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

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
Reinar, William Brynildsen; Olsson, Vilde; Reitan, Trond; Jakobsen, Kjetill Sigurd & Butenko, Melinka Alonso (2021). Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana. The Plant Cell. ISSN 1040-4651. 33(7), p. 2221–2234. doi: 10.1093/plcell/koab107. Full text in Research Archive
Tørresen, Ole K.; Star, Bastiaan; Mier, Pablo; Andrade-Navarro, Miguel A.; Bateman, Alex & Jarnot, Patryk [Show all 13 contributors for this article] (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(21), p. 10994–11006. doi: 10.1093/nar/gkz841. Full text in Research Archive
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

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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
The predominant view in biology has been that genetic variation caused by point mutations are the main source for evolutionary change. Yet, point mutations alone cannot account for the genetic variation necessary to deal with rapid environmental changes. Genes and promoters are enriched with the tandem repeats (TRs), which are sets of trinucleotides repeated in tandem and that can mutate 10 to 100 000 times faster than point mutations. A working hypothesis is that such sequences serves as evolutionary hotspots that facilitate adaptation by fine-tuning gene function. To test this hypothesis, we are surveying the repeat length variation present in genes from more than a thousand Arabidopsis individuals spread mainly across the northern hemisphere. We are exploring associations between repeat length variation and ecological clines, such as variation in temperature and precipitation. We will investigate the functional importance of the repeat lengths in a set of candidate genes, representing the variation observed in the wild, by introducing them into Arabidopsis and monitoring phenotypic changes at the molecular and morphological level. We will further expose the Arabidopsis plants to various physical and biological stress, and screen for phenotypic and genetic changes relating to trinucleotide TRs.
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
The predominant view in biology has been that genetic variation caused by point mutations are the main source for evolutionary change. Yet, point mutations alone cannot account for the genetic variation necessary to deal with rapid environmental changes. Genes and promoters are enriched with the tandem repeats (TRs), which are sets of trinucleotides repeated in tandem and that can mutate 10 to 100 000 times faster than point mutations. A working hypothesis is that such sequences serves as evolutionary hotspots that facilitate adaptation by fine-tuning gene function. To test this hypothesis, we are surveying the repeat length variation present in genes from more than a thousand Arabidopsis individuals spread mainly across the northern hemisphere. We are exploring associations between repeat length variation and ecological clines, such as variation in temperature and precipitation. We will investigate the functional importance of the repeat lengths in a set of candidate genes, representing the variation observed in the wild, by introducing them into Arabidopsis and monitoring phenotypic changes at the molecular and morphological level. We will further expose the Arabidopsis plants to various physical and biological stress, and screen for phenotypic and genetic changes relating to trinucleotide TRs.
Reinar, William Brynildsen (2017). Short tandem repeat length variation in Arabidopsis thaliana genomes.

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

Participants

Detailed list of participants