Download How the loss of genes has shaped the genome as we know it

How the loss of genes has shaped the genome as we know it
SUPERVISOR
Antonio Marco, School of Biological Sciences, University of Essex, UK
DESCRIPTION:
Genomes are the product of a long evolutionary process. Many genes have multiple copies, reflecting
the importance of gene duplication during genome evolution. The duplication of genes with regulatory
functions has been associated with the development of novel functions. However, there is strong
evidence that the loss of gene functions has also influenced the evolution of species. Gene loss is
often associated with redundant functions, but the loss of non-redundant regulatory genes also
happens with relative frequency. In recent years, the characterization of novel types of regulatory
genes, such as microRNAs or long-non-coding RNAs, showed that gene loss is much more important
that previously thought. Nevertheless, gene loss as a driving evolutionary force has not been
systematically explored.
This project aims to understand how gene losses have shaped genomes. A PhD student will compare
the genomes of related species and characterize which genes have been lost in specific lineages. The
work will focus in transcription factors as well as in other regulatory genes such as microRNAs. By
analysing the function, evolutionary age and regulatory connections of lost genes, we will be able to
generate a model of genome evolution by gene loss. The candidate will be trained in computational
biology / bioinformatics, with a focus on evolutionary genetics and comparative genomics. No prior
knowledge of computer programming is required, but the candidate will have the chance to learn one
programming language and state-of-the-art computational approaches. Depending on the interest of
the student, the project may also involve molecular genetics in Drosophila melanogaster.
REFERENCES:
- Marco A, Ninova M, Ronsaugen M, Griffiths-Jones S (2013) Clusters of microRNAs emerge by new
hairpins in existing transcripts. Nucleic Acids Res, 41:7745-7752.
- Marco A (2012) Regulatory RNAs in the light of Drosophila genomics. Brief Func Genomics, 11:356365.
- Hahn MW, Han MV, Han S-G (2007) Gene family evolution across 12 Drosophila genomes. PLoS
Genetics 3:e197.