An updated reference genome of Barbatula barbatula (Linnaeus, 1758)

Abstract

The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species' available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species' available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species' publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species' biodiversity and support conservation efforts.

Fig. 1

Stone loach Barbatula barbatula (Linnaeus, 1758) from the upper catchment of the Tarna river, Parádfürdő, Hungary (a). Photo taken by P.S. and Á.M. Tarna river in Tarnaszentmária, Hungary. One of the typical habitats of the stone loach, a gravel-bottom stream within a hilly and woody landscape (b). Photo taken by P.S. and Á.M.

Fig. 2

Structural comparison of the publicly available mitochondrial genome of Barbatula barbatula and the de novo assembled mitochondrial genome. The figure reconstructed using clinker 0.0.27 was further edited with Inkscape 1.2.2 to improve readability.

Fig. 3

Functional annotation of the predicted genes in the chromosome scaffolds. The figure shows the total number of predicted genes in the newly assembled contigs, chromosome scaffolds and reference genome (GCA_947034865.1) as a bar chart stacked to represent the ratio of genes that received a GO term after functional annotation. (a) The ratio of GO terms belonging to different ontologies is shown as a bar chart (b), and the 50 most frequent functions found in each ontology (biological process – BP, cell composition – CC, molecular function – MF) are shown as a word cloud (c), where the font size is proportional to the frequency of each function in the annotation.

Fig. 4

Genome and annotation completeness as assessed by BUSCO (a) and OMArk (b).