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.

Objectives

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.

Financing

This Project is funded by the Research Council of Norway (RCN) FRIMEDBIO

RCN Project Number: 251076 (Project data bank at RCN)

UiO Project Number: 144337

Publications

  • Ole K. Tørresen; Bastiaan Star; Pablo Mier; Miguel A. Andrade-Navarro; Alex Bateman; Patryk Jarnot; Aleksandra Gruca; Marcin Grynberg; Andrey V. Kajava; Vasilis J. Promponas; Maria Anisimova; Kjetill Sigurd Jakobsen & Dirk Linke (2019). Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Research (NAR).  ISSN 0305-1048.  47, s 10994- 11006
  • Ole K. Tørresen; Marine Servane Brieuc; Monica Hongrø Solbakken; Elin Sørhus; Alexander Johan Nederbragt; Kjetill Sigurd Jakobsen; Sonnich Meier; Rolf Edvardsen & Sissel Jentoft (2018). Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics.  ISSN 1471-2164.  19, s 1- 17
  • Andrè M. Machado; Ole K. Tørresen; Naoki Kabeya; Alvarina Couto; Bent Petersen; Mónica Felício; Paula F. Campos; Elza Fonseca; Narcisa Bandarra; Mónica Lopes-Marques; Renato Ferraz; Raquel Ruivo; Miguel M. Fonseca; Sissel Jentoft; Óscar Monroig; Rute R. Da Fonseca & L. Filipe C. Castro (2018). “Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes.  ISSN 2073-4425.  9, s 1- 13

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  • William Brynildsen Reinar; Ole K. Tørresen; Michael Matschiner; Sissel Jentoft; Alexander Johan Nederbragt & Kjetill Sigurd Jakobsen (2018). The impact of repetitive DNA on speciation rates in teleost fish.
  • Ole K. Tørresen (2018). De novo genome assemblies of Atlantic cod.
  • William Brynildsen Reinar (2017). Trinucleotide repeat variation in the global Arabidopsis thaliana population: Associations with the environment.
  • Jonfinn Mordekai Blix Knutsen (2017). Evolutionary and functional importance of simple repeats in 1135 Arabidopsis thaliana genomes.
  • Jonfinn Mordekai Blix Knutsen (2017). Evolutionary and functional importance of simple repeats in eukaryotic genomes.
  • William Brynildsen Reinar (2017). Short tandem repeat length variation in Arabidopsis thaliana genomes.
  • Ole K. Tørresen (2017). Long reads: dream or reality?.

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Published Jan. 15, 2021 2:32 PM - Last modified Feb. 2, 2021 10:31 AM