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Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus).
Han L
,
Sun Y
,
Cao Y
,
Gao P
,
Quan Z
,
Chang Y
,
Ding J
.
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Breeding of polyploid aquatic animals is still an important approach and research hotspot for realizing the economic benefits afforded by the improvement of aquatic animal germplasm. To better understand the molecular mechanisms of the growth of triploid sea cucumbers, we performed gene expression and genome-wide comparisons of DNA methylation using the body wall tissue of triploid sea cucumbers using RNA-seq and MethylRAD-seq technologies. We clarified the expression pattern of triploid sea cucumbers and found no dosage effect. DEGs were significantly enriched in the pathways of nucleic acid and protein synthesis, cell growth, cell division, and other pathways. Moreover, we characterized the methylation pattern changes and found 615 differentially methylated genes at CCGG sites and 447 differentially methylated genes at CCWGG sites. Integrative analysis identified 23 genes (such as Guf1, SGT, Col5a1, HAL, HPS1, etc.) that exhibited correlations between promoter methylation and expression. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions in the growth of triploid sea cucumbers. Our data provide new insights into the epigenetic and transcriptomic alterations of the body wall tissue of triploid sea cucumbers and preliminarily elucidate the molecular mechanism of their growth, which is of great significance for the breeding of fine varieties of sea cucumbers.
Figure 1. Ploidy test results of diploid sea cucumbers (A) and triploid sea cucumbers (B).
Figure 2. Distribution of FPKM expression. The horizontal axis represents the sample name, the vertical axis represents the number of protein-coding genes, and different colors represent different ranges of FPKM.
Figure 3. GO enrichment analysis of the top 30 differentially expressed genes. The X-axis is the GO entry name and the Y-axis is -log10 p-value (A: down-regulated DEGs; B: up-regulated DEGs).
Figure 4. Top 20 differentially expressed genes in the KEGG enrichment analysis. The X-axis is the enrichment score. The larger the bubble, the more differential protein-encoding genes contained in the item. The color of bubbles changes from purple to blue to green to red, with the smaller p-value corresponding to greater significance.
Figure 5. Pie charts of the distribution of the differentially methylated sites on different functional components (A: CCGG sites; B: CCWGG sites).
Figure 6. GO functional classification histograms of differentially methylated genes, the X-axis is the GO entry name and the Y-axis is -log10 p-value. (A: CCGG sites; B: CCWGG sites).
Figure 7. Bubble map of KEGG top 20 differentially methylated genes in CCGG sites (A) and CCWGG sites (B).
Figure 8. Differentially expressed genes and differential methylation quadrants (A: CCGG site; B: CCWGG site). Red indicates the locus of negatively correlated differentially expressed genes, and blue indicates the locus of positively correlated differentially expressed genes.
Figure 9. Comparison of mRNA expression levels among the 10 DEGs obtained using qRT-PCR validation and RNA-seq. Log2 Fold Change are expressed as the ratio of gene expression after normalization to Cytb.
Anders,
HTSeq--a Python framework to work with high-throughput sequencing data.
2015, Pubmed
Anders,
HTSeq--a Python framework to work with high-throughput sequencing data.
2015,
Pubmed
Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014,
Pubmed
Chatchaiphan,
De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864).
2017,
Pubmed
Cheng,
Fibronectin enhances healing of excised wounds in rats.
1988,
Pubmed
Cingolani,
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
2012,
Pubmed
Covelo-Soto,
Genome-wide methylation study of diploid and triploid brown trout (Salmo trutta L.).
2015,
Pubmed
Dell'Angelica,
Molecular characterization of the protein encoded by the Hermansky-Pudlak syndrome type 1 gene.
2000,
Pubmed
Du,
Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
2012,
Pubmed
,
Echinobase
Eivers,
Insulin-like growth factor (IGF) signalling is required for early dorso-anterior development of the zebrafish embryo.
2004,
Pubmed
Esclatine,
Macroautophagy signaling and regulation.
2009,
Pubmed
Flanagan,
An epigenetic role for noncoding RNAs and intragenic DNA methylation.
2007,
Pubmed
Florea,
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.
2013,
Pubmed
García-Arrarás,
Cellular mechanisms of intestine regeneration in the sea cucumber, Holothuria glaberrima Selenka (Holothuroidea:Echinodermata).
1998,
Pubmed
,
Echinobase
Gavery,
DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas).
2010,
Pubmed
Haltaufderhyde,
Data set for the genome-wide transcriptome analysis of human epidermal melanocytes.
2014,
Pubmed
Herman,
Promoter-region hypermethylation and gene silencing in human cancer.
2000,
Pubmed
Holliday,
Evidence for gene silencing by endogenous DNA methylation.
1998,
Pubmed
Jiang,
Inheritance and Variation of Genomic DNA Methylation in Diploid and Triploid Pacific Oyster (Crassostrea gigas).
2016,
Pubmed
Jo,
Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants.
2017,
Pubmed
,
Echinobase
Kammel,
Early hypermethylation of hepatic Igfbp2 results in its reduced expression preceding fatty liver in mice.
2016,
Pubmed
Kanehisa,
KEGG for linking genomes to life and the environment.
2008,
Pubmed
Kang,
Development of Genetic Markers for Triploid Verification of the Pacific Oyster, Crassostrea gigas.
2013,
Pubmed
Keshet,
Effect of regional DNA methylation on gene expression.
1985,
Pubmed
Kim,
HISAT: a fast spliced aligner with low memory requirements.
2015,
Pubmed
Li,
Phosphorylation of MCM3 protein by cyclin E/cyclin-dependent kinase 2 (Cdk2) regulates its function in cell cycle.
2011,
Pubmed
Li,
The Sequence Alignment/Map format and SAMtools.
2009,
Pubmed
Li,
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.
2011,
Pubmed
Marandel,
Remodelling of the hepatic epigenetic landscape of glucose-intolerant rainbow trout (Oncorhynchus mykiss) by nutritional status and dietary carbohydrates.
2016,
Pubmed
Matos,
Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish.
2016,
Pubmed
Olson,
Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes.
2014,
Pubmed
Osborn,
Understanding mechanisms of novel gene expression in polyploids.
2003,
Pubmed
Palacios,
Interplay between DNA methylation and transcription factor availability: implications for developmental activation of the mouse Myogenin gene.
2010,
Pubmed
Pinheiro,
Demethylation of the coding region triggers the activation of the human testis-specific PDHA2 gene in somatic tissues.
2012,
Pubmed
Roberts,
Improving RNA-Seq expression estimates by correcting for fragment bias.
2011,
Pubmed
Sarda,
The evolution of invertebrate gene body methylation.
2012,
Pubmed
Seetharam,
A unique signal transduction from FLT tyrosine kinase, a receptor for vascular endothelial growth factor VEGF.
1995,
Pubmed
Severino,
MicroRNA expression profile in head and neck cancer: HOX-cluster embedded microRNA-196a and microRNA-10b dysregulation implicated in cell proliferation.
2013,
Pubmed
Sheu,
The Dbf4-Cdc7 kinase promotes S phase by alleviating an inhibitory activity in Mcm4.
2010,
Pubmed
Stingele,
Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells.
2012,
Pubmed
Sun,
Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus.
2011,
Pubmed
,
Echinobase
Tang,
Gene copy-number alterations: a cost-benefit analysis.
2013,
Pubmed
Trapnell,
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
2010,
Pubmed
Wang,
MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes.
2015,
Pubmed
Yi,
[High glucose induce the demethylation of CTGF promoter and gene expression].
2011,
Pubmed
Yin,
DNA repair gene O6-methylguanine-DNA methyltransferase: promoter hypermethylation associated with decreased expression and G:C to A:T mutations of p53 in brain tumors.
2003,
Pubmed
Yoder,
Cytosine methylation and the ecology of intragenomic parasites.
1997,
Pubmed
Zhao,
RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.
2014,
Pubmed
,
Echinobase
Zhou,
Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.
2016,
Pubmed
,
Echinobase
