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Identifier 000451979
Title Μελέτη της ετεροπλασμίας του μιτοχονδριακού DNA σε εργαστηριακά στελέχη Drosophila και σε φυσικούς υβριδικούς πληθυσμούς
Alternative Title A study of mtDNA heteroplasmy in Drosophila lab strains and in hybrid natural popoulations
Author Παρακατσελάκη, Μαρία-Ελένη Ε
Thesis advisor Λαδουκάκης, Εμμανουήλ
Reviewer Πουλακάκης, Νίκος
Δελιδάκης, Χρήστος
Παυλίδης, Παύλος
Ηλιόπουλος, Ιωάννης
Κωτούλας, Γεώργιος
Παρμακέλης, Αριστείδης
Abstract In animals, mtDNA is maternally transmitted, therefore all progeny carries one single mitochondrial haplotype, or otherwise mitotype. As a result, all progeny is expected to carry only one mitotype, a condition described as homoplasmy. However, more and more individuals are found to carry more than one mitotypes, namely they are heteroplasmic. Heteroplasmy can emerge in two different ways. The first one is due to mutations. The second one is due to circumstancial transmission of paternal mtDNA, along with the inheritance of maternal mtDNA, which is described by the term ‘paternal leakage’. Studying paternal leakage is interesting, since it can have great impact on mtDNA fitness and on its evolution, in general. Specifically, mtDNA accumulates deleterious mutations faster compared to nDNA, because of its asexual mode of transmission, however mtDNA remains functional. Leakage may contribute to mtDNA’s preservation, since when two mitotypes are co-existing in an individual, recombination between the different mtDNA molecules may occur. In turn, the detrimental accumulation of mutations can be mitigated. Consequently, studying heteroplasmy and its pattern is of great significance. In the first set of experiments, we used chimeric Drosophila lines that possess nDNA from D. melanogaster and mtDNA from D. simulans, to study heteroplasmy. The lines used carry a specific nuclear background (DGRP-820) and have been found to be heteroplasmic after replacing their original mtDNA with mtDNA from D. simulans. On the contrary, other lines that did not carry this particular nuclear background were homoplasmic for the inserted mitotype. After the first series of experiments, we deduced that the emergence of the mel mitotype from the DGRP-820 line was associated with the X chromosome, and specifically with the region between the phenotypic markers f and mal. However, the fact that only the mel mitotype leaked to the next generation from the heteroplasmic lines, and not the si mitotype, led to the hypothesis the observed patterns were not due to true heteroplasmy, but due to a mtDNA fragment embedded in the nDNA (Nuclear Mitochondrial, NUMT). In order to resolve this issue, we designed another set of experiments and found that there is a large NUMT embedded in a 3.15Mb region of the X chromosome, between f and mal markers. We estimated that the NUMT should be at least 16225bp in size, which is the largest NUMT found in the D. melanogaster species. Given the abundance of NUMTs among genomes, heteroplasmy data should be handled with caution, so they are not interpreted as heteroplasmy, while they are truly NUMTs. In the next set of experiments, we tried to resolve the problem that arose with heteroplasmy in chimeric lines, using a bioinformatic approach. Specifically, whole-genome sequencing data were used in order to detect the presence of chimeril reads that align in both the mtDNA and the X chromosome. For the analysis, we used reads that were flagged as unmapped after mapping with a reference genome and we performed a BLAST search in order to find reads with similarities with the X chromosome and the mtDNA. Several filters were applied, so that we could detect pairs of reads that correspond to the junctions of the NUMT. However, BLAST hits were hard to reduce even after filtering and, furthermore, positive control showed that reads that correspond to the junctions are probably eliminated during the filtering process. We assumed that the major cause for the inability to detect chimeric reads is the relatively short reads that were used, compared to the large size of the NUMT that we were trying to locate. In the last set of experiments, we used Drosophila collected from a wild population to assess if paternal leakage happens with a different frequency, dependent on the nuclear genome. For this purpose, we constructed isofemale lines of D. simulans and we crossed females from these lines with D. mauritiana males. In total, we analysed 2292 individuals for the presence of the paternal mtDNA, which came from 15 different isofemale lines. Statistical analysis of the results showed that paternal leakage is more frequently detected in males from three specific lines compared to the other lines. A similar difference was detected when analysing all progeny, regardless of sex. Interestingly, we found two lines where there was no difference in leakage detected between males and females, opposed to what was expected from previous studies. We deduced that paternal leakage is associated with the nuclear background of the D. simulans lines, suggesting that leakage does not happen randomly due to failure of mechanisms that eliminate paternal mtDNA from transmitting to the next generation, but it is a process cotrolled by the nDNA.
Language Greek
Subject Biparental transmission
Drosophila melanogaster
NUMT
Ένθεση
Αμφιγονεϊκή κληρονόμηση
Ετεροπλασμία
Μιτοχονδριακό DNA
Issue date 2022-11-23
Collection   School/Department--School of Sciences and Engineering--Department of Biology--Doctoral theses
  Type of Work--Doctoral theses
Permanent Link https://elocus.lib.uoc.gr//dlib/d/1/3/metadata-dlib-1667490603-615485-29295.tkl Bookmark and Share
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