REPEAT: Evolutionary and functional importance of simple repeats in the genome
About the project
More than 150 years since Darwin published his famous work 'The Origin Of Species' the causal relationship between the genotype (genome) and the phenotype (phenome) is still basically a mystery.
In particular, even though the role of natural selection in evolution is widely accepted, we do not understand how changes in the phenotype relate to genetic change and how this may cause adaptation and speciation under natural selection. However, what we do better understand, due to recent whole genome investigations using high throughput sequencing (HTS), is the dynamic nature of genome architectural changes. These include, gene copy numbers, inversions, transposable element dynamics and simple repeat variations.
Here we propose to investigate variations in simple trinucleotide repeats residing inside (coding) and in the vicinity (or in introns) of genes. We will relate such length variations to functional modulation of regulatory mechanisms affecting the phenotype. Specifically, we will test the hypothesis that hypervariable coding/regulatory repeats are promoting the ability of a species or population to adapt to a changing environment.
The project is cross-disciplinary and will utilize genomic, bioinformatics, statistics and experimental approaches. The goal is to understand how new mechanisms drives genomic architecture and divergence, taking into account fluctuations in the selection regimes. We aim to obtain new fundamental biological insights as well as novel bioinformatics, and statistical methodology.
The primary objectives are to address
(i) how adaptational processes affect genome dynamics, and
(ii) to test if adaptation drives evolution (through selection) of length variants of amino
acid-coding simple repeats or regulatory associated simple repeats.
The goal is to understand how new mechanisms drives genomic architecture and divergence – taking into account fluctuations in the selection regimes.
We aim to obtain new fundamental biological insights as well as novel bioinformatics, and statistical methodology.
This Project is funded by the Research Council of Norway (RCN) FRIMEDBIO
UiO Project Number: 144337
Sætre, Camilla Lo Cascio; Eroukhmanoff, Fabrice; Rönkä, Katja; Kluen, Edward; Thorogood, Rose & Torrance, James [Show all 12 contributors for this article] (2021). A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus). Genome Biology and Evolution (GBE). ISSN 1759-6653. 13(9), p. 1–7. doi: 10.1093/gbe/evab212. Full text in Research Archive
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Tørresen, Ole K.; Brieuc, Marine Servane; Solbakken, Monica Hongrø; Sørhus, Elin; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd [Show all 9 contributors for this article] (2018). Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics. ISSN 1471-2164. 19(240), p. 1–17. doi: 10.1186/s12864-018-4616-y. Full text in Research Archive
Machado, Andrè M.; Tørresen, Ole K.; Kabeya, Naoki; Couto, Alvarina; Petersen, Bent & Felício, Mónica [Show all 17 contributors for this article] (2018). “Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes. ISSN 2073-4425. 9(10), p. 1–13. doi: 10.3390/genes9100485. Full text in Research Archive
Reinar, William Brynildsen; Tørresen, Ole K.; Matschiner, Michael; Jentoft, Sissel; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd (2018). The impact of repetitive DNA on speciation rates in teleost fish.
Tørresen, Ole K. (2018). De novo genome assemblies of Atlantic cod.
Tørresen, Ole K. (2017). Long reads: dream or reality?
Knutsen, Jonfinn Mordekai Blix (2017). Evolutionary and functional importance of simple repeats in 1135 Arabidopsis thaliana genomes. Show summary
Reinar, William Brynildsen (2017). Trinucleotide repeat variation in the global Arabidopsis thaliana population: Associations with the environment.
Knutsen, Jonfinn Mordekai Blix (2017). Evolutionary and functional importance of simple repeats in eukaryotic genomes. Show summary
Reinar, William Brynildsen (2017). Short tandem repeat length variation in Arabidopsis thaliana genomes.