E-Locus - Institutional Repository of the University of Crete - Evolution of conserved non-coding elements in teleost fish

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Identifier

000444172

Title

Evolution of conserved non-coding elements in teleost fish

Alternative Title

Εξέλιξη των συντηρημένων μη κωδικών στοιχείων στους τελεοστέους

Author

Ηλιοπούλου, Ελισάβετ

Thesis advisor

Ηλιόπουλος, Ιωάννης

Reviewer

Παυλίδης, Παύλος
Μανουσάκη, Τερέζα

Abstract

Many genes associated with evolutionarily conserved functions are proximal to highly Conserved Non-coding Elements (CNE), which often act as enhancers of their neighboring genes. A small number of studies have suggested loss and rapid evolutionary divergence of CNE in teleost fish. Here, we focused on identifying and studying the teleost CNE repertoire, taking advantage of the recent increase in high-quality genomes. We developed a comparative genomics pipeline to align genomes and detect CNEs. Moreover, we built CNE-based phylogenomic trees, to test their potential in resolving teleost phylogenetic placements and study CNE loss, gain and evolutionary divergence across teleosts. Finally, we attempted to gain information on the potential of identified CNE as developmental enhancers, by associating them with proximal developmental genes. This study provided insight on CNE evolution in teleost fish and a set of putative conserved developmental cis-regulatory elements that show promise for further experimental testing.

Language

English

Subject

Enhancers

Pairwise whole genome alignment

Phylogenomic analysis

Vertebrates

Ολόκληρος διπλασιασμός του γονιδιώματος

Σπονδυλωτά

Συντηρημένα μη κωδικά στοιχεία

Τελεόστεοι

Φυλογενωμική ανάλυση