Improved Assembly of the Pungitius Pungitius Reference Genome

Overview

Journal G3 (Bethesda)

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2024 Jun 11

PMID 38861393

Authors

Dandan Wang

Pasi Rastas

Xueling Yi

Ari Loytynoja

Mikko Kivikoski

Xueyun Feng

Kerry Reid

Juha Merila

Affiliations

Soon will be listed here.

Abstract

The nine-spined stickleback (Pungitius pungitius) has been increasingly used as a model system in studies of local adaptation and sex chromosome evolution but its current reference genome assembly is far from perfect, lacking distinct sex chromosomes. We generated an improved assembly of the nine-spined stickleback reference genome (98.3% BUSCO completeness) with the aid of linked-read mapping. While the new assembly (v8) was of similar size as the earlier version (v7), we were able to assign 4.4 times more contigs to the linkage groups and improve the contiguity of the genome. Moreover, the new assembly contains a ∼22.8 Mb Y-linked scaffold (LG22) consisting mainly of previously assigned X-contigs, putative Y-contigs, putative centromere contigs, and highly repetitive elements. The male individual showed an even mapping depth on LG12 (pseudo X chromosome) and LG22 (Y-linked scaffold) in the segregating sites, suggesting near-pure X and Y representation in the v8 assembly. A total of 26,803 genes were annotated, and about 33% of the assembly was found to consist of repetitive elements. The high proportion of repetitive elements in LG22 (53.10%) suggests it can be difficult to assemble the complete sequence of the species' Y chromosome. Nevertheless, the new assembly is a significant improvement over the previous version and should provide a valuable resource for genomic studies of stickleback fishes.

Citing Articles

The genome sequence of the nine-spined stickleback, (Linnaeus, 1758).

Hanfling B, Smith A Wellcome Open Res. 2024; 8:555.

PMID: 39114814 PMC: 11303943. DOI: 10.12688/wellcomeopenres.20354.1.

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