New publication: A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome

By Srinidhi Varadharajan, Pasi Rastas, Ari Löytynoja, Michael Matschiner, Federico C F Calboli, Baocheng Guo, Alexander J. Nederbragt, Kjetill S. Jakobsen, and Juha Merilä in Genome Biology and Evolution (GBE)

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Abstract

The 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.


Genome Biology and Evolution, evz240
DOI: 10.1093/gbe/evz240
Published: 5 November 2019
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By Srinidhi Varadharajan*, Pasi Rastas, Ari Löytynoja, Michael Matschiner*, Federico C F Calboli, Baocheng Guo, Alexander J. Nederbragt*, Kjetill S. Jakobsen*, and Juha Merilä

* Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
See the publication webpage for full author information.

Tags: Genome Biology and Evolution (GBE);
Published Nov. 7, 2019 10:46 AM - Last modified Nov. 7, 2019 10:46 AM