Chromosome-level genome assembly with telomeric repeats at scaffold ends for Rhabdosargus sarba

Abstract

Rhabdosargus sarba, the goldlined seabream, is a euryhaline marine fish of great aquaculture potential. Genome sequencing and assembly of R. sarba was carried utilizing a multi-platform sequencing strategy that included long-read sequencing (PacBio HiFi), short-read sequencing (Illumina), and chromatin interaction mapping (Hi-C). The final genome assembly size after scaffolding was 764.59 Mb in 31 scaffolds with an N50 length of 33.98 Mb. Repeat profiling of primary assembly showed that 28.71% of the genome comprises of repeat elements. Gene prediction utilising the evidence from ab initio prediction and transcriptome data revealed 26,913 protein encoding genes and functional annotation and pathway analysis showed their participation in 332 pathways. This genome is an excellent resource for future research on genetic improvement and molecular breeding programmes for R. sarba.

Fig. 1

A specimen of goldlined seabream (Rhabdosargus sarba).

Fig. 2

The genome size estimation profiles of Rhabdosargus sarba (a) Flowcytometry graph depicting the fluorescent peaks of R. sarba and Chicken erythrocytes, (b) K-mer based analysis profile for genome size estimation of R. sarba using Jellyfish and Genomescope.

Fig. 3

(a) Hi-C contact map representing the assembled genome of R. sarba into 24 chromosome level scaffolds. The blue line and the green line indicate scaffold borders and contig borders respectively. (b) Circos plot of the Goldlined seabream genome. From the outermost: Track1: The 24 chromosomes of the seabream genome. Track2: Contigs corresponding to the 24 chromosomes represented as tiles. Track3: The protein encoding genes shown as heatmap with progressive colors (yellow–orange–red) indicating length of genes. Track4: Full length isoform sequences supporting the genes of seabream shown as line diagram with incremental isoform lengths shown from purple to dark purple. Track5: Transcripts generated from RNAseq data supporting the genes of seabream shown as line diagram with incremental transcripts lengths shown from blue to dark blue. Track6: GC content of seabream genome shown as line diagram plotted with 50 kb sliding window. The GC values below 35 and above 45 are shown in dark green color, and remaining in green color.

Fig. 4

The functional annotation levels using Omicsbox tool. Pie chart depicting the percentage of transcripts with GO annotation, with only GO mapping, with only blast hits and No hits.

Fig. 5

The graph depicting the telomeric repeats present at the ends of the chromosomes assembled in the R. sarba genome.

Fig. 6

Graph depicting BUSCO analysis for estimating genome completeness of R. sarba against Actinopterygii_odb10 orthologous database.

Fig. 7

Synteny map of R. sarba (goldlined seabream) with Sparus aurata (gilthead seabream).