Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome

Abstract

The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for this species. Sequencing involved a combination of long reads with Oxford Nanopore Technologies, Illumina paired-end short reads (2 × 151 bp), Hi-C and RNA-seq from different tissues. The nuclear genome assembly has a scaffold N50 of 34.33 Mb, a total assembly span of 775.53 Mb and 99.63% of the sequence assembled into 24 superscaffolds, consistent with its known karyotype. Quality metrics revealed a consensus accuracy (QV) of 42.92 and gene completeness > 98%. The genome annotation resulted in 26,690 protein-coding genes and 12,737 non-coding transcripts. The coding regions encoded 39,613 unique protein products, 93% of them with assigned function. Overall, the publication of the X. novacula's reference genome will broaden the scope and impact of genomic research conducted on this iconic and colourful species.

Keywords: Hi-C scaffolding; Labridae; Xyrichtys novacula; chromosome-level assembly; genome annotation.

Figure 1.

Xyrichtys novacula. Specimen of X. novacula used to generate the genome (ID: XN0914), deposited at the Mediterranean Institute for Advanced Studies Collection (Ref. IMEDEA 109264). Scale bar in cm.

Figure 2.

Assembly workflow. Summary of the main steps followed to obtain the curated chromosome-level assembly. See the Snakemake pipeline for detailed information (https://github.com/cnag-aat/assembly_pipeline).

Figure 3.

Annotation workflow. Summary of the main steps followed to annotate the Xyrichtys novacula genome.

Figure 4.

Summary of assembly results. (A) Hi-C contact map for genome assembly fXyrNov1_1 visualized in PretextView. The map shows 24 superscaffolds, ordered from longest to shortest, in agreement with the karyotype of the species (n = 24). (B) Snail plot summary of assembly statistics for assembly fXyrNov1_1. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 775,535,542 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (40,352,512 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (34,328,652 and 28,232,734 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the actinopterygii_odb10 set is shown in the top right.