Additional file 1 of Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish
Creators: name: Ren, Li
name: Zhang, Hong
name: Luo, Mengxue
name: Gao, Xin
name: Cui, Jialin
name: Zhang, Xueyin
name: Liu, Shaojun
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1. DNA methylation level of regions of TEs. A.TE distributions in each orthologous chromosomes of genomes R (2nRR) and C (2nCC). TE distributions were identified using 0.1 Mb sliding windows. B.The total methylation ratio (the combination of two homoeologs) in the two triploids and their inbred parents.C.The methylation ratio of homoeologs R vs.C in the two triploids and the total expressions in the two parents. Fig. S2. The cluster of DNA methylation of gene element among the two triploids and their inbred parents. DNA methylation in subgenomes R and C of the triploids. Black boxes indicate the DMRs, in which the similar trends of DNA methylation were in subgenomes/genomes R and C, respectively. Green box indicates the other DMRs in among these fishes. “Up in 2 k” represents 2 kb upstream of transcription start site. “Down in 2 k” represents 2 kb downstream of transcription termination site. “First exon” and “First intron” represent the first exon and intron in gene body, respectively. “Inner exon” represents all exons, except first and last exons. “Inner intron” represents all introns, except first intron. “Last exon” represents last exon in gene body. Each region was divided into twenty bins based on length. Fig. S3. GO annotation (Biological Process in level 3) of gene regulated by DNA methylation. Fig. S4. Correlation analyses between the values of differential expression (DE) and values of differential methylation (DM). A.Negative correlation between values of DE and DM (24 genes) in group of 3nR2C vs.2nCC.B.Negative correlation between values of DE and DM (5 genes) in group of 3nRC2vs.2nCC. C.Negative correlation between values of DE and DM (15 genes) in group of 3nR2C vs.2nRCC. D.Negative correlation between values of DE and DM (183 genes) in group of 3nRC2vs.2nRR. Red dot indicates the negative correlation between values of DE and DM. black dot indicates the positive correlation between values of DE and DM. Fig. S5. Differential expression (DE) analysis of miRNAs among the two triploids and their inbred parents. A.The number represents the number of up-regulated genes in the sample of the corresponding comparison. For example, the number “18” reflects that the 18 genes were higher expression in 2nRRthan in 3nRC2. B.The distribution of DE miRNAs in the five comparisons (3nR2Cvs.3nRC2, 3nR2Cvs. 2nRR, 3nRC2 vs.2nRR, 3nR2Cvs. 2nCC and 3nRC2 vs.2nCC). Fig. S6. GO annotation (Biological Process in level 3) in homoeologous recombinant genes (HRGs). Fig. S7. The distribution ofthe six DMGs in pathway of growth hormone synthesis, secretion and action (map04935). Red presents the hyper-DMGs. Green presents the HRGs in hypo-DMGs, while pink presents the other hypo-DMGs. PRKCA(K02677): classical protein kinase C alpha type; ATF4(K04374): cyclic AMP-dependent transcription factor ATF-4; CACNA1F(K04853): voltage-dependent calcium channel L type alpha-1F; PLCB(K05858): phosphatidylinositol phospholipase C, beta; CREB1(K05870): cyclic AMP-responsive element-binding protein 1; STAT5A(K11223): signal transducer and activator of transcription 5A. Fig. S8. The distribution of the nine DMGs in pathway of insulin secretion (map04911).Green presents the HRGs in hypo-DMGs, while pink presents the other hypo-DMGs. ATP1B(K01540): sodium/potassium-transporting ATPase subunit beta; PRKCA(K02677): classical protein kinase C alpha type; ATF4(K04374): cyclic AMP-dependent transcription factor ATF-4; STX1A(K04560): syntaxin 1A; CACNA1F(K04853): voltage-dependent calcium channel L type alpha-1F; KCNN2(K04943): potassium intermediate/small conductance calcium-activated channel subfamily N member 2; PLCB(K05858): phosphatidylinositol phospholipase C, beta; CREB1(K05870): cyclic AMP-responsive element-binding protein 1; SNAP25(K18211): synaptosomal-associated protein 25. Table S1. The mapping information of Methyl-seq data. Table S2. Summary of methylated and unmethylated cytosines. Table S3. The TE distribution of C. auratus red var. and C. carpio haematopterus. Table S4. The distribution of methylated and unmethylated cytosines (CpG) in the two triploids and their inbred parents. Table S5. The summary of miRNA-seq data. Table S6. The pathway distributions of hyper-DMGs and hypo-DMGs (more than 5 in each pathway).