Workshop cycle of molecular biology

Workshop cycle of molecular biology (Spanish) (23rd June-21st June 2021)

Molecular biology tools have become almost indispensable in any deep taxonomic study of fungi. Nevertheless, the use of molecular techniques requires a previous training and education, something sometimes not at hand of all mycologists. The goal of this cycle of workshops is show how to clean chromatograms, edit consensus sequences, conduct Blast (Basic Local Alignment Search Tool) searches, make alignments, conduct preliminary analyses of sequence data, edit phylogenetic trees and how to deposit sequences in the GenBank. Freely downloadable software will be utilized. The talks will be held in the Zoom platform, in Spanish. Each one will last 1:30-2:00 h. The first two will be open to everyone and free, while for the participation in the 3rd, 4th and 5th sessions it will be necessary either to be member of the society (initial fee 45 €, yearly 30 € afterwards) or to pay a fee of 30 € (only not mebers). A previous inscription will be mandatory for all sessions (inscription 30rd June, inscription 30rd June, inscription 7th June , inscripción 14th July, inscription 21st July).

The fee for not members to be able to attend sessions 3, 4 and 5 is 30 € in total. This amount should be put into the bank account of the Iberian Mycological Society, (ES93 2085 8017 5803 3034 7032) with the following notation: Curso molecular-Name

A more detailed program is provided below:

Session 1. The study of fungi using DNA (please sign up here)

23rd June (19:00 h). Dr. Ibai Olariaga Ibarguren (Rey Juan Carlos University)

Adding DNA techniques to the study of fungi has revolutioned fungal taxonomy. Sequencing DNA regions has become an easily accessible tool even for amateur mycologists, who use DNA data to study fungi more and more frequently. Nevertheless, a correct interpretation of molecular results requieres a background on the biological sense of the DNA. This introductory session aims at explaining in a straightforward manner what DNA is and what kind of questions can be addressed using DNA techniques. Hence, this talk will go through basic concepts that will be employed in other sessions.

Session 2. Chromatogram cleaning and consensus sequences (please sign up here)

30 de junio (19:00 h). Dr. Isaac Garrido Benavent (València university)

The first step after sending PCR products for sequencing is the receipt of DNA sequences. More precisely, an electropherogram in ab1 format is received, which must be visualized and edited in order to obtain a reliable sequence in a format that can be used for analysis (for example, FASTA format). The edition of electropherograms imply the detection of ambiguous nucleotides, double peaks or double bands that are very common when sequencing fungi, whereas the sequence ends must be trimmed as they usually suffer from poor quality. Likewise, if one counts on two reads (“forward” and “reverse” reads), a consensus sequence must be obtained. The session will show how to carry out all those steps using free software.

Session 3. BLAST searches and alignments (please sign up here)

7th July (19:00 h). Dr. Juan Carlos Zamora Señoret (Conservatoire et Jardin botaniques de la Ville de Genève, Suiza)

Once we have appropriately edited DNA sequences, several analyses can be conducted.

A first and easy step is to conduct on-line BLAST search to compare our sequence with all public sequences in a NCBI database (National Center for Biotechnology Information) called GenBank. This session will show to conduct BLAST searches and how to interpret the results being aware of its potential and limitations.

This talk will also show how to search for sequences of interest in GenBank, how to download them and to compare them locally. The first step, of paramount importance in sequence analysis is to construct an data matrix called alignment. The significance of the matrix will be explored, and automatic and manual alignments will be made. Freely downloadable bioinformatic programmes will be utilized to visualize and edit alignments.

Session 4. Phylogenetic analyses and tree edition (please sign up here)

14th July (19:00 h). Dra. María Prieto Álvaro (Rey Juan Carlos university)

This workshop will show the participants to conduct preliminary analyses and to edit phylogenetic trees. It will contain the next contents:

1.-Phylogenetic inference: Maximum Likelihood approach
2.-Evolution models
3.-Statistic support: bootstrap values
4.-Using IQ-Tree for analyses
5.-Result interpretation: phylogenetic trees
6.-Edition of phylogenetic trees

Session 5. Publication of DNA sequences in GenBank (please sign up here)

21st July (19:00 h). Dr. Ibai Olariaga Ibarguren (Rey Juan Carlos university)

DNA sequence deposits are of paramount importance and imply progress and acknoledgment of sequences generated by mycologists. This last session will show all steps that must be followed to deposit sequences in GenBank. The GenBank and BankIt platforms will be employed to submit sequences of nuclear ribosomal genes (nrITS, nrLSU, nrSSU), as well as sequences of protein-coding genes (for example, RPB2, RPB1, tef-1).

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