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. 2023 Jun 6;10(1):360.
doi: 10.1038/s41597-023-02278-w.

Gap-free genome assembly of anadromous Coilia nasus

Fengjiao Ma #  1 , Yinping Wang #  1   2 , Bixiu Su #  3 , Chenxi Zhao #  3 , Denghua Yin  2 , Chunhai Chen  3 , Yanping Yang  2 , Chenhe Wang  3 , Bei Luo  3 , Hongqi Wang  3 , Yanmin Deng  4 , Pao Xu  5   6   7 , Guojun Yin  8   9 , Jianbo Jian  10 , Kai Liu  11   12   13
Affiliations

Gap-free genome assembly of anadromous Coilia nasus

Fengjiao Ma et al. Sci Data. .

Abstract

The Chinese tapertail anchovy, Coilia nasus, is a socioeconomically important anadromous fish that migrates from near ocean waters to freshwater to spawn every spring. The analysis of genomic architecture and information of C. nasus were hindered by the previously released versions of reference genomes with gaps. Here, we report the assembly of a chromosome-level gap-free genome of C. nasus by incorporating high-coverage and accurate long-read sequence data with multiple assembly strategies. All 24 chromosomes were assembled without gaps, representing the highest completeness and assembly quality. We assembled the genome with a size of 851.67 Mb and used BUSCO to estimate the completeness of the assembly as 92.5%. Using a combination of de novo prediction, protein homology and RNA-seq annotation, 21,900 genes were functionally annotated, representing 99.68% of the total predicted protein-coding genes. The availability of gap-free reference genomes for C. nasus will provide the opportunity for understanding genome structure and function, and will also lay a solid foundation for further management and conservation of this important species.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The sampling site and otolith profiles of C. nasus. (A) Morphological photograph of C. nasus. (B) Location of the sampling site (red dot) and migration direction (direction of the arrow) of C. nasus. (C) Otolith Sr: Ca profiles of C. nasus collected from the Taizhou section in the Yangtze River.
Fig. 2
Fig. 2
Hi-C chromatin interaction map and circos plot of the genome assembly. (A) Hi-C chromatin interaction map of the C. nasus assembly. (B) The circos plot of the C. nasus genome assembly. The rings from outside to inside indicate (a) chromosomes of the Coilia nasus genome, (b) gene density, (c) TE density, (d) GC density, and (e) paralogous genes on different chromosomes; b-d were drawn in 500-kb sliding windows.
Fig. 3
Fig. 3
Venn diagram of functional annotation of the C. nasus protein-coding genes. The Venn diagram shows the shared and unique annotations among InterPro, KEGG, KOG, NR and SwissProt.
Fig. 4
Fig. 4
Chromosome comparison of C. nasus to Clupea harengus using protein-coding gene synteny. The chromosome ID of C. nasus was sorted by sequence length.
See this image and copyright information in PMC

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