Detection of structural variants in genomes of two nightingale species

• Thesis title in Czech: Detekce strukturálních variant v genomech dvou druhů slavíků
• Thesis title in English: Detection of structural variants in genomes of two nightingale species
• Key words: strukturální varianty, speciace, adaptace, variant calling, slavík obecný, slavík tmavý
• English key words: structural variants, speciation, adaptation, variant calling, inversions, common nightingale, thrush nightingale
• Academic year of topic announcement: 2019/2020
• Thesis type: diploma thesis
• Thesis language: angličtina
• Department: Department of Cell Biology (31-151)
• Supervisor: RNDr. Radka Reifová, Ph.D.
• Author: hidden - assigned by the advisor
• Date of registration: 15.09.2020
• Date of assignment: 25.09.2020
• Date of electronic submission: 11.08.2021
• Date of proceeded defence: 13.09.2021
• Opponents: Ing. Petr Jansa, CSc., Ph.D.

Preliminary scope of work

Cílem práce je detekovat strukturální varianty, které zahrnují větší chromozomální inzerce, delece, inverze a translokace, v genomech dvou blízce příbuzných druhů slavíků. Student bude analyzovat již dostupná celogenomová 10X linked-read a Oxford Nanopore sekvenční data, a také sestavené genomy obou druhů. Bude aplikovat různé výpočetní metody k detekci strukturálních variant mezi genomy obou druhů, které mohou mít důsledky pro reprodukční izolaci mezi druhy.

Preliminary scope of work in English

The aim of the thesis is to detect structural variants, which include large chromosomal insertions, deletions, inversions and translocations, in the genomes of two closely related nightingale species. The student will analyze already available whole genome 10X linked-read sequencing data, Oxford Nanopore sequencing data as well as assembled genomes of both species. He/she will apply several computational methods to reveals structural variants between the genomes of the two species, which may have consequences for the reproductive isolation of the two species.