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Project updates: 15. January 2019 – Project finished 

The project has officially finished and all the planned milestones were completed. We are now happy to have comprehensive molecular raw data available and further extensive analyses are underway. We are excited with the obtained results while we are drafting our manuscripts. The presentation of the preliminary results was done at the 7th Balkan Botanical Congress in Novi Sad, Serbia, and the next presentation will be at the 6th Croatian botanical symposium in Zagreb, Croatia, and at the XVI OPTIMA Meeting in Athens, Greece.

Project updates: Last Aurinia A4 & A5 libraries finished in Innsbruck

Ivana Rešetnik finished the last two RADseq Aurinia A3 A4 & A5 libraries at the Research Group Evolutionary Systematics, Institute of Botany, University of Innsbruck. In total 2x96 samples representing species A. saxatilis were included in the library.

Photos: Gel electrophoresis after the library PCR amplification of the selected fragment sizes. The results of the final step of checking the library quality with the Agilent High Sensitivity DNA Kit on the Bioanalyzer before sending the library for sequencing to the CSF Vienna facility, the sample is checked before and after the final SPRI size selection process.



 

Project updates: Analyses of AFLPs in progress

The analysis of the obtained AFLP fragments is in progress at the Laboratory for systematic botany at the Faculty of Science, University of Zagreb.
Photo: An example of the fragments of four samples.

Project updates: Aurinia A3 library finished in Innsbruck

Ivana Rešetnik finished the third RADseq Aurinia A3 library at the Research Group Evolutionary Systematics, Institute of Botany, University of Innsbruck. In total 96 samples representing species A. sinuata were included in the library.
Photos: The final step of checking the library quality with the Agilent High Sensitivity DNA Kit on the Bioanalyzer before sending the library for sequencing to the CSF Vienna facility.

Project updates: Analyses of ITS and cpDNA sequences in progress

The master student Paolo Bartolić is checking and assembling the ndhF sequences. The obtained results will be a part of his master’s thesis. Meanwhile Ivana Rešetnik is analysing the obtained ITS sequences.
Photo: The sequence assembly in the Geneious programme.

Project updates: Aurinia A2 library finished in Innsbruck

Ivana Rešetnik, Daniela Pirkebner and Eliška Záveská finished the second RADseq Aurinia A2 library at the Research Group Evolutionary Systematics, Institute of Botany, University of Innsbruck. In total 96 samples representing species A. corymbosa, A. leucadea, A. microcarpa and A. petraea were included in the library.
Photo: Daniela Pirkebner performing the sonification of the A2 library with the Covaris Ultrasonicator.

Project updates: MidTerm – we are half way through wink

All the planned work and milestones for the first part of the project were done according to the work plan and now we are looking forward to the next planned library preparations, analyses and first preliminary results.

Project updates: Aurinia AFLPs done in Zagreb

The AFLP fragment analysis was carried out according to the standard protocol at the Laboratory for Systematic Botany at the Faculty of Science, University of Zagreb. In total 960 samples were included in the analysis. The fluorescently labelled selective PCR fragments were sent to Macrogen facility where they were separated on a capillary sequencer.
Photos: Two 384 plates ready for the preselective PCR amplification in the Applied Biosystems Thermocycler; gel electrophoreses of the preselective PCR amplification.

Project updates: Aurinia cpDNA and ITS sequences in progress

The master student Paolo Bartolić is conducting the PCR amplification of the ndhF region for at least one individual per population. Ivana Rešetnik is doing the PCR amplification of the additional cpDNA region and the nuclear ITS region. The purified PCR products are sent to Macrogen facility where BigDye Terminator chemistry is employed, and sequences are generated on a capillary sequencer.
Photos: The preparation of the PCR master mix; PCR amplification in the Applied Biosystems Thermocycler; gel electrophoresis of the PCR products.

 

Project updates: First Aurinia A1 library finished in Innsbruck

Ivana Rešetnik and Daniela Pirkebner finished the first RADseq Aurinia A1 library at the Research Group Evolutionary Systematics, Institute of Botany, University of Innsbruck. In total 54 samples representing all Aurinia taxa were included in this library.
Photos: Magnetic size selection of desired DNA fragments with SPRI beads.

Project updates: Aurinia DNA extractions finished

The DNA from 375 individuals from all Aurinia taxa are extracted.

Project updates: Aurinia DNA extractions on the way

The extractions of 145 Aurinia populations with 5 to 10 individuals per population sampled in silica gel has started. 
Photos: DNA extractions done at the Laboratory for Systematic Botany at the Faculty of Science, University of Zagreb. The measuring of silica gel dried plant tissue; grinding of plant tissue in the Qiagen TissueLyser; incubation at 65 °C; filtration columns of the Sigma GenElute™ Plant Genomic DNA Miniprep Kit; samples in the Eppendorf centrifuge; measuring of DNA concentration of the extracted samples with Implen NanoPhotometer.


 

Project activities update: Genus Aurinia herbarium specimens from ZA and ZAHO herbaria were databased and digitalized by the students of the Faculty of Science in the frame of their practical work. The herbarium specimens are accessible though the Herbarium Croaticum Virtual Herbarium http://herbariumcroaticum.biol.pmf.hr/virtualni-herbarij/