Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Feb 3;13(2):evaa272.
doi: 10.1093/gbe/evaa272.

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

Xinghua Lin  1   2   3   4 , Yang Huang  1   2   3   4   5 , Dongneng Jiang  1   2   3   4   5 , Huapu Chen  1   2   3   4   5 , Siping Deng  1   2   3   4   5 , Yulei Zhang  1   3   4   5 , Tao Du  1   2   3   4   5 , Chunhua Zhu  1   2   3   4   5 , Guangli Li  1   2   3   4   5 , Changxu Tian  1   2   3   4   5
Affiliations

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

Xinghua Lin et al. Genome Biol Evol. .

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 Sillago sinica ∼7.92 Ma. 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.

Keywords: Hi-C; PacBio; chromosomal assembly; genome; silver sillago.

PubMed Disclaimer

Figures

<sc>Fig</sc>. 1
Fig. 1
Genome landscape and evolutionary analysis of Sillago sihama. (A) Genome landscape of S. sihama. (a) Chromosome length, (b) GC content, (c) gene density, (d) repeat sequence, (e) long terminal repeated (LTE), (f) long interspersed nuclear elements (LINE), and (g) simple sequence repeat (SSR). (B) Phylogenetic analysis of 11 teleost fishes. At each branch point, the predicted species divergence time (million years ago) is marked. The red number on each evolutionary branch represents the number of expanding gene families, and the blue number represents the number of contracting gene families. (C) Collinearity analysis of S. sihama and Larimichthys crocea genomes. Blue and orange outer circles represent the chromosome of S. sihama and L. crocea, respectively.
See this image and copyright information in PMC

References

    1. Alioto T, Blanco E, Parra G, Guigó R. 2018. Using geneid to identify genes. Curr Protoc Bioinformatics. 64(1):e56. - PubMed
    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410. - PubMed
    1. Boeckmann B. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31(1):365–370. - PMC - PubMed
    1. Burge C, Karlin S. 1997. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 268(1):78–94. - PubMed
    1. Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR. 2006. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7(1):327. - PMC - PubMed

Publication types