Comparative transcriptome analysis of albino northern snakehead (Channa argus) reveals its various collagen-related DEGs in caudal fin cells

Abstract

The albino northern snakehead (Channa argus) is an aquaculture species characterized by heritable albino body color, in contrast to the typical coloration. Additionally, there are gray- and golden-finned individuals, which exhibit distinct coloration in their caudal fins. We performed RNA-seq to profile the transcriptome of caudal fin tissues in albino gray-finned and golden-finned C. argus, contrasting these with normal morphs to elucidate the differences between the two groups. A total of 137,130 unigenes were identified in this study. Gene Ontology (GO) analysis showed that the identified DEGs were significantly enriched in cellular components related to cytoplasm. So far, 379 common DEGs have been identified in all three groups. Notably, we observed more DEGs in golden-finned individuals compared to gray-finned individuals. We also revealed that golden-finned individuals were enriched in collagen-related pathways compared with normal individuals. The enriched DEGs of collagen components include collagen I of COL1A1 and COL1A2, collagen II of COL2A1, collagen V of COL5A1 and COL5A2, collagen VI of COL6A1 and COL6A3, collagen IX of COL9A3, collagen X of COL10A1, collagen XI of COL11A2, collagen XII of COL12A1, collagen XVI of COL16A1, collagen XVIII of COL18A1 and decorin (DCN), all of which play a role in modulating the collagen matrix. In golden-finned albino fish, collagen-related genes were downregulated, suggesting that despite the abundance of collagen types in their caudal fin cells, gene expression was slightly limited. This work provides valuable genetic insights into collagen variation in albino C. argus, lays the foundation for research on collagen genes and is crucial for the development and utilization of fish-derived collagen as a biomaterial for tissue engineering and biomedical applications.

Fig 1. Chana argus was used in this study.

Three distinct color morphs of C. argus were identified: Group H included three gray-finned albinos, Group J included three golden-finned albinos, and Group W included three black-whites.

Fig 2

A. Venn diagram based on 5 databases: NR, NT, SwissProt, KOG and UniProt; numbers in the overlapping regions refer to those unigenes that were expressed in more than one database, and 68700 shared unigenes matched with all five databases; B. Correlations of the samples between the H (H1, H2, H3), J (J1, J2, J3) and W (W1, W2, W3) groups. The change in the correlation coefficient is indicated by the change in color from blue (1.0) to red (-1.0), and a deeper color indicates a higher correlation between samples.

Fig 3. Genes were classified according to three major GO categories: Biological process (BP), cellular component (CC), and molecular function (MF).

The y-axis indicates the number of genes in each category.

Fig 4. Heatmap of differentially expressed gene clustering.

The colors can only be compared horizontally with the same clustering of genes for expression values (TPM) in the high (blue) and low (yellow) colors. Axes: Bottom, variable groups; top, hierarchical clusters for closeness between groups; left, hierarchical clustering among the expressed genes.

Fig 5. Differential genetic Venn diagram of groups J and H compared with group W and GO enrichment histogram of differentially expressed genes.

A. Venn diagram between group J vs. group W and group H vs. group W. The number of genes expressed uniquely within each group is shown and overlapping regions indicate the number of genes expressed in both groups. B. Comparison of GO enrichment analysis for up-and down-regulated genes between groups H and W. C. Comparison of GO enrichment analysis for up- and downregulated genes between groups J and W. X-axis: number of genes; Y-axis: GO categories.

Fig 6. Bubble diagram of the GO enrichment analysis results for group J compared with those for group W.

The 20 most significantly enriched GO pathway entries are presented in this figure. The value of p-adjust ranges from 0 to 1, and the closer it is to zero, the more significant the enrichment. GeneRatio is the ratio of the number of differentially expressed genes in pathway entry to the total number of genes involved in pathway entry for all annotated genes.

Fig 7. Directed acyclic graph (DAG) of topGO in group J compared to group W for classification of CCs (cell components).

The branches represent inclusion relationships and the functional descriptions defined from top to bottom become increasingly specific. Each node represents a GO term. The specific DEGs involved in enrichment are shown alongside functional descriptions. The most important terms are represented by red nodes, whereas the less significant terms are represented by elliptical nodes. Colors represent the degree of enrichment, with darker colors representing higher enrichment.

Fig 8. Downregulation of collagen genes in golden-finned C argus.

Axis: x-axis, gene expression level based on log2-fold change value; y-axis, gene names.

Fig 9

(A-M). Phylogenetic studies of collagen-related genes. These correspond to A. COL1A1, B. COL1A2, C. COL2A1, D. COL5A1, E. COL5A2, F. COL6A1, G. COL6A3, H. COL9A3, I. COL10A1, J. COL11A1, K. COL11A2, L. COL16A1 and M. COL18A1.