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Structural variants in the great tit genome and their effect on seasonal timing

da Silva, Vinicius Henrique (2020). Structural variants in the great tit genome and their effect on seasonal timing. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis Agriculturae Sueciae, 1652-6880 ; 2020:1
ISBN 978-91-7760-520-1
eISBN 978-91-7760-521-8
[Doctoral thesis]

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Abstract

The biodiversity of our planet has been increasingly endangered by human actions. This nature biodiversity is strictly correlated with genomic diversity of all the species in the ecosystem. Thus, a broader understanding on the genome of wild species may be extremely useful to understand selection and plasticity in the natural species of our changing world. The great tit (Parus major ) is a songbird that has been extensively explored in ecological and evolutionary studies, shedding light on the effects of the global warming on nature. The seasonal timing of the great tit has been shifting under the global warming, but the knowledge on particular genes associated with timing is still limited. Although the effect of single nucleotide changes on the breeding timing of great tits has been investigated, the effect of more complex structural variants is largely unknown. In fact, the genomic structural variability was never explored in detail in these species. The aim of this thesis was to detect, map, characterize and associate, with seasonal timing, structural variants that are present in the great tit genome such as copy number variations (CNVs) and inversions. First, this thesis presents a genome-wide map of CNV regions in the great tit genome, showing how these variants are associated with genomic architecture that underlies their molecular formation. Great tit CNVs, in accordance to reported in several mammalian species, are enriched at evolutionary breakpoints. Although it supports the importance of CNVs during speciation like is described in mammals, a remarkable difference is that neuronal related genes may play a central role on the great tit speciation. Second, CNVs were associated with breeding timing. Although no strong association was found, suggestive associations such as a copy number gain in a gene related to circadian clock deserves further investigation. Finally, this thesis investigate in detail the genomic complexity of a large (≈64 Mb) and widespread (≈5%) inversion in the Chromosome 1A. Interestingly, this inversion is a recessive lethal selfish structural rearrangement (i.e. breaks the Mendel’s law). The inversion is inherited twice more than expected from male carriers but are normally inherited from female carriers, suggesting that a meiotic drive mechanism during spermatogenesis maintains this large inversion in great tit populations.

Authors/Creators:da Silva, Vinicius Henrique
Title:Structural variants in the great tit genome and their effect on seasonal timing
Year of publishing :2020
Number:2020:1
Number of Pages:173
Papers/manuscripts:
NumberReferences
Ida Silva, Vinicius, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson, Luciana Regitano, Luiz Coutinho, Ralf Zimmer, Levi Waldron, and Ludwig Geistlinger. 2019. CNVRanger: Association Analysis of CNVs with Gene Expression and Quantitative Phenotypes. Bioinformatics btz632:1–2.
IIPértille, Fàbio, Vinicius H. da Silva, Anna M. Johansson, Tom Lindström, Dominic Wright, Luiz L. Coutinho, Per Jensen, and Carlos Guerrero-Bosagna. 2019. Mutation Dynamics of CpG Dinucleotides during a Recent Event of Vertebrate Diversification. Epigenetics 14(7):685–707.
IIIda Silva, Vinicius H., Veronika N. Laine, Mirte Bosse, Lewis G. Spurgin, Martijn F. L. Derks, Kees van Oers, Bert Dibbits, Jon Slate, Richard P. M. A. Crooijmans, Marcel E. Visser, and Martien A. M. Groenen. 2019. The Genomic Complexity of a Large Inversion in Great Tits. Genome Biology and Evolution 11(7):1870–81.
IVda Silva, Vinicius H., Veronika N. Laine, Mirte Bosse, Kees van Oers, Bert Dibbits, Marcel E. Visser, Richard P. M. A. Crooijmans, and Martien A. M. Groenen. 2018. CNVs Are Associated with Genomic Architecture in a Songbird. BMC Genomics 19(S2):195.
VSchurink, Anouk, Vinicius H. da Silva, Brandon D. Velie, Bert W. Dibbits, Richard P. M. A. Crooijmans, Liesbeth Franois, Steven Janssens, Anneleen Stinckens, Sarah Blott, Nadine Buys, Gabriella Lindgren, and Bart J. Ducro. 2018. Copy Number Variations in Friesian Horses and Genetic Risk Factors for Insect Bite Hypersensitivity. BMC Genetics 19(1):49.
VIGeistlinger, Ludwig, Vinicius Henrique da Silva, Aline Silva Mello Cesar, Polyana Cristine Tizioto, Levi Waldron, Ralf Zimmer, Luciana Correia de Almeida Regitano, and Luiz Lehmann Coutinho. 2018. Widespread Modulation of Gene Expression by Copy Number Variation in Skeletal Muscle. Scientific Reports 8(1):1399.
VIIUpadhyay, Maulik, Vinicus H. da Silva, Hendrik-Jan Megens, Marleen H. P. W. Visker, Paolo Ajmone-Marsan, Valentin A. Bâlteanu, Susana Dunner, Jose F. Garcia, Catarina Ginja, Juha Kantanen, Martien A. M. Groenen, and Richard P. M. A. Crooijmans. 2017. Distribution and Functionality of Copy Number Variation across European Cattle Populations. Frontiers in Genetics 8
VIIIda Silva, Vinicius Henrique, Luciana Correia de Almeida Regitano, Ludwig Geistlinger, Fàbio Pértille, Poliana Fernanda Giachetto, Ricardo Augusto Brassaloti, Natàlia Silva Morosini, Ralf Zimmer, and Luiz Lehmann Coutinho. 2016. Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLOS ONE 11(6):e0157711.
VIIIIPértille, Fàbio, Carlos Guerrero-Bosagna, Vinicius Henrique da Silva, Clarissa Boschiero, José de Ribamar da Silva Nunes, Mônica Corrêa Ledur, Per Jensen, and Luiz Lehmann Coutinho. 2016. High-Throughput and Cost-Effective Chicken Genotyping Using Next-Generation Sequencing. Scientific Reports 6:26929
Place of Publication:Uppsala
Publisher:Department of Animal Breeeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-7760-520-1
ISBN for electronic version:978-91-7760-521-8
ISSN:1652-6880
Language:English
Additional Information:This research was conducted under the joint auspices of Swedish University of Agricultural Sciences and the Graduate School Wageningen Institute of Animal Sciences of Wageningen University & Research and is part of the Erasmus Mundus Joint Doctorate program “EGS-ABG”
Publication Type:Doctoral thesis
Article category:Other scientific
Full Text Status:Public
Agris subject categories.:L Animal production > L10 Animal genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:biodiversity
URN:NBN:urn:nbn:se:slu:epsilon-p-103259
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-103259
ID Code:16534
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:03 Jan 2020 10:29
Metadata Last Modified:14 Jan 2020 14:19

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