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Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilian Univ Munich, Fac Biol, Div Evolutionary Biol, D-82152 Planegg Martinsried, Germany..
BioNano Genom, San Diego, CA 91121 USA..
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 5, p. 697-708Article in journal (Refereed) Published
Abstract [en]

Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [ OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (rho) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.

Place, publisher, year, edition, pages
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT , 2017. Vol. 27, no 5, p. 697-708
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-323040DOI: 10.1101/gr.215095.116ISI: 000400392400005PubMedID: 28360231OAI: oai:DiVA.org:uu-323040DiVA, id: diva2:1104721
Funder
Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)Swedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536Available from: 2017-06-01 Created: 2017-06-01 Last updated: 2019-01-07Bibliographically approved
In thesis
1. Evolutionary genomics in Corvids: – From single nucleotides to structural variants
Open this publication in new window or tab >>Evolutionary genomics in Corvids: – From single nucleotides to structural variants
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Heritable genetic variation is the raw material of evolution and can occur in many different forms, from altering single nucleotides to rearranging stretches of millions at once. DNA mutations that result in phenotypic differences are the basis upon which natural selection can act, leading to a shift of the frequency of those mutations.

In this thesis I aim to comprehensively characterize and quantify genetic variation in a natural system, the songbird genus Corvus.

First, we expand on previous work from a hybrid zone of different populations of Eurasian crows. All black carrion crows and black-and-grey hooded crows meet in a narrow hybrid zone in central Europe, and also in central and Southeast Asia. Comparing population genetic data acquired from these three hybrid zones yielded no single genetic region as a candidate responsible for phenotypic divergence, yet a parallelism in sets of genes and gene networks was evident.

Second, we capitalize on varying evolutionary timescales to investigate the driver of the heterogeneous genetic differentiation landscape observed in multiple avian species. Genetic diversity, and thus differentiation, seems to be correlated both between populations within single species and between species which diverged 50 million years ago. This pattern is best explained by conserved broad-scale recombination rate variation, which is in turn likely associated with chromosomal features such as centromeres and telomeres.

Third, we introduce a de-novo assembly of the hooded crow based on long-read sequencing and optical mapping. The use of this technology allowed a glimpse into previously hidden regions of the genome, and uncovered large-scale tandem repeat arrays consisting of a 14-kbp satellite repeat or its 1.2-kpb subunit. Furthermore, these tandem repeat arrays are associated with regions of reduced recombination rate.

Lastly, we extend the population genetic analysis to structural genomic variation, such as insertions and deletions. A large-scale population re-sequencing data set based on short-read and long-read technologies, spread across the entire genus is the foundation of a fine-scale genome-wide map of structural variation. A differentiation outlier approach between all-black carrion and black-and-grey hooded crows identified a 2.25-kilobase LTR retrotransposon inserted 20-kb upstream of the NDP gene. The element, which is fixed in the hooded crow population, is associated with decreased expression of NDP and may be responsible for differences in plumage color.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 42
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1762
Keywords
evolutionary genetics, genomics, population genetics, selection, recombination, chromosomal features, colouration, insertion, deletion, inversion, crow, tandem repeat, transposable element, gene expression
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-369878 (URN)978-91-513-0550-9 (ISBN)
Public defence
2019-02-25, Ekmansalen, Norbyvägen 14 A, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2019-02-04 Created: 2019-01-07 Last updated: 2019-02-18

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Weissensteiner, Matthias H.Bunikis, IgnasHöijer, IdaPettersson, Olga VinnereSuh, AlexanderWolf, Jochen B. W.

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Weissensteiner, Matthias H.Bunikis, IgnasHöijer, IdaPettersson, Olga VinnereSuh, AlexanderWolf, Jochen B. W.
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Evolutionary BiologyScience for Life Laboratory, SciLifeLabDepartment of Immunology, Genetics and Pathology
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