Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama)

Abstract

Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93% of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51% of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of S. sinica about 7.92 million years ago. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.

Genomic Comparison and Genetic Marker Identification of the White-Spotted Bamboo Shark Chiloscyllium plagiosum

“…We hypothesized that the difference in genome size and repeat ratio of this species should be due to different (i.e., natural vs. artificial) habitat environments of samples. Similar genomic patterns were also revealed in the silver sillago (Sillago sihama) (Li et al, 2019b;Lin et al, 2020), in which the genome size of the natural sample was 521.63 Mb with a repeat ratio of 13.78%, while the domesticated one had a genome size of about 680 Mb and a repeat ratio of 29.60%. Chalopin et al (2015) discovered a positive correlation between repeat elements and genome size in 26 vertebrate species, suggesting that repeat sequences largely contribute to the genome size of vertebrates.…”

Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama)

“…All available OR gene sequences of six teleost fish were downloaded from the National Center for Biotechnology Information (NCBI) ( (accessed on 20 May 2022)) and Ensemble ( (accessed on 20 May 2022)), including large yellow croaker ( Larimichthys crocea ), tilapia ( Oreochromis niloticus ), zebrafish ( Danio rerio ), medaka ( Oryzias latipes ), stickleback ( Gasterosteus aculeatus ), and fugu ( Takifugu rubripes ) ( Table S1 ). Genomic and genome annotation data of S. sihama were obtained from Lin et al [ 25 ] ( Table S2 ). The OR gene-coding sequences of S. sihama were translated to obtain amino acid sequences using the EditSeq program of DNASTAR Lasergene 7.…”

“…A total of 542 OR gene protein sequences from L. crocea ( n = 111), O. niloticus ( n = 266), and D. rerio ( n = 165) were used as query sequences to conduct a TBLASTN search (Version: 2.7.1+) in the S. sihama genome, with an e-value cut-off of 1 × 10 −5 , and the predictive limit of intron size at default parameters [ 25 ]. Fasta Extract functions in the TBtools (v1.098696) software were used to extract these gene regions from the genome [ 25 ]. Then, the obtained OR genes were annotated based on the existing S. sihama genome annotation results.…”

“…The chromosomal location and structure information of OR genes were obtained from the genome annotation data [ 25 ]. The OR genes were mapped to S. sihama chromosomes, which were visualized by the Mapchart software [ 31 ].…”

“…S. sihama is sensitive to environmental stimuli and has the habit of drilling sand to avoid seine-net and other environmental hazards [ 24 ]. Lin et al [ 25 ] reported the genome sequence of this species and found that OR genes were significantly expanded in the genome. In this study, the members of the OR gene family were identified and analyzed to unravel phylogenetic relationships, gene structures, conserved motifs, chromosomal locations, and gene duplications in the S. sihama genome.…”