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MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout (Oncorhynchus mykiss).

Ma H, Weber GM, Hostuttler MA, Wei H, Wang L, Yao J - BMC Genomics (2015)

Bottom Line: The objective of this study was to identify miRNAs that are associated with egg qualities in rainbow trout using post-ovulatory aged eggs.Four known miRNAs (omy-miR-193b-3p, omy-miR-203c-3p, omy-miR-499-5p and omy-miR-7550-3p) and two novel miRNAs (omy-miR-nov-95-5p and omy-miR-nov-112-5p) showed significantly higher expression in D1PO eggs relative to D14PO eggs as revealed by both deep sequencing and real time quantitative PCR analysis.Further characterization of the differentially expressed miRNAs and their target genes may provide valuable information on the role of these miRNAs in controlling egg quality, and ultimately lead to the development of biomarkers for prediction of egg quality in rainbow trout.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA. hao.ma@mail.wvu.edu.

ABSTRACT

Background: Egg quality is an important aspect in rainbow trout farming. Post-ovulatory aging is one of the most important factors affecting egg quality. MicroRNAs (miRNAs) are the major regulators in various biological processes and their expression profiles could serve as reliable biomarkers for various pathological and physiological conditions. The objective of this study was to identify miRNAs that are associated with egg qualities in rainbow trout using post-ovulatory aged eggs.

Results: Egg samples from females on day 1, day 7, and day 14 post-ovulation (D1PO, D7PO and D14PO), which had the fertilization rates of 91.8%, 73.4% and less than 50%, respectively, were collected and small RNAs isolated from these samples were subjected to deep sequencing using the Illumina platform. The massive sequencing produced 27,342,477, 26,910,438 and 29,185,371 reads from the libraries of D1PO, D7PO and D14PO eggs, respectively. A three-way comparison of the miRNAs indicated that the egg samples shared 392 known and 236 novel miRNAs, and a total of 414, 481, and 470 known and 243, 298, and 296 novel miRNAs were identified from D1PO, D7PO and D14PO eggs, respectively. Four known miRNAs (omy-miR-193b-3p, omy-miR-203c-3p, omy-miR-499-5p and omy-miR-7550-3p) and two novel miRNAs (omy-miR-nov-95-5p and omy-miR-nov-112-5p) showed significantly higher expression in D1PO eggs relative to D14PO eggs as revealed by both deep sequencing and real time quantitative PCR analysis. GO analysis of the predicted target genes of these differentially expressed miRNAs revealed significantly enriched GO terms that are related to stress response, cell death, DNA damage, ATP generation, signal transduction and transcription regulation.

Conclusions: Results indicate that post-ovulatory ageing affects miRNA expression profiles in rainbow trout eggs, which can in turn impact egg quality. Further characterization of the differentially expressed miRNAs and their target genes may provide valuable information on the role of these miRNAs in controlling egg quality, and ultimately lead to the development of biomarkers for prediction of egg quality in rainbow trout.

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Top 3 GO terms (second level) of the target genes of 6 miRNAs highly expressed in high quality eggs (D1PO) compared with the same GO terms of whole transcriptome in rainbow trout. (A) Molecular function. (B) Biological process. (C) Cellular component. Solid fill bar: Top 3 GO terms of the target genes of 6 differentially expressed miRNAs; Pattern fill bar: the corresponding GO terms analyzed using whole genome transcriptome. ** indicates significant difference at P < 0.001.
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Fig5: Top 3 GO terms (second level) of the target genes of 6 miRNAs highly expressed in high quality eggs (D1PO) compared with the same GO terms of whole transcriptome in rainbow trout. (A) Molecular function. (B) Biological process. (C) Cellular component. Solid fill bar: Top 3 GO terms of the target genes of 6 differentially expressed miRNAs; Pattern fill bar: the corresponding GO terms analyzed using whole genome transcriptome. ** indicates significant difference at P < 0.001.

Mentions: PITA and miRanda algorithms were used to predict the target genes of the 6 differentially expressed miRNAs that were validated by RT-qPCR analysis, A total of 178 gene entries from gene index database (http://www.animalgenome.org/repository) were predicted, which represent 114 known genes and 23 unknown genes (Additional file 1: Table S3). In addition, when mitochondrial genome was used as a query, a gene encoding cytochrome c oxidase subunit 1 (COX6B1) was predicted as the target of omy-miR-nov-95-5p. GO functional enrichment analysis of the target genes was carried out using Blast2GO software [46]. The results indicated that the top three GO terms (second level) in biological process include cellular process, metabolic process, and single organismal process, and the most significant GO terms in molecular function are binding, catalytic activity, and transporter activity (Figure 5). In comparison with the recent transcriptome data in rainbow trout [47], the significantly enriched GO terms are single-organism process and membrane. Interestingly, the GO term of cell death, which is one of the indicators of egg quality, is under the children branches of single-organism process.Figure 5


MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout (Oncorhynchus mykiss).

Ma H, Weber GM, Hostuttler MA, Wei H, Wang L, Yao J - BMC Genomics (2015)

Top 3 GO terms (second level) of the target genes of 6 miRNAs highly expressed in high quality eggs (D1PO) compared with the same GO terms of whole transcriptome in rainbow trout. (A) Molecular function. (B) Biological process. (C) Cellular component. Solid fill bar: Top 3 GO terms of the target genes of 6 differentially expressed miRNAs; Pattern fill bar: the corresponding GO terms analyzed using whole genome transcriptome. ** indicates significant difference at P < 0.001.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4374207&req=5

Fig5: Top 3 GO terms (second level) of the target genes of 6 miRNAs highly expressed in high quality eggs (D1PO) compared with the same GO terms of whole transcriptome in rainbow trout. (A) Molecular function. (B) Biological process. (C) Cellular component. Solid fill bar: Top 3 GO terms of the target genes of 6 differentially expressed miRNAs; Pattern fill bar: the corresponding GO terms analyzed using whole genome transcriptome. ** indicates significant difference at P < 0.001.
Mentions: PITA and miRanda algorithms were used to predict the target genes of the 6 differentially expressed miRNAs that were validated by RT-qPCR analysis, A total of 178 gene entries from gene index database (http://www.animalgenome.org/repository) were predicted, which represent 114 known genes and 23 unknown genes (Additional file 1: Table S3). In addition, when mitochondrial genome was used as a query, a gene encoding cytochrome c oxidase subunit 1 (COX6B1) was predicted as the target of omy-miR-nov-95-5p. GO functional enrichment analysis of the target genes was carried out using Blast2GO software [46]. The results indicated that the top three GO terms (second level) in biological process include cellular process, metabolic process, and single organismal process, and the most significant GO terms in molecular function are binding, catalytic activity, and transporter activity (Figure 5). In comparison with the recent transcriptome data in rainbow trout [47], the significantly enriched GO terms are single-organism process and membrane. Interestingly, the GO term of cell death, which is one of the indicators of egg quality, is under the children branches of single-organism process.Figure 5

Bottom Line: The objective of this study was to identify miRNAs that are associated with egg qualities in rainbow trout using post-ovulatory aged eggs.Four known miRNAs (omy-miR-193b-3p, omy-miR-203c-3p, omy-miR-499-5p and omy-miR-7550-3p) and two novel miRNAs (omy-miR-nov-95-5p and omy-miR-nov-112-5p) showed significantly higher expression in D1PO eggs relative to D14PO eggs as revealed by both deep sequencing and real time quantitative PCR analysis.Further characterization of the differentially expressed miRNAs and their target genes may provide valuable information on the role of these miRNAs in controlling egg quality, and ultimately lead to the development of biomarkers for prediction of egg quality in rainbow trout.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA. hao.ma@mail.wvu.edu.

ABSTRACT

Background: Egg quality is an important aspect in rainbow trout farming. Post-ovulatory aging is one of the most important factors affecting egg quality. MicroRNAs (miRNAs) are the major regulators in various biological processes and their expression profiles could serve as reliable biomarkers for various pathological and physiological conditions. The objective of this study was to identify miRNAs that are associated with egg qualities in rainbow trout using post-ovulatory aged eggs.

Results: Egg samples from females on day 1, day 7, and day 14 post-ovulation (D1PO, D7PO and D14PO), which had the fertilization rates of 91.8%, 73.4% and less than 50%, respectively, were collected and small RNAs isolated from these samples were subjected to deep sequencing using the Illumina platform. The massive sequencing produced 27,342,477, 26,910,438 and 29,185,371 reads from the libraries of D1PO, D7PO and D14PO eggs, respectively. A three-way comparison of the miRNAs indicated that the egg samples shared 392 known and 236 novel miRNAs, and a total of 414, 481, and 470 known and 243, 298, and 296 novel miRNAs were identified from D1PO, D7PO and D14PO eggs, respectively. Four known miRNAs (omy-miR-193b-3p, omy-miR-203c-3p, omy-miR-499-5p and omy-miR-7550-3p) and two novel miRNAs (omy-miR-nov-95-5p and omy-miR-nov-112-5p) showed significantly higher expression in D1PO eggs relative to D14PO eggs as revealed by both deep sequencing and real time quantitative PCR analysis. GO analysis of the predicted target genes of these differentially expressed miRNAs revealed significantly enriched GO terms that are related to stress response, cell death, DNA damage, ATP generation, signal transduction and transcription regulation.

Conclusions: Results indicate that post-ovulatory ageing affects miRNA expression profiles in rainbow trout eggs, which can in turn impact egg quality. Further characterization of the differentially expressed miRNAs and their target genes may provide valuable information on the role of these miRNAs in controlling egg quality, and ultimately lead to the development of biomarkers for prediction of egg quality in rainbow trout.

Show MeSH
Related in: MedlinePlus