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Reinar WB, Tørresen OK, Nederbragt AJ, Matschiner M, Jentoft S, Jakobsen KS. Teleost genomic repeat landscapes in light of diversification rates and ecology. Mob DNA 2023; 14:14. [PMID: 37789366 PMCID: PMC10546739 DOI: 10.1186/s13100-023-00302-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.
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Affiliation(s)
| | - Ole K Tørresen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Alexander J Nederbragt
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Matschiner
- Department of Biosciences, University of Oslo, Oslo, Norway
- University of Oslo, Natural History Museum, Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, University of Oslo, Oslo, Norway
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Reinar WB, Greulich A, Stø IM, Knutsen JB, Reitan T, Tørresen OK, Jentoft S, Butenko MA, Jakobsen KS. Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis. Sci Adv 2023; 9:eadd6960. [PMID: 36947624 PMCID: PMC10032594 DOI: 10.1126/sciadv.add6960] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Intrinsically disordered protein regions are of high importance for biotic and abiotic stress responses in plants. Tracts of identical amino acids accumulate in these regions and can vary in length over generations because of expansions and retractions of short tandem repeats at the genomic level. However, little attention has been paid to what extent length variation is shaped by natural selection. By environmental association analysis on 2514 length variable tracts in 770 whole-genome sequenced Arabidopsis thaliana, we show that length variation in glutamine and asparagine amino acid homopolymers, as well as in interaction hotspots, correlate with local bioclimatic habitat. We determined experimentally that the promoter activity of a light-stress gene depended on polyglutamine length variants in a disordered transcription factor. Our results show that length variations affect protein function and are likely adaptive. Length variants modulating protein function at a global genomic scale has implications for understanding protein evolution and eco-evolutionary biology.
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Affiliation(s)
- William B. Reinar
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Anne Greulich
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ida M. Stø
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Jonfinn B. Knutsen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Trond Reitan
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Melinka A. Butenko
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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Reinar WB, Lalun VO, Reitan T, Jakobsen KS, Butenko MA. Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana. Plant Cell 2021; 33:2221-2234. [PMID: 33848350 PMCID: PMC8364236 DOI: 10.1093/plcell/koab107] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately influences the phenotype and thus the local adaptation of natural populations. Short tandem repeats (STRs) consisting of repetitive DNA motifs have been shown to regulate gene expression. STRs are variable in length within a population and serve as a heritable, but semi-reversible, reservoir of standing genetic variation. For sessile organisms, such as plants, STRs could be of major importance in fine-tuning gene expression as a response to a shifting local environment. Here, we used a transcriptome dataset from natural accessions of Arabidopsis thaliana to investigate population-wide gene expression patterns in light of genome-wide STR variation. We empirically modeled gene expression as a response to the STR length within and around the gene and demonstrated that an association between gene expression and STR length variation is unequivocally present in the sampled population. To support our model, we explored the promoter activity in a transcriptional regulator involved in root hair formation and provided experimentally determined causality between coding sequence length variation and promoter activity. Our results support a general link between gene expression variation and STR length variation in A. thaliana.
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Affiliation(s)
- William B. Reinar
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Vilde O. Lalun
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Trond Reitan
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Melinka A. Butenko
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, Nederbragt AJ. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 2017; 18:95. [PMID: 28100185 PMCID: PMC5241972 DOI: 10.1186/s12864-016-3448-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. RESULTS By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual. CONCLUSIONS The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.
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Affiliation(s)
- Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
- Department of Natural Sciences, University of Agder, Kristiansand, NO-4604 Norway
| | - William B. Reinar
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Harald Grove
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, NO-1432 Norway
| | - Jason R. Miller
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, 20850 MD USA
| | - Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 MD USA
| | - James Knight
- Yale School of Medicine, Yale University, New Haven, 06520 CT USA
| | | | | | | | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Morten Skage
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, NO-1432 Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
| | - Alexander J. Nederbragt
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NO-0316 Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Oslo, NO-0316 Norway
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