrived approximately 3 or 4 metres from us, suddenly stopped, , gazed at us, looked at us for a couple of seconds, turned around and then run away.
25:37: So that was the, , , one of the one of the occasion in which we were basically actually attacked by these by these species.
25:49: But, , , this piece is basically these animals didn’t realise what we were.
25:56: We were the what the he or she was basically confusing us as a prey that we were in a play but actually human being in that in that case are kind of.
26:07: , top predator as they are.
26:11: Well, fantastic.
26:12: That’s a fight or flight situation that you experience.
26:18: OK, let’s move on to the, to the last question.
26:20: So before we wrap up, if you could have any historical or fictional or contemporary character as your intern in your lab in your sequencing centre for a week, who would be it and why?
26:36: It, I, I don’t think it will be someone technical, say someone that knows about techniques, let’s say in the lab but some more some someone that could inspire, say.
26:51: Our, our conservation work in general, I would think of, , , say scientist or conservationist who has inspired me during my, , academic career as well.
27:06: , Gerard Darrell is one of these.
27:08: , Gerard Darry was a, you know, a British naturalist, , writer, a conservationist, and Was the one basically who envisaged the first zoos that’s not just a showcase for the public, let’s say, but it was aimed to captive breeding and reintroduction of endangered species into the wild and that inspired me quite a lot so .
27:34: , conservation biology and conservation genetics were in their infancies in the late 70s, in the, in the, in between the late 70s and the late 80s.
27:49: And Darl was one character which basically inspired my, my, my career, basically my studies.
27:59: Also, , Michael, Michael Sule, , , he is, , he was an American biology.
28:08: He, he died a few years ago actually, but he’s mainly known for his work promoting the idea of conservation biology.
28:15: , he was the co-founder of the first, , and the first president also the Society for Conservation Biology.
28:22: So, , , scientists basically that.
28:26: Won’t help us in the lab actually but will mainly help us to have a vision basically for the future for conservation of, of, of endangered species in general.
28:37: Thank you, Claudia.
28:41: This podcast is brought together by Biodiversity Genomics Europe, a project funded by the European Union, the Swiss Confederation, and the United Kingdom.
