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| Author(s): |
Henry Angel Bonilla Bruno
Total Authors: 1
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| Document type: | Master's Dissertation |
| Press: | São Paulo. |
| Institution: | Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) |
| Defense date: | 2023-06-27 |
| Examining board members: |
Maria Dulcetti Vibranovski;
Antonio Bernardo de Carvalho;
Ariane Machado Lima;
Cesar Martins
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| Advisor: | Maria Dulcetti Vibranovski |
| Abstract | |
Drosophila miranda is considered a model species for the study of genomic, transcriptomic, or epigenetic processes that occur in the early evolution of sex chromosomes due to the presence of the so-called neo-chromosomes. Two chromosome fusion events, occurring approximately 15 and 2 million years ago, between sex chromosomes and autosomes produced the sex chromosomes XL/XR, Neo-X, and Y (YD and Neo-Y), respectively. Fluorescent in situ hybridization (FISH) represents a valuable tool, allowing the investigation of chromosomal evolution, chromosomal behavior and, ultimately, for assessing the quality of genome assembly. Currently, complex libraries of synthetic probes are becoming increasingly popular. Thus, oligopaint probes represent a new generation of custom-made, versatile, and highly specific probes. Using the OligoMiner software and inspired by its modification according to the pipeline OligoY, it was possible to design single-copy and repetitive oligos to completely cover sex chromosomes of different evolutionary ages. FISH experiments on metaphase chromosome spreads from 3rd instar larval brains showed that all oligo libraries are highly specific for their target region. The repetitive oligos label those locations with a low amount of single-copy oligos. We propose that a density of 0.5 hits/Kb, with distances smaller than 2500 nucleotides between oligos and concentrated in the median according to a violin plot, is sufficient to observe labeling in a target region at the Megabase (Mb) level. This finding decreases the value of oligo density commonly used (1 hit/Kb). Our FISH experiments on the Y chromosome showed that the Neo-Y region (Muller C) is interspersed by YD. The use of our oligo libraries in the sister species D. pseudoobscura and analyses of alignments between chromosomes allowed us to develop a hypothesis about the fusion event between YD and Muller C that gave rise to the Y chromosome of D. miranda. After the telomere-to-telomere fusion, it is highlyprobable that a pericentric inversion and subsequent overlapping inversions played a fundamental role in the reorganization of the Y. Our oligo libraries are the first oligos designed for D. miranda and the only ones besides the model species D. melanogaster in Drosophila, thus representing a valuable resource that will allow future research on chromosomal behavior. (AU) | |
| FAPESP's process: | 19/10559-1 - Evolution of the meiotic X-chromosome inactivation in Drosophila |
| Grantee: | Henry Angel Bonilla Bruno |
| Support Opportunities: | Scholarships in Brazil - Master |