A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome

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Varadharajan , S , Rastas , P , Löytynoja , A , Matschiner , M , Calboli , F C F , Guo , B , Nederbragt , A J , Jakobsen , K S & Merilä , J 2019 , ' A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome ' , Genome Biology and Evolution , vol. 11 , no. 11 , pp. 3291-3308 . https://doi.org/10.1093/gbe/evz240

Title: A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome
Author: Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F.; Guo, Baocheng; Nederbragt, Alexander J.; Jakobsen, Kjetill S.; Merilä, Juha
Contributor: University of Helsinki, Ecological Genetics Research Unit
University of Helsinki, Institute of Biotechnology
University of Helsinki, Faculty of Biological and Environmental Sciences
University of Helsinki, Faculty of Biological and Environmental Sciences
University of Helsinki, Organismal and Evolutionary Biology Research Programme
Date: 2019-11
Number of pages: 18
Belongs to series: Genome Biology and Evolution
ISSN: 1759-6653
URI: http://hdl.handle.net/10138/313602
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," whereas 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 = 1.2Mbp) 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 about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with 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.
Subject: genome assembly
stickleback
Pungitius pungitius
comparative genomics
TRANSPOSABLE ELEMENTS
GENETIC ARCHITECTURE
EUKARYOTIC GENOMES
PELVIC REDUCTION
TANDEM REPEATS
DATING METHODS
EVOLUTION
DNA
MICROSATELLITES
SEQUENCE
1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
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