The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids

• Published in: G3 Genes|Genomes|Genetics
• Main Authors: Sävilammi, Tiina, Primmer, Craig R., Varadharajan, Srinidhi, Guyomard, René, Guiguen, Yann, Sandve, Simen R., Vøllestad, L. Asbjørn, Papakostas, Spiros, Lien, Sigbjørn
• Other Authors: Department of Biology, University of Memphis, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, HiLIFE - Institute of Biotechnology Helsinki (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Biosciences, University of Kent Canterbury, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Centre for Integrative Genetics (CIGENE), This work was supported by the Academy of Finland (project numbers 287342 and 302873). We thank the Finnish Centre for Scientific Computing for providing computational resources. SV and LAV are supported by Center for Computational Inference in Evolutionary Life Science (CELS) and the Department of Biosciences, University of Oslo. YG and RG contributions were supported by the Agence Nationale de la Recherche (ANR Blanc SVSE 7 2011, project SDS)., ANR-15-CE37-0004,SmellBrain,Dissection fonctionnelle des circuits codant pour la récompense dans le système olfactif(2015)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2019
• Subjects: karyotyping of the cells; salmonids; fish; rétrotransposon; caryotype; séquençage du génome; chromosome; génomique fonctionnelle; gène sdY; structure chromosome; évolution du génome; évolution chromosomique; reproduction; ombre commun; salmonidae; poisson; thymallus thymallus; [SDV]Life Sciences [q-bio]; Atlantic salmon; Salmo salar
• Online Access: https://hal.science/hal-02154636; https://hal.science/hal-02154636/document; https://hal.science/hal-02154636/file/S%C3%A4vilammi_2019_3G_1.pdf; https://doi.org/10.1534/g3.118.200919

Supplemental material available at Figshare: https://doi.org/10.25387/g3.7728512 Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.