In silico analysis of Hsp70 genes in Ctenopharyngodon idella and their expression profiles in response to environmental stresses

Figures & data

Table 1. Summary of the CiHSP genes in grass carp genome.

Gene name	Chromosome segment	Locus	Exons	Length
CiHSP1a1	CI01000069	CI01000069:00000091–00001650	1	520
CiHSP1a2	CI01000035	CI01000035:00018796–00020662	2	523
CiHSP1b	CI01000052	CI01000052:01925657–01927599	1	646
CiHSP4a	CI01000040	CI01000040:01160713–01185710	23	930
CiHSP4b	CI01000000	CI01000000:17884239–17897080	19	841
CiHSP4l	CI01000315	CI01000315:00177207–00200023	19	829
CiHSP5	CI01000205	CI01000205:00910423–00913491	6	459
CiHSP8	CI01000352	CI01000352:00558495–00562831	7	585
CiHSP8a	CI01000304	CI01000304:14352375–14355516	8	649
CiHSP8b	CI01000053	CI01000053:00808245–00813766	7	528
CiHSP9	CI01000032	CI01000032:02253454–02272958	16	718
CiHSP12	CI01000312	CI01000312:00452710–00476302	14	796
CiHSP13	CI01000053	CI01000053:02891966–02895382	5	438
CiHSP14	CI01000066	CI01000066:01339972–01347463	14	504
CiHSPh1	CI01000095	CI01000095:00219520–00237347	18	838
CiHSPhyou1	CI01000304	CI01000304:14304022–14317252	23	1046

Figure 1. Phylogenetic analysis of the CiHSP genes in grass carp.

Note: Molecular phylogeny analysis of CiHSP genes was performed using MEGA11. Red circles represent subfamily HSP1; Light green squares represent subfamily HSP8; Blue triangles represent subfamily HSP5; Purple triangles represent subfamily HSP9; Pink diamonds represent subfamily HSP13; Brown green circles represent subfamily HSPh1; Yellow circles represent subfamily HSP4; Blackish green diamonds represent subfamily HSP14; Cyan hollow circles represent HSPhyou1; Deep blue hollow squares represent subfamily HSP12.

Figure 2. Distribution of conserved motifs in CiHSP genes.

Note: The conserved motifs in CiHSP genes were identified and characterized using MEME software. Each colored box represents the putative motifs detected in the protein sequence.

Figure 3. Chromosomal distribution and gene duplication analysis of the CiHSP genes in grass carp.

Note: All genes duplications were scanned and identified using MCSanX software, and they were displayed using CIRCOS software. All CiHSP genes were labeled with red short line, and genes with duplication event were linked with a black curve.

Figure 4. Gene regulatory network analysis of CiHSP genes in grass carp.

Note: Gene regulatory network of grass carp was reconstructed using zebrafish gene regulatory network (GRN) in STRING database. The pink nodes were CiHSP genes, and the light blue nodes were function genes interacting with CiHSP genes in grass carp.

Figure 5. GO analysis of gene regulatory networks of CiHSP genes in grass carp.

Note: GO enrichment analysis was performed using topGO package. Red dot, BP (biological process); green dot, MF (molecular function), and blue dot, CC (cellular component) represent three types of GO terms. The dot size represents the number of genes enriched in the GO term. The ordinate is the term of GO, and the abscissa is the p-value of topGO enrichment analysis, −log10 (p).

Figure 6. Expression profile of CiHSP genes in grass carp.

Note: The expression levels of CiHSP genes were downloaded from grass carp genome website and SRA database;, all expression data were clustered and plotted using the heatmap function in R platform. (A) Expression profile of CiHSP genes in six tissues; (B), expression profile of CiHSP genes response to high density stress; S group: Grass carp high-density culture (40 kg m⁻³); B group: normal culture (3 kg m⁻³); MUS represents muscle in S group, MUB represents muscle in B group; INS represents intestine in S group, INB represents intestine in B group; BRS represents brain in S group, BRB represents brain in B group; (C), expression profile of CiHSP genes response to high temperature stress; T18 represents lower temperature (18 °C) while T28 represents higher temperature (28 °C), R1-R3 represent replaces.

Data availability statement

All data that support the findings reported in this study are available from the corresponding author upon reasonable request.