GENOMIKA I OSOBITOSTI PONAVLJAJUĆIH DNA ŠKOLJKAŠA IZ PORODICE OSTREIDAE

doctoral thesis

• Title (english): GENOMICS AND PECULIARITIES OF THE REPETITIVE DNAs OF THE OYSTERS IN THE FAMILY OF OSTREIDAE
• Author: Monika Tunjić Cvitanić
• Mentor: Miroslav Plohl (mentor)
• Mentor: Eva Šatović Vukšić (komentor)
• Committee member: Višnja Besendorfer (predsjednik povjerenstva)
• Committee member: Đurđica Ugarković (član povjerenstva)
• Committee member: Petra Korać (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2024, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology
• Universal decimal classification (UDC): 577 - Biochemistry. Molecular biology. Biophysics

Abstract

Ponavljajuća DNA u mnogim organizmima čini velik, ali neistražen dio genoma. Za vrstu
Crassostrea gigas bioinformatički je utvrđeno da repeatom dominantno grade satDNA i PGE, a
najbrojnija satDNA je Cg170. Bioinformatički su utvrđeni satelitomi srodnih vrsta kamenica C.
gigas, Crassostrea angulata, Crassostrea virginica i Ostrea edulis. U sklopu centromere C.
gigas najbrojnije DNA su transpozoni i satDNA, a u heterokromatinu najbrojniji su DNA
transpozoni. Više od 75 % satelitoma te vrste pokazalo je sličnost s elementima Helitron.
Analizom postranih regija monomera ili nizova satDNA utvrđeno je da se samo jedna satDNA
nalazi isključivo u sklopu elementa Helitron, dvjema je većina monomera/nizova monomera
samostalna, a osam satDNA u podjednakim je omjerima prisutno samostalno i u sklopu
elementa. Niz satDNA zajednički je svim ispitanim vrstama, a C. gigas i C. angulata dijele
najveći broj zajedničkih satDNA. U C. gigas nije otkriveno tipično nakupljanje satDNA na
određenim kromosomskim pozicijama, čime je u ovoj vrsti ustanovljen novi (visokoraspršeni)
obrazac organizacije satDNA na razini genoma.

Abstract (english)

Repetitive DNA constitutes big, but still uninvestigated genome part. For the oyster Crassostrea
gigas it was bioinformatically determined that the repeatome is mainly constituted of satDNAs
and mobile elements, and the most abundant satDNA is Cg170. The satellitomes of four closely
related species, C. gigas, Crassostrea angulata, Crassostrea virginica and Ostrea edulis, were
bioinformatically determined. The most abundant sequences in the centromere of C. gigas are
DNA transposons and satDNAs, while in heterochromatin the most abundant are DNA
transposons. More than 75% of satellitome of this species showed similarity to Helitrons.
Analysis of conserved boxes adjacent to monomers or tandem repeats of satDNAs showed that
only one satDNA exists integrated into Helitrons, two have majority of their monomers/tandem
repeats as standalone organizational form, and eight satDNAs have equally present
monomers/tandem repeats in both forms. All analyzed species have several satDNAs in
common, but C. gigas and C. angulata share the highest number of common satDNAs. SatDNAs
in C. gigas did not show typical clustering at certain chromosomal positions but new
organizational pattern: highly scattered across the genome.

• Keywords: školjkaši; satelitom; repeatom; centromere; heterokromatin
• Keywords (english): bivalves; satellitome; repeatome; centromere; heterochromatin
• Language: croatian
• URN:NBN: urn:nbn:hr:217:270005
• Promotion: 2024
• Project: Number: IP-2014-09-3183; Title: Centromerna genomika beskralježnjaka; Title: Invertebrate centromere genomics; Acronym: CENGEN; Leader: Miroslav Plohl; Jurisdiction: Croatia; Funder: HRZZ; Funding stream: IP
• Project: Number: IP-2019-04-5522; Title: Rasvjetljavanje evolucije satelitnih DNA visokoprotočnim analizama satelitoma srodnih vrsta; Title: Satellite DNA evolution illuminated by high-throughput satellitome analyses of related species; Acronym: EvoSat; Leader: Brankica Mravinac; Jurisdiction: Croatia; Funder: HRZZ; Funding stream: IP
• Study programme: Title: Doctoral study; Study programme type: university; Study level: postgraduate; Academic / professional title: doktor/doktorica znanosti u području prirodnih znanosti (doktor/doktorica znanosti u području prirodnih znanosti)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-04-02 09:53:00