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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.


Heritable parental ELD genes in hybrids.(A) Venn diagram of ELD-B genes among F1 and F2. (B) Venn diagram of ELD-T genes among F1 and F2. (C) Enriched GO terms of heritable parental ELD genes in hybrids.
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f5: Heritable parental ELD genes in hybrids.(A) Venn diagram of ELD-B genes among F1 and F2. (B) Venn diagram of ELD-T genes among F1 and F2. (C) Enriched GO terms of heritable parental ELD genes in hybrids.

Mentions: Meanwhile, the patterns of 79 ELD-B and 118 ELD-T genes were heritable across F1 to F2 (Fig. 5A,B). Subsequently, we assigned the heritable parental ELD genes into GO terms. Ten GO categories were found significant difference in these genes, including DNA binding, hydrolase activity, integral to membrane, membrane, metal ion binding, nucleus, protein binding, regulation of transcription DNA-dependent, transferase activity and zinc ion binding (Fig. 5C). The ELD-B set contained more genes for DNA binding, metal ion binding, nucleus and regulation of transcription DNA-dependent than the ELD-T genes. Interestingly, in the regulation of transcription DNA-dependent category, several genes involved in cell development were found, including cyclin D1, TNF receptor-associated factor 6 (TRAF6), signal transducer and activator of transcription 6 (STAT6), and period homolog 1a (per1a), suggesting the ELD-B genes may be mainly involved in the development of hybrids (Fig. 5C; Supplementary Dataset 2). By contrast, the other 6 categories, including hydrolase activity, integral to membrane, membrane, protein binding, transferase activity and zinc ion binding were more represented by ELD-T genes compared with their ELD-B counterparts (Fig. 5C; Supplementary Dataset 2). The zinc ion binding category, which is associated with disease and stress resistance, included zinc finger, DHHC domain containing 16a, tripartite motif containing 35–28 (trim 35–28), tumor necrosis factor, alpha-induced protein 3 (TNFAIP3), ring-box 1 (RBX1), E3 ubiquitin protein ligase, bloodthirsty-related gene family, member 32, DNL-type zinc finger, CREB binding protein and zinc finger, DHHC-type containing 18a. In addition, ELD-T genes also included some oxidation-reduction genes, such as WW domain containing oxidoreductase, Parkinson disease (autosomal recessive, juvenile) 2, parkin, oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) and cholesterol 25-hydroxylase (Supplementary Dataset 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)

Heritable parental ELD genes in hybrids.(A) Venn diagram of ELD-B genes among F1 and F2. (B) Venn diagram of ELD-T genes among F1 and F2. (C) Enriched GO terms of heritable parental ELD genes in hybrids.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Heritable parental ELD genes in hybrids.(A) Venn diagram of ELD-B genes among F1 and F2. (B) Venn diagram of ELD-T genes among F1 and F2. (C) Enriched GO terms of heritable parental ELD genes in hybrids.
Mentions: Meanwhile, the patterns of 79 ELD-B and 118 ELD-T genes were heritable across F1 to F2 (Fig. 5A,B). Subsequently, we assigned the heritable parental ELD genes into GO terms. Ten GO categories were found significant difference in these genes, including DNA binding, hydrolase activity, integral to membrane, membrane, metal ion binding, nucleus, protein binding, regulation of transcription DNA-dependent, transferase activity and zinc ion binding (Fig. 5C). The ELD-B set contained more genes for DNA binding, metal ion binding, nucleus and regulation of transcription DNA-dependent than the ELD-T genes. Interestingly, in the regulation of transcription DNA-dependent category, several genes involved in cell development were found, including cyclin D1, TNF receptor-associated factor 6 (TRAF6), signal transducer and activator of transcription 6 (STAT6), and period homolog 1a (per1a), suggesting the ELD-B genes may be mainly involved in the development of hybrids (Fig. 5C; Supplementary Dataset 2). By contrast, the other 6 categories, including hydrolase activity, integral to membrane, membrane, protein binding, transferase activity and zinc ion binding were more represented by ELD-T genes compared with their ELD-B counterparts (Fig. 5C; Supplementary Dataset 2). The zinc ion binding category, which is associated with disease and stress resistance, included zinc finger, DHHC domain containing 16a, tripartite motif containing 35–28 (trim 35–28), tumor necrosis factor, alpha-induced protein 3 (TNFAIP3), ring-box 1 (RBX1), E3 ubiquitin protein ligase, bloodthirsty-related gene family, member 32, DNL-type zinc finger, CREB binding protein and zinc finger, DHHC-type containing 18a. In addition, ELD-T genes also included some oxidation-reduction genes, such as WW domain containing oxidoreductase, Parkinson disease (autosomal recessive, juvenile) 2, parkin, oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) and cholesterol 25-hydroxylase (Supplementary Dataset 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.