Barcoding of tropical woods

Barbora Legezová

Bachelor's thesis

Abstract:

The method of DNA barcoding was initially introduced in 2003 in the effort to facilitate the species identification. It is a molecular method of species identification based on a short region of DNA sequences. These DNA barcodes should be unique for each species. This method has since proven very effective mainly among animal species – however, further development is required for plant species. This thesis aims to describe the current knowledge of the barcoding technique, in the field of plant identification, with a special focus on tropical trees. Moreover, it aims to test the information gained by isolating DNA from dead wood material, select useful barcode loci for amplification, amplify the isolates by polymerase chain reaction (PCR) and verify the success of the reaction by agarose gel electrophoresis. This study evaluates the positive and negative aspects of the DNA barcoding method. It shows different plant barcodes proposed and provides examples of its successes in the use for wood barcoding. Moreover, this thesis explores the practical uses of DNA barcoding ranging from ecological studies, biosecurity, biomonitoring, biodiversity sciences, diet analysis, illegal trade and forensics, and databases in which barcode sequences are stored. The successes of DNA extractions were quantified using NanoDrop spectrophotometer and PCR amplifications were visualized using electrophoresis. Results show that out of the two DNA extraction methods (CTAB and DNeasy Mini Kit-Qiagen), the CTAB method isolates greater quantity of DNA, however both methods produced DNA of not ideal quality. Even though the poor quality of DNA, PCR amplification worked perfectly, therefore CTAB extraction was successful. The trnL approach chosen for this study has proven effective, PCR amplification worked well with chosen sequences. To improve this method, further optimization of DNA isolation may help with better results, mainly the optimization of ‘medium sequence’ (approximate length 400 base pair).

Keywords

dead wood, DNA isolation, PCR, plant barcode, species identification, taxonomy, trnL approach

Language used: English

Date on which the thesis was submitted / produced: 19. 4. 2018

Thesis defence

• Supervisor: doc. Ing. Bohdan Lojka, Ph.D.

Czech University of Life Sciences Prague

Faculty of Tropical AgriSciences

Bachelor programme / field:
Agricultural Specialization / Agriculture in Tropics and Subtropics