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) are recently described in China, providing us with valuable materials to analyze genetic diversification of the family Sillaginidae. Herein, we constructed a reference genome for the Chinese sillago, with the aim to setup a platform for comparative analysis of all species in this family.
Using the single-molecule real-time DNA sequencing platform 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 taking advantage of complementary strengths of two genome assembly programs Canu and FALCON. The genome size was consistent with the estimated genome size based on Kmer 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 de novo method and with RNA-seq data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, Chinese sillago was closely related to Larimichthys Crocea and Dicentrarchus labrax, and Chinese sillago diverged from their ancestor around 69.5 - 82.6 million years ago.
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.

Keywords:

• chinese sillago
• pacbio sequencing
• canu
• falcon
• genetic diversification

Read the peer-reviewed publication(s):

(PubMed: 30202912)

Accessions (data generated as part of this study):

BioProject: PRJNA437933