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

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.

Assembly of a young vertebrate Y chromosome reveals convergent signatures of sex chromosome evolution

“…Divergence times for each of the strata can be approximated based on divergence rates 461 between the threespine stickleback fish and the ninespine stickleback fish (Pungitius pungitius), al. 2009; Varadharajan et al 2019). Combined with a mean genome-wide estimate of Using the same calibration, stratum two formed less than 5.9 million years ago and stratum three 467 formed less than 4.7 million years ago.…”

Automated improvement of stickleback reference genome assemblies with Lep-Anchor software

“…The improved assembly brings noticeable gains, and we could now successfully map the centromere associated repeat and unambiguously identify the centromere positions in all linkage groups (previously missing from LG1 and LG16, and incoherent in LG10 and LG14, Fig. 1b; see reference (17)). Removal of haplotypes and other changes in the genome assembly affects read mapping and single nucleotide variant calling.…”

“…The starting point for this reference was the genomic DNA sequence data from Varadharajan et al (17) In short, sequence data on one male individual from Pyöreälampi pond (66 a large inversion in LG19 was characterized and the region was reassembled (see below), and the mitochondrial genome was reassembled (see below). The resulting contig-assembly was anchored using Lep-Anchor (9) following the standard pipeline (https://sourceforge.net/p/lep-anchor/wiki/Home) with default parameters (exception: minQuality=1 for Map2Bed to assign more contigs into chromosomes).…”

“…The parental genotypes were called using ParentCall2 module utilizing half-sib families (halfsibs=1) and calling also sex markers (XLimit=2). After running Fil-tering2 on default parameters, 50568 markers were retained and SeparateChromosomes2 module with LOD score limit 40 (lodLimit) clustered these markers into 21 linkage groups (LGs), matching the chromosome number of the species (33,17). JoinSingles2All with lodLimit=20 and lodDifference=4 assigned 22753 markers to the LGs and each LG was then ordered with OrderMarkers2, producing the first maps.…”

“…JoinSingles2All with lodLimit=20 and lodDifference=4 assigned 22753 markers to the LGs and each LG was then ordered with OrderMarkers2, producing the first maps. After genome anchoring with the novel maps and maps from Varadharajan et al (17), OrderMarkers2 was run one more time, separately for each LG, with physically ordered markers (parameter evaluateOrder). This yielded the final map from which the crossover locations were acquired.…”