Fish genomes : a powerful tool to uncover new functional elements in vertebrates

Leiden Repository

Fish genomes : a powerful tool to uncover new functional elements in vertebrates

Type: Doctoral Thesis
Title: Fish genomes : a powerful tool to uncover new functional elements in vertebrates
Author: Stupka, Elia
Publisher: Department of Computer Science, Leiden Institute of Advanced Computer Science (LIACS), Faculty of Science, Leiden University
Issue Date: 2011-05-11
Keywords: Genomics
Bioinformatics
Comparative genomics
Regulatory elements
De novo assembley
Transcription
Abstract: This thesis spans several years of work dedicated to understanding fish genomes. In the first chapter it describes the genome of the first fish for which the entire genome was sequenced through a large-scale international project, Fugu rubripes. the pufferfish. In particular, it highlights how this fish has a genome that contains as many genes as the human genome, although it is ten times smaller. It also shows that the majority of genes that are found in the human genome can be found in this fish genome as well. In the second chapter we compared fish genomes to the human genome to find regions that have been preserved during evolution and which are therefore likely to have a function, even though they are not genes. We showed that indeed they are functional, and they help to regulate other genes. Knowing all the genes in the genome we could then interrogate how they are expressed, i.e. if they are switched “on” or “off” and in particular in chapter 4 we looked at how a specific gene is in charge of gradually switching off genes that are inherited from the mother in a newborn fish embryo. Finally in the last chapter since genome sequencing is now becoming much cheaper and simpler to achieve we set out to map the genome of the common carp and we discuss the best approaches and strategies to obtain a good genome sequence for this species. The common carp is a candidate model system for high-troughput screening.
Description: Promotor: J.N. Kok, Co-promotor: F.J. Verbeek
Faculty: Faculteit der Wiskunde en Natuurwetenschappen
Citation: Stupka, E., 2011, Doctoral Thesis, Leiden University
ISBN: 978908892771
Sponsor: This work was carried out with support from the Euopean Commission Framework VI grant TRANSCODE (LSHG-CT-2004-511990 ) as well support from A-STAR Singapore and Temasek Life Sciences Laboratory, Singapore
Handle: http://hdl.handle.net/1887/17640
 

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