Evolucija satelitnih DNA u vrstama oblića roda Meloidogyne

master's thesis

• Title (english): Evolution of satellite DNAs in nematode species of the genus Meloidogyne
• Author: Marino Korlević
• Mentor: Nevenka Meštrović Radan (mentor)
• Committee member: Kristian Vlahoviček (predsjednik povjerenstva)
• Committee member: Mirjana Kalafatić (član povjerenstva)
• Committee member: Dubravka Hranilović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2009, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Oblići korijenovih kvržica roda Meloidogyne su biljni paraziti od iznimne agronomske važnosti koji imaju vrlo raznolike načine reprodukcije, od klasičnog spolnog razmnožavanje do mitotske partenogeneze. Vrsta Meloidogyne incognita nedavno je odabrana kao modelni organizam te je njezin genomski projekt postao dostupan. U ovom radu, provedena je cjelokupna analiza satelitnih DNA u vrstama roda Meloidogyne koja je sadržavala analize novootkrivenih satelitnih DNA izlučenih iz baze podataka sekvenciranog genoma zajedno s ranije opisanih satelitnim sljedovima. Analize monomernih varijanti izlučenih iz contig-a koji su sadržavali ranije opisanu INC satelitnu DNA otkrile su varijabilnost jedinica ponavljanja koja je specifična za niz što ukazuje na homogenizacijske procese na razini niza. Kako bi se odredio položaj INC satelitne DNA na holocentričnim kromosomima vrste Meloidogyne incognita provedena je FISH analiza. Rezultati su pokazali lokalizaciju signala na samo dva kromosoma. Nadalje, contig-zi koji su sadržavali predvidivo nove sljedove satelitnih DNA izlučeni su programima Repeat Scout i Tandem Repeat Finder te su karakterizirani in silico analizom. Sljedovi novih satelitnih DNA (R1, R5, R7 i R8) pokazuju nisku unutarsatelitnu varijabilnost monomera, visok udio A i T nukleotida, beznačajnu međusobnu sličnost u nukleotidnim sljedovima te nizak udio u genomu (<0,1%). Nadalje, međuvrsna rasprostranjenost novih satelitnih DNA u pet srodnih vrsta roda Meloidgyne provedena je metodom PCR-a i hibridizacijskom analizom po Southernu. Na temelju rasprostranjenosti novih satelitnih DNA (R1, R5, R7, R8) i onih opisanih ranije potvrđena je hipoteza prema kojoj rasprostranjenost satelitnih DNA može biti relevantni kriterij za određivanje evolucijskih odnosa.

Abstract (english)

Root-knot nematodes (RKN) of the genus Meloidogyne are plant parasites of major agricultural importance, which exhibit different modes of reproduction, from classical amphimixis to mitotic parthenogenesis. Recently, Meloidogyne incognita was selected as a model organism and its genome project became available. In this work, comprehensive analyses of satellite DNAs based on data published in the genome project including already characterized satellite DNAs were performed. Analyses of monomer variants retrieved from contigs containing already characterized INC satellite DNA revealed array specific variability pointing out that sequences are predominantly homogenized on the array level. To define the localization of INC satellite DNA on holocentric M. incognita chromosomes, FISH analyses were performed. Results showed localization of INC satellite DNA on only two chromosomes. In addition, contigs with candidate satellite DNA sequences were extracted by RepeatScout and Tandem Repeat Finder and further characterized in silico. Sequences of newly described satellite DNAs (R1, R5, R7 and R8) exhibit low intrasatellite monomer variability, high A+T content, insignificant mutual sequence similarity and each of them makes up <0,1% of the genome. In addition, the interspecific distribution of new satellite DNAs detected in five congeneric Meloidogyne species was performed by PCR and Southern hybridization. Based on genomic distribution of four satellite DNAs (R1, R5, R7 and R8) together with results concerning distribution of previously characterized satellites we tested the hypothesis that the distribution of satellite DNA could be a relevant criterion to resolve evolutionary relationships.

• Keywords: evolucija; rod Meloidogyne; "biblioteka" satelitnih DNA
• Keywords (english): evolution; genus Meloidogyne; satellite DNA library
• Language: croatian
• URN:NBN: urn:nbn:hr:217:645332
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2018-03-13 08:59:12