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dc.date.accessioned2020-06-24T18:24:59Z
dc.date.available2020-06-24T18:24:59Z
dc.date.created2019-11-06T14:35:06Z
dc.date.issued2019
dc.identifier.citationVaradharajan, Srinidhi Rastas, Pasi Löytynoja, Ari Matschiner, Michael Calboli, Federico C. F. Guo, Baocheng Nederbragt, Alexander Johan Jakobsen, Kjetill Sigurd Merilä, Juha . A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome. Genome Biology and Evolution. 2019, 11(11), 3291-3308
dc.identifier.urihttp://hdl.handle.net/10852/77193
dc.description.abstractThe Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the ‘ecology’s supermodel’, while the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and ca. 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromeric-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years (MYA) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 MYA. Compared to the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
dc.languageEN
dc.rightsAttribution-NonCommercial 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.titleA high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome
dc.typeJournal article
dc.creator.authorVaradharajan, Srinidhi
dc.creator.authorRastas, Pasi
dc.creator.authorLöytynoja, Ari
dc.creator.authorMatschiner, Michael
dc.creator.authorCalboli, Federico C. F.
dc.creator.authorGuo, Baocheng
dc.creator.authorNederbragt, Alexander Johan
dc.creator.authorJakobsen, Kjetill Sigurd
dc.creator.authorMerilä, Juha
cristin.unitcode185,15,29,50
cristin.unitnameCentre for Ecological and Evolutionary Synthesis
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.qualitycode1
dc.identifier.cristin1744629
dc.identifier.bibliographiccitationinfo:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Genome Biology and Evolution&rft.volume=11&rft.spage=3291&rft.date=2019
dc.identifier.jtitleGenome Biology and Evolution
dc.identifier.volume11
dc.identifier.issue11
dc.identifier.startpage3291
dc.identifier.endpage3308
dc.identifier.doihttps://doi.org/10.1093/gbe/evz240
dc.identifier.urnURN:NBN:no-80280
dc.type.documentTidsskriftartikkel
dc.type.peerreviewedPeer reviewed
dc.source.issn1759-6653
dc.identifier.fulltextFulltext https://www.duo.uio.no/bitstream/handle/10852/77193/2/A%2BHigh-Quality%2BAssembly%2Bof%2Bthe%2BNine-Spined%2BStickleback-evz240.pdf
dc.type.versionPublishedVersion
dc.relation.projectNFR/275869
dc.relation.projectEC/FP7/PIEF-GA-2013-624073


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