Limits...
Global transcriptional and miRNA insights into bases of heterosis in hybridization of Cyprinidae.

Zhou Y, Ren L, Xiao J, Zhong H, Wang J, Hu J, Yu F, Tao M, Zhang C, Liu Y, Liu S - Sci Rep (2015)

Bottom Line: Interestingly, the ELD pattern could inherit from F1 to F2, which guaranteed a stable appearance in progenies.The ELD-B genes were found to contribute to cell development, while the ELD-T genes were enriched in function of stress and adaptability. microRNAs (miRNA) also had similar expression patterns to genes.A high proportion of miRNAs showed nonadditive expression upon hybridization, and were found to target important genes with diverse roles potentially involved in stress adaption and development.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China.

ABSTRACT
Hybrid Megalobrama amblycephala × Culter alburnus represents a population newly formed by interspecific crossing between two different genera. Here we assessed the expression pattern of mRNA and small RNA in newly formed F1, F2 and their progenitors. Large amounts of nonadditively expressed protein-coding genes showed parental expression level dominance (ELD). Interestingly, the ELD pattern could inherit from F1 to F2, which guaranteed a stable appearance in progenies. The ELD-B genes were found to contribute to cell development, while the ELD-T genes were enriched in function of stress and adaptability. microRNAs (miRNA) also had similar expression patterns to genes. A high proportion of miRNAs showed nonadditive expression upon hybridization, and were found to target important genes with diverse roles potentially involved in stress adaption and development. Taken together, the gene and miRNA expression divergence contributes to heterosis in the newly formed hybrid, promising the successful existence of hybrid speciation.

No MeSH data available.


Global characterization of specific gene expression among M. amblycephala, C. alburnus, F1 and F2. BB, M. amblycephala, TT, C. alburnus. (A) Venn diagram analyses of specific genes in M. amblycephala, C. alburnus, F1 and F2. (B,C) Functional categories of specific genes in F1 (B) and F2 (C) except the 5566 co-expressed genes in all the samples. *P < 0.05 and **P < 0.01 to indicate the significant difference. Observed, indicated percentage of genes in the present study; Expected, indicated percentage of genes in the same category in GO enrichment analysis program.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4561955&req=5

f2: Global characterization of specific gene expression among M. amblycephala, C. alburnus, F1 and F2. BB, M. amblycephala, TT, C. alburnus. (A) Venn diagram analyses of specific genes in M. amblycephala, C. alburnus, F1 and F2. (B,C) Functional categories of specific genes in F1 (B) and F2 (C) except the 5566 co-expressed genes in all the samples. *P < 0.05 and **P < 0.01 to indicate the significant difference. Observed, indicated percentage of genes in the present study; Expected, indicated percentage of genes in the same category in GO enrichment analysis program.

Mentions: Then, we BLAST the annotated genes of F1 and F2 against the unigenes of B and T reciprocally (Supplementary Fig. 1). We defined the genes except the 5566 co-expressed genes across all the samples as specific genes for each species (Fig. 2A). To compare expression quantities, the numbers of reads were normalized to relative abundance measured using fragments per transcript kilobase per million fragments mapped (FPKM)20. We also used Gene Ontology (GO) functional categories to identify gene function. The specific genes were identified by pairwise comparison among the species. In both F1 and F2, the specific genes (2593 in F1 and 3170 in F2) were significantly enriched for methylation, cell cycle, stress responses, and DNA and RNA modification (Fig. 2B,C). The specific genes in the two progenitors (1042 in BB and 1868 in TT) were significantly enriched for activities involving cellular macromolecules, oxidation-reduction, and activation of nucleic acids and proteins (Supplementary Fig. 2).


Global transcriptional and miRNA insights into bases of heterosis in hybridization of Cyprinidae.

Zhou Y, Ren L, Xiao J, Zhong H, Wang J, Hu J, Yu F, Tao M, Zhang C, Liu Y, Liu S - Sci Rep (2015)

Global characterization of specific gene expression among M. amblycephala, C. alburnus, F1 and F2. BB, M. amblycephala, TT, C. alburnus. (A) Venn diagram analyses of specific genes in M. amblycephala, C. alburnus, F1 and F2. (B,C) Functional categories of specific genes in F1 (B) and F2 (C) except the 5566 co-expressed genes in all the samples. *P < 0.05 and **P < 0.01 to indicate the significant difference. Observed, indicated percentage of genes in the present study; Expected, indicated percentage of genes in the same category in GO enrichment analysis program.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4561955&req=5

f2: Global characterization of specific gene expression among M. amblycephala, C. alburnus, F1 and F2. BB, M. amblycephala, TT, C. alburnus. (A) Venn diagram analyses of specific genes in M. amblycephala, C. alburnus, F1 and F2. (B,C) Functional categories of specific genes in F1 (B) and F2 (C) except the 5566 co-expressed genes in all the samples. *P < 0.05 and **P < 0.01 to indicate the significant difference. Observed, indicated percentage of genes in the present study; Expected, indicated percentage of genes in the same category in GO enrichment analysis program.
Mentions: Then, we BLAST the annotated genes of F1 and F2 against the unigenes of B and T reciprocally (Supplementary Fig. 1). We defined the genes except the 5566 co-expressed genes across all the samples as specific genes for each species (Fig. 2A). To compare expression quantities, the numbers of reads were normalized to relative abundance measured using fragments per transcript kilobase per million fragments mapped (FPKM)20. We also used Gene Ontology (GO) functional categories to identify gene function. The specific genes were identified by pairwise comparison among the species. In both F1 and F2, the specific genes (2593 in F1 and 3170 in F2) were significantly enriched for methylation, cell cycle, stress responses, and DNA and RNA modification (Fig. 2B,C). The specific genes in the two progenitors (1042 in BB and 1868 in TT) were significantly enriched for activities involving cellular macromolecules, oxidation-reduction, and activation of nucleic acids and proteins (Supplementary Fig. 2).

Bottom Line: Interestingly, the ELD pattern could inherit from F1 to F2, which guaranteed a stable appearance in progenies.The ELD-B genes were found to contribute to cell development, while the ELD-T genes were enriched in function of stress and adaptability. microRNAs (miRNA) also had similar expression patterns to genes.A high proportion of miRNAs showed nonadditive expression upon hybridization, and were found to target important genes with diverse roles potentially involved in stress adaption and development.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China.

ABSTRACT
Hybrid Megalobrama amblycephala × Culter alburnus represents a population newly formed by interspecific crossing between two different genera. Here we assessed the expression pattern of mRNA and small RNA in newly formed F1, F2 and their progenitors. Large amounts of nonadditively expressed protein-coding genes showed parental expression level dominance (ELD). Interestingly, the ELD pattern could inherit from F1 to F2, which guaranteed a stable appearance in progenies. The ELD-B genes were found to contribute to cell development, while the ELD-T genes were enriched in function of stress and adaptability. microRNAs (miRNA) also had similar expression patterns to genes. A high proportion of miRNAs showed nonadditive expression upon hybridization, and were found to target important genes with diverse roles potentially involved in stress adaption and development. Taken together, the gene and miRNA expression divergence contributes to heterosis in the newly formed hybrid, promising the successful existence of hybrid speciation.

No MeSH data available.