View of the Abruzzo, Lazio and Molise National Park. Photo by Giorgio Bertorelle
In these days at the UniFi cytogenetics labs we have set the cell cultures of Bombina pachypus fibroblasts using a small muscle biopsy. The cells, once grown sufficiently, will be blocked in their metaphase in order to obtain the chromosome preparations, from which the individual chromosomes will be microdissected and then sequenced. The cells seem … Continue reading Setting up Bombina pachypus fibroblast cell coltures for chromosome isolation 24.10.2020
As for the other species of the project, the study design requires the analysis of the genomes from a small endangered population (S) to be compared with a large population (L). We were very lucky to be successful in sampling a small population of Hipparchia sbordonii from the island of Ponza on 24 June 2019 … Continue reading Fieldwork: sampling Hipparchia butterflies from the “large” population in Central Italy 4.10.2020
On August 25th, the Dovetail Genomics Omni-C™ library preparation kits were delivered to the University of Trieste. Learning how to master this complex library preparation protocol, that requires a two-days workflow to be completed, will be of fundamental importance to further improve the quality of the draft genome assemblies obtained with PacBio reads.Omni-C can be … Continue reading Getting familiar with the Omni-C™ library preparation kit 22.09.2020
One of the most important lessons we have learned over the past few years in Trieste is that storage space is never enough when you work with -omic data! Raw sequencing data, mapping, assembly and annotation data often usually end up taking several hundred Gb disk space, even for relatively small projects.On a very hot … Continue reading Ongoing work in the server room at Trieste 13.09.2020
Fieldwork: sampling Bombina pachypus from the “small” population in Northern Italy (part 2 of 2) 03.09.2020
Observing or collecting the Appennine yellow-bellied toad in its natural northern habitats is not trivial as it is mimetic and very rare. It lives in freshwater, shallow ponds in forest creeks (as the one we explored in our expedition in Emilia Romagna, northern Italy, see picture below) but also in equivalent artificial pools along ditches. … Continue reading Fieldwork: sampling Bombina pachypus from the “small” population in Northern Italy (part 2 of 2) 03.09.2020
Fieldwork: sampling Bombina pachypus from the “small” population in Northern Italy (part 1 of 2) 29.08.2020
One of the most exciting parts of this project is fieldwork, which provides the opportunity to observe these unique endemic species in their natural habitat. Our most recent sampling expedition aimed to collect the Apennine yellow-bellied toad Bombina pachypus from Northern Italy, in Emilia-Romagna.B. pachypus is endemic to the Italian Apennine chain. It is characterized by its bright … Continue reading Fieldwork: sampling Bombina pachypus from the “small” population in Northern Italy (part 1 of 2) 29.08.2020
After approximately a week from the reproductions, the first eggs started to hatch. The larvae are very different from the adults: it is evident the yolk sac that will be their first source of sustenance and will be reabsorbed in the next few days.
On a extremely hot day of June we went to the aquaculture plant ‘Storione Ticino’ in order to obtain eggs fertilized by different combinations of six pairs of siblings previously chosen through parental analyses, paired to produce six inbred and six outbred lineages.This aquaculture plant, located within the area of the natural park ‘Valle del … Continue reading Breeding Adriatic sturgeons 14.08.2020
Part of the Endemixit project at the University of Padova unit involves in vivo fitness studies of twelve outbred and inbred crosses of Adriatic sturgeon (Acipenser naccarii). For this reason, we set up a specific fish room which will allow us to rear the offspring resulting from our crosses. The room is provided with mechanical … Continue reading The fish room for the Adriatic sturgeons rearing is ready! 07.08.2020
Small but with a huge genome: the challenge of sequencing the Apennine yellow-bellied toad (part 4 of 4) 04.08.2020
As you may have noticed in the previous posts 1-3 on Bombina pachypus sequencing, the protocols use short read sequencing approaches to genotype the fragments produced by the library step. These approaches are useful as they provide high amount of very accurate sequences, but at the same time the short length doesn’t allow to be … Continue reading Small but with a huge genome: the challenge of sequencing the Apennine yellow-bellied toad (part 4 of 4) 04.08.2020
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