Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae

Abstract

Golden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5 Mb with the contig N50 of 1.80 Mb and the scaffold N50 of 5.05 Mb. The assembly covers 98.9% of the estimated genome size (655 Mb). Based on Hi-C data, 99.4% of the assembled bases are anchored into 24 pseudo-chromosomes. The annotation includes 21,915 protein-coding genes, in which 95.7% of 2,586 BUSCO vertebrate conserved genes are complete. This genome is expected to contribute to the comparative analysis of the Carangidae family.

Fig. 1

The pipelines of the chromosome-level pompano genome assembly.

Fig. 2

The K-mer distribution of Illumina paired-end reads using GenomeScope based on k value of 31. Frequency distribution of k-mers of different occurrences in two pair-end libraries. K-mer occurrences (x axis) were plotted against their frequencies (y axis).

Fig. 3

Hi-C chromosome contact map. Each block represents a Hi-C contact between two genomic loci within a 100-kb window. Darker color of a block indicates higher contact intensity.

Fig. 4

K-mer spectra copy number plot. Different color on the stacked bars represents copy number on the assembly. Frequency counts (spectral distribution) are computed on the Illumina paired-end reads.

Fig. 5

Alignment frequency distribution of Pacbio long reads and Illumina short reads.

Fig. 6

Distribution of insert sizes of sequencing reads in five libraries.

Fig. 7

Whole genome plot of four Carangiformes genomes compared to pompano genome. Alignment dot plots show the genome comparisons between four Carangiformes assemblies (y-axis) and pompano assembly (x-axis). Dotted lines (vertical and horizontal, respectively) are the boundaries of chromosome and of scaffolds in the assemblies. (a) Plot between the assemblies of Seriola quinqueradiata and pompano. (b) Plot between Seriola rivoliana assembly and pompano assembly. (c) Plot between Seriola dumerili assembly and pompano assembly. (d) Plot between Echeneis naucrates assembly and pompano assembly.