A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes

Abstract

Background: Sillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family.

Findings: Using the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated ∼27.3 Gb genomic DNA sequences for the Chinese sillago. We reconstructed a genome assembly of 534 Mb using a strategy that takes advantage of complementary strengths of two genome assembly programs, Canu and FALCON. The genome size was consistent with the estimated genome size based on k-mer analysis. The assembled genome consisted of 802 contigs with a contig N50 length of 2.6 Mb. We annotated 22,122 protein-coding genes in the Chinese sillago genomes using a de novo method as well as RNA sequencing data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, the Chinese sillago is closely related to Larimichthys crocea and Dicentrarchus labrax and diverged from their ancestor around 69.5-82.6 million years ago.

Conclusions: Using long reads generated with PacBio sequencing technology, we have built a draft genome assembly for the Chinese sillago, which is the first reference genome for Sillaginidae species. This genome assembly sets a stage for comparative analysis of the diversification and adaptation of fishes in Sillaginidae.

Figure 1:

A representative individual of the Chinese sillago.

Figure 2:

Comparing genome assemblies between Chinese sillago and other fish species. The y-axis represents the contig N50 (A) and contig number (B). Only the top 20 public genomes are shown (x-axis) ordered by contig N50 length (A) and contig number (B).

Figure 3:

Gene family comparison between Chinese sillago and other fish species (x-axis). The y-axis represents the gene number for each class: single-copy (one gene for each species), multiple-copy (more than one gene for each species), unique paralogs (no genes in other species), other orthologs (other cases in gene clusters), and unclustered genes (genes that did not cluster with other genes).

Figure 4:

The phylogenetic relationship of Chinese sillago with other fish. The estimated divergence time (million years ago) is shown in the lower coordinates. The blue bars at each branch represent the 95% confidence interval of the species divergence time.