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. 2021 Oct 21;10(10):giab070.
doi: 10.1093/gigascience/giab070.

Chromosome-level genome assemblies of Channa argusandChanna maculata and comparative analysis of their temperature adaptability

Mi Ou  1 , Rong Huang  2 , Cheng Yang  2 , Bin Gui  2 , Qing Luo  1 , Jian Zhao  1 , Yongming Li  2 , Lanjie Liao  2 , Zuoyan Zhu  2 , Yaping Wang  2   3 , Kunci Chen  1
Affiliations

Chromosome-level genome assemblies of Channa argusandChanna maculata and comparative analysis of their temperature adaptability

Mi Ou et al. Gigascience. .

Abstract

Background: Channa argus and Channa maculata are the main cultured species of the snakehead fish family, Channidae. The relationship between them is close enough that they can mate; however, their temperature adaptability is quite different.

Results: In this study, we sequenced and assembled the whole genomes of C. argus and C. maculata and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, and scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for C. argus and C. maculata, respectively. Our analyses showed that C. argus and C. maculata have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in C. argus correspond to 3 chromosomes in C. maculata, suggesting that 3 chromosomal fusion events occurred in C. maculata. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to C. maculata, such as genes related to herpes simplex infection. Analysis of the transcriptome differences related to temperature adaptation revealed that the brain and liver of C. argus rapidly produced more differentially expressed genes than C. maculata. Genes in the FoxO signalling pathway were significantly enriched in C. argus during the cooling process (P < 0.05), and the expression of 3 transcription factor genes in this pathway was significantly different between C. argus and C. maculata (P < 0.01).

Conclusions: C. maculata may have higher resistance to certain diseases, whereas C. argus has a faster and stronger response to low-temperature stress and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae and provides important clues regarding differences in the low-temperature adaptations of fish.

Keywords: Channa argus; Channa maculata; genome; low-temperature adaptation; transcriptome.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1:
Figure 1:
Genome assembly and evolutionary analysis of C. argus and C. maculata. Genome-wide Hi-C heat maps of C. argus (A) and C. maculata (B). Chr 1–24 and Chr 1–21 refer to chromosome 1–24 and chromosome 1–21. (C) Evolutionary tree including C. argus and C. maculata. The black number at each branch represents the divergence time supported by 95% of the highest posterior density (HPD). The top of the tree is absolute age, separated by the shadow of each geological period. The number on the branch shows the number of expanded (red) and contracted (blue) gene families for each clade. The 2 red asterisks indicate C. argus and C. maculata.
Figure 2:
Figure 2:
Comparative analysis of the C. argus and the C. maculata genomes. (A) KEGG enrichment analysis of the unique, expansion, and contraction gene families. The ordinate is KEGG terms, the abscissa is the number of genes in the pathway, and the colour represents the corresponding P-value. Left, enrichment result for C. argus; right, enrichment result for C. maculata, same asterisks indicate same terms. (B) There was a high collinearity between the 2 species. Chr 2 and 3 of C. argus correspond to Chr 2 of C. maculata, Chr 4 and 5 of C. argus correspond to Chr 3 of C. maculata, Chr 18 and 19 of C. argus correspond to Chr 16 of C. maculata.
Figure 3:
Figure 3:
Verification of chromosome structure differences between C. argus and C. maculata genomes. (A) Complete collinearity map. (B) Partial collinearity map showing only the chromosomes with structural differences. (C) C. argus chromosomes were set as the reference sequence to which the Hi-C data of C. argus and C. maculata were mapped.
Figure 4:
Figure 4:
Low-temperature experiment and transcriptome sequencing of C. argus and C. maculata. (A) Cumulative mortality of C. argus and C. maculata during cooling. Abscissa represents temperature and ordinate represents cumulative mortality. (B) Principal component analysis (PCA) of expression genes in brain and liver at different temperatures. Coordinates are the first 3 principal components PC1, PC2, and PC3 of PCA, and the scale value represents the contribution of the sample to the principal component.
Figure 5:
Figure 5:
Number of DEGs in brain and liver of C. argus (A) and C. maculata (B) during cooling. The abscissa represents temperature and the ordinate represents the number of genes. Red indicates up-regulated genes and blue indicates down-regulated genes. FC: fold change.
Figure 6:
Figure 6:
GO and KEGG enrichment analysis of DEGs. The genes with noticeable differences between C. argus and C. maculata were selected for display. (A) Enrichment results for C. argus (green for brain, red for liver). The area of the circle indicates the number of genes. (B) Enrichment results for C. maculata. (C) The expression of 3 transcription factor genes in C. argus and C. maculata. The abscissa represents the tissue samples at different temperatures, and the ordinate represents the expression quantity. The asterisk indicates a significant difference (P < 0.01).
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