Filogeografska metaanaliza mitogenoma koza

master's thesis

• Title (english): Phylogeographical metaanalysis of goat mitogenomes
• Author: Mirta Vulje
• Mentor: Vladimir Brajković (mentor)
• Committee member: Vladimir Brajković (predsjednik povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Committee member: Ino Čurik (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Animal Science); Zagreb
• Defense date and country: 2024-09-27, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Analiza cijelog mitogenoma pruža uvide u genetičku raznolikost, evoluciju i filogeografiju različitih pasmina koza i divljih srodnika. Metaanaliza 564 sekvenci mitogenoma koza i 5 ovaca obuhvatila je i devet mitogenoma hrvatskih pasmina koza, koji su bioinformatičkim alatima Galaxy platforme mapirani iz cijelih genoma, uz prosječnu duljinu pokrivenosti od 100% i prosječnu dubina pokrivenosti od 1630.62. BEAST analizom utvrđena je prisutnost A, B, C, D, F i G haplogrupe uzimajući u obzir posteriori vrijednost 1 kao signifikantno razdvajanje haplogrupa, no uz pojavu dvije nepoznate skupine azijskog podrijetla. Procijenjeno je vrijeme divergencije između svih parova haplogrupa, dok je razdvajanje ovaca i koza procijenjeno na prije 833892 godina. U području Bliskog istoka detektirane su sve haplogrupe dok su hrvatske koze pokazale pripadnost samo haplogrupi A. Istraživanje je obuhvatilo i 110 drevnih sekvenci koza koje pokazuju ravnomjerniju zastupljenost haplogrupa u usporedi s modernim kozama iako je haplogrupa A ostala dominantna i najraširenija na cijelom području Euroazije. MJ mreža jasno je razdvojila navedene haplogrupe te potvrdila evolucijske odnose i ukazala na genetsku sličnost između domaće koze i njezinih srodnika. Najveću raznolikost haplotipova pokazala je regija mtDNA D-petlja (Hd=0.9992) nakon koje slijedi segment ND5. Ovom metaanalizom stvorena je baza sekvenci mitogenoma za buduće arheogenetičke analize te za razvoj SNP-ova mitogenoma na SNP čip panelu za komercijalnu upotrebu u analizama i praćenju genetske raznolikosti.

Abstract (english)

Analysing the entire mitogenome provides insights into the genetic diversity, evolution and phylogeography of the different goat breeds and their wild relatives. The meta-analysis of 564 goat and 5 sheep mitogenome sequences also included nine mitogenomes of Croatian goat breeds mapped from whole genomes using the Galaxy platform bioinformatics tools, with an average length of coverage of 100% and an average depth of coverage of 1630.62. The BEAST analysis revealed the presence of haplogroups A, B, C, D, F and G, with the a posteriori value of 1 indicating a significant separation of haplogroups, but also revealing two unknown groups of Asian origin. The time of divergence was estimated between all pairs of haplogroups, while the divergence between sheep and goats was estimated at 833892 years ago. In the Middle East region, all haplogroups were detected, while the Croatian goats belonged only to haplogroup A. The study included 110 ancient sequences of goats, which showed a more even representation of haplogroups compared to modern goats, although haplogroup A remained dominant and most widespread across Eurasia. The MJ network clearly separated the aforementioned haplogroups, confirmed the evolutionary relationships and showed the genetic similarity between the domestic goat and its relatives. The greatest diversity of haplotypes was found in the mtDNA D-loop region (Hd=0.9992), followed by the ND5 segment. This meta-analysis created a database of mitogenome sequences for future archaeogenetic analyses and for the development of mitogenome SNPs on the SNP chip panels for commercial use to analyse and monitor genetic diversity.

• Keywords: varijabilnost; mitogenom; koza; BEAST; haplogrupa
• Keywords (english): variability; mitogenome; goat; BEAST; haplogroup
• Language: croatian
• URN:NBN: urn:nbn:hr:204:671602
• Study programme: Title: Animal Genetics and Breeding; Study programme type: university; Study level: graduate; Academic / professional title: magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja (magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to authenticated users
• Created on: 2024-10-17 07:51:10