Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)

- Dynamic transcriptome sequencing and analysis during early development in the bighead carp ( Hypophthalmichthys nobilis.
- Background: Early development is a key process of the life history of fish.
- However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hypophthalmichthys nobilis).
- In the present study, we performed transcriptome analysis of six development stages in H.
- In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during H.
- Unfortunately, a serious de- cline in the fishery resources of this species has been ob- served in its natural distribution waters in the past few decades, mainly caused by habitat loss or shrinkage, water pollution, and long-time overfishing [3].
- Full list of author information is available at the end of the article.
- proportion of farms, which caused degradation of seed quality, including a decline in growth performance and abnormally high mortality in the embryogenesis period..
- Significant effort has been made in the gen- etic improvement of H.
- Early development is a key process of the life history of fish related to embryogenesis, larval development and growth, and is likely to determine the early survival rate associated with physiological and environmental changes..
- Many studies have in- vestigated gene expression in the early development of teleost species, related to the basal processes and mecha- nisms of embryogenesis and larval development [13–18]..
- nobilis have been well described by line drawings based on live individuals [19], and the devel- opmental rate and behavior of the early life stages in H..
- The decline in the wild resources of H.
- nobi- lis have so far focused on the juvenile or sub adult stages [11, 12], and no data is currently available on the tran- scriptomic changes in the early development of H.
- nobilis, the present study performed a transcriptomic analysis in the early life stages of this species.
- The results of the present study should lead to a deeper understanding of the biological processes and mechanisms of the dynamic changes dur- ing the early development of H.
- Overview of the RNA-Seq data.
- Ultimately, more of the.
- The statistic of the annotation results for the databases are shown in Fig.
- The majority of the unigenes (41,655.
- The outcome of the homology search of unigenes in the NR databases showed that all of the top ten matching spe- cies were teleosts (Additional file 5: Figure S3a).
- The majority of the unigenes were matched to the class of “function un- known” in the eggNOG database (Additional file 5: Figure S3e).
- Correlation and principal component analysis of the samples.
- To evaluate the consistency of the sample collection and investigate the transcriptomic relationship among the.
- Both ana- lyses could provide an overview of the reliability of the experimental results and the rationality of sampling.
- The Pearson correlation coefficient between the five bio- logical replicates of the six groups in this study had very high repeatability, i.e., all R >.
- The statistical information and Venn diagram of the pairwise comparative DETs are shown in Fig.
- Bar chart (b) and Venn diagram (c) of the annotation statistics for unigenes mapped to public databases.
- the number of down-regulated transcripts for each com- parison, especially in the earlier stages..
- Based on the GO (BP) terms enriched, we constructed a rough transcrip- tomic dynamic map for the early developmental period in the H.
- In view of the largest difference detected be- tween DS2 and DS1, the top specific GO (BP) and KEGG pathway enrichments in DS2 vs.
- We noticed that several biological processes (egg coat formation, gene silencing by RNA, miRNA mediated inhibition of translation, and piRNA metabolic process, etc.) and metabolic pathways (estrogen signaling pathway, progesterone-mediated oocyte maturation, and prolactin signaling pathway) might be related to maternal mRNA expression and degradation in the down-regulated DETs in the pairwise comparison.
- “ribosome”, and “oxidative phosphorylation” pathways were enriched in the up-regulated terms.
- and “progester- one-mediated oocyte maturation” pathways was enriched in the down-regulated terms, as shown in Fig.
- 0.05) based on the mean FPKM values of the unigenes in each stage (Fig.
- We noticed that profile_48 might be related to hatching in the early development of H.
- There was no available PPI information related to HCE in the STRING database.
- Figure S4), which confirmed the high reliability of the RNA-seq data obtained in the present study..
- In terms of the long unigene count (>.
- biology process) (a) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway (b, and c for down- and up-regulated, respectively) enrichments for the differentially expressed transcripts (DETs) detected in the DS2 vs.
- The unigene count detected in this study fell in the range of counts reported in two previous studies [11, 12].
- Hom- ology searching using the NR databases showed that all of the top ten matching species were teleosts (Additional file 5: Figure S3a).
- The qPCR results validated the high reliability of the transcriptome data and the DETs ana- lyses (Additional file 9: Figure S4).
- In the present study, the gene expression pattern iden- tification and comparative transcriptome analyses were carried out for early development stages in H.
- The correlation and PCA results for the samples demon- strated high homogeneity among the samples from the same stage, especially in the early embryo stages (Fig.
- For each pairwise comparison, the enriched biological process and pathway terms of down- and up-regulated conditions indicated the change trends in the given pe- riods, and some biological processes related to ontogen- esis, organogenesis, morphological change, and immune and nervous system development were regulated.
- As reported in the studies of zebrafish embryogenesis, MZT mostly occurs from the blastula to gastrula stages [13, 16].
- There- fore, the specific and highly expressed unigenes detected in the DS1 stage, could be regarded as maternal tran- scripts in H.
- The biological processes in the early stages of vertebrate development rely exclusively on ma- ternal transcripts (maternal mRNAs and ma- ternal mRNAs are also responsible for the zygote genome activation (ZGA) during the MZT [25].
- A pro- portion of the maternal mRNAs are essential for normal embryogenesis and development in fish.
- For the down-regulated DETs in the DS2 vs.
- nobilis, e.g., the biological processes of “gene silencing by RNA”, “miRNA mediated inhibition of translation”,.
- The onset of the ZGA is tightly coordinated with maternal transcripts degradation in zebrafish [16]..
- “translation” biology process and “ribosome” pathway are enriched for up-regulated DETs in the period from DS1 to DS2, and are probably related with ZGA of early development in H.
- A similar overrepresentation of the ribosomal pathway was found previously in zebra- fish [16].
- Those genes mapped in the PPI networks in this study, that were enriched with “cell cycle”, “oocyte meiosis”, and “progesterone-mediated oocyte maturation” path- ways might be related to reproductive potential in H..
- The PPIs among ribosomal proteins (RPs) de- tected in the present study (enriched in the “ribosome”.
- The eukaryotic translation initiation factor 3 complex (eIF3, enriched in the “RNA transport”.
- The mitochondrial ribosome proteins (MRPs, enriched in the “ribosome” pathway) are essential for mitochondrial ribosome assembly, and offer translation sites for mitochondrial DNA genes.
- Furthermore, the in- tegrated process of oxidative phosphorylation for ATP production (enriched in the “oxidative phosphorylation”.
- pathway) is executed in the mitochondria, which meets most of the energy requirements for cell growth, differ- entiation, and development.
- “proteasome” pathway in the PPI networks, which also reported play important roles to modulate ZGA and ma- ternal mRNA degradation in embryogenesis and devel- opment [43]..
- In the present study, the largest enriched pathway was “protein pro- cessing in endoplasmic reticulum (ER)” (Fig.
- patterns of unigenes coincided closely with that of hce1 in profile_48, which showed high expression in the hatching stages (Fig.
- Among those genes detected in the co-expression ana- lysis (Fig.
- Another subunit of the TRAP complex (TRAPβ) in zebrafish embryogenesis was reported to show enhanced expression in hatching gland precursors [48].
- Moreover, a unigene (CL37Contig19) annotated as encoding an LCE, was not clustered into profile_48, and showed low expression in the analyzed samples.
- The present report is the first to describe combined transcriptome profiling of the early developmental stages in H.
- All sequencing reads were exported in the FASTQ format.
- The se- quence data were deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers SRP143548..
- The statistics for FPKM value of unigenes, hier- archical clustering (Pearson correlation), and PCA (Prin- cipal component analysis) for the 30 samples used in the.
- present study were performed using stats, reshape2, dplyr, and ggplot2 packages in the R program (http://.
- The Venn diagram was depicted using the VennDiagram package in the R program..
- to classify the differentially expressed genes in different clusters based on the FPKM change tendency of the genes in the six development stages, set with default pa- rameters.
- A heatmap of genes expression was con- structed using the pheatmap package in the R program..
- Gene co-expression network analysis was performed to track the interactions among the DETs in specific profile, according to their dynamic expression changes in the six developmental stages.
- A Pearson correlation matrix among genes was calculated using the stats pack- age in the R programs, and the significantly correlated pairs (R >.
- The Shapiro-Wilk normality test and Levene’s test for homogeneity of variances was carried out using the stats and car packages in the R program, respectively.
- DS3) were performed using the stats package in the R program.
- The Pearson correlations were calculated using the stats package in the R program..
- SSRs in the transcriptome were identified using MISA (http://pgrc.ipk-gatersleben.de/misa.
- The length distribution of unigenes assembled in the early developmental stages of H.
- The statistic of simple sequence repeat (SSR) loci detected in the unigenes from transcriptome sequencing..
- The funding bodies had no role in the experimental.
- The dataset supporting the conclusions of this article is available in the NCBI and Sequence Read Archive (SRA) repository, accession number SRP143548 (Release data https://www.ncbi.nlm.nih.gov/sra/SRP143548..
- Food and agriculture Organization of the United Nations, Rome 2017..
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