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Variant calling using NGS data in European aspen (Populus tremula)
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). (Molecular Ecology Group)
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0001-6031-005X
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
2015 (English)In: Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches / [ed] Sablok, G., Kumar, S., Ueno, S., Kuo, J., Varotto, C. (Eds.), Springer, 2015, 1, 43-61 p.Chapter in book (Refereed)
Abstract [en]

Analysis of next-generation sequencing (NGS) data is rapidly becoming an important source of information for genetics and genomics studies. The utility of such data does, however, rely crucially on the accuracy and quality of SNP and genotype calling. Identification of genetic variants (SNPs and short indels) from NGS data is an area of active research and many recent statistical methods have been developed to both improve and quantify the large uncertainty associated with genotype calling. The detection of genetic variants from NGS data is prone to errors, due to multiple factors such as base-calling, alignment errors and read coverage. Here we highlight some of the issues and review and exemplify some of the recent methods that have been developed for genotype calling. We also provide guidelines for their application to whole-genome re-sequencing data using a data set based on a number of European aspen (Populus tremula) individuals each sequenced to a depth of about 20x coverage per individual.

Place, publisher, year, edition, pages
Springer, 2015, 1. 43-61 p.
Keyword [en]
Next generation sequencing, variant calling, single nucleotide polymorphism (SNP), pre-processing, alignment, post-processing, filtering
National Category
Biological Sciences
URN: urn:nbn:se:umu:diva-102803DOI: 10.1007/978-3-319-17157-9_4ISBN: 978-3-319-17156-2OAI: diva2:809757
Available from: 2015-05-05 Created: 2015-05-05 Last updated: 2016-05-16Bibliographically approved
In thesis
1. The genomic signatures of adaptive evolution in Populus
Open this publication in new window or tab >>The genomic signatures of adaptive evolution in Populus
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the genetic basis of adaptive evolution, and how natural selection has shaped patterns of polymorphism and divergence within and between species are enduring goals of evolutionary genetics. In this thesis, I used whole genome re-sequencing data to characterize the genomic signatures of natural selection along different evolutionary timescales in three Populus species: Populus tremula, P. tremuloides and P. trichocarpa. First, our study shows multiple lines of evidence suggesting that natural selection, due to both positive and purifying selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. Second, we characterize the evolution of genomic divergence patterns between two recently diverged aspen species: P. tremula and P. tremuloides. Our findings indicate that the two species diverged ~2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. We further explore different mechanisms that may explain the heterogeneity of genomic divergence, and find that variation in linked selection and recombination likely plays a key role in generating the heterogeneous genomic landscape of differentiation between the two aspen species. Third, we link whole-genome polymorphic data with local environmental variables and phenotypic variation in an adaptive trait to investigate the genomic basis of local adaptation in P. tremula along a latitudinal gradient across Sweden. We find that a majority of single nucleotide polymorphisms (SNPs) (>90%) identified as being involved in local adaptation are tightly clustered in a single genomic region on chromosome 10. The signatures of selection at this region are more consistent with soft rather than hard selective sweeps, where multiple adaptive haplotypes derived from standing genetic variation sweep through the populations simultaneously, and where different haplotypes rise to high frequency in different latitudinal regions. In summary, this thesis uses phylogenetic comparative approaches to elucidate how various evolutionary forces have shaped genome-wide patterns of sequence evolution in Populus.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2016. 52 p.
Populus, adaptive evolution, natural selection, genomic diversity and divergence, recombination, Next-generation sequencing, local adaptation
National Category
urn:nbn:se:umu:diva-120286 (URN)978-91-7601-463-9 (ISBN)
Public defence
2016-06-08, KB3B1, KBC-huset, Umeå, 13:00 (English)

The research in this thesis was supported by the Swedish research council (to Pär K. Ingvarsson) and the JC Kempe Memorial Scholarship Foundation (to Jing Wang). The PhD study of Jing Wang in Sweden was funded by the State Scholarship from China Scholarship council.

Available from: 2016-05-18 Created: 2016-05-13 Last updated: 2016-05-26Bibliographically approved

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Wang, JingStreet, NathanielIngvarsson, Pär
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Department of Ecology and Environmental SciencesUmeå Plant Science Centre (UPSC)Department of Plant Physiology
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