Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii)
Objective Sturgeons are considered living fossils, and have a very high conservation and economic value. Studies on the molecular mechanism of sturgeon gonadal development and sex differentiation would not only aid in understanding vertebrate sex determination but also benefit sturgeon aquaculture....
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PeerJ Inc.
2019-04-01
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| Online Access: | https://peerj.com/articles/6709.pdf |
| _version_ | 1797421023919865856 |
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| author | Lihong Yuan Linmiao Li Xiujuan Zhang Haiying Jiang Jinping Chen |
| author_facet | Lihong Yuan Linmiao Li Xiujuan Zhang Haiying Jiang Jinping Chen |
| author_sort | Lihong Yuan |
| collection | DOAJ |
| description | Objective Sturgeons are considered living fossils, and have a very high conservation and economic value. Studies on the molecular mechanism of sturgeon gonadal development and sex differentiation would not only aid in understanding vertebrate sex determination but also benefit sturgeon aquaculture. Piwi-interacting RNAs (piRNAs) have been shown to function in germline or gonadal development. In this study, we performed small RNA deep sequencing and microarray hybridization to identify potential sturgeon piRNAs. Methods Male and female sturgeon gonads were collected and used for small RNA sequencing on an Illumina HiSeq platform with the validation of piRNA expression by microarray chip. The program Bowtie and k-mer scheme were performed to filter small RNA reads and discover potential sturgeon piRNAs. A known piRNA database, the coding sequence (CDS), 5′ and 3′ untranslated region (UTR) database of the A. Schrenckii transcriptome, Gene Ontology (GO) database and KEGG pathway database were searched subsequently to analyze the potential bio-function of sturgeon piRNAs. Results A total of 875,679 putative sturgeon piRNAs were obtained, including 93 homologous to known piRNAs and hundreds showing sex-specific and sex-biased expression. Further analysis showed that they are predominant in both the ovaries and testes and those with a sex-specific expression pattern are nearly equally distribution between sexes. This may imply a relevant role in sturgeon gonadal development. KEGG pathway and GO annotation analyses indicated that they may be related to sturgeon reproductive processes. Conclusion Our study provides the first insights into the gonadal piRNAs in a sturgeon species and should serve as a useful resource for further elucidation of the gene regulation involved in the sex differentiation of vertebrates. These results should also facilitate the technological development of early sex identification in sturgeon aquaculture. |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:10:59Z |
| publishDate | 2019-04-01 |
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| spelling | doaj.art-09a434b7cf6b4486a8d0cff21042d7172023-12-03T09:07:23ZengPeerJ Inc.PeerJ2167-83592019-04-017e670910.7717/peerj.6709Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii)Lihong Yuan0Linmiao Li1Xiujuan Zhang2Haiying Jiang3Jinping Chen4School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, ChinaGuangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, ChinaGuangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, ChinaGuangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, ChinaGuangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, ChinaObjective Sturgeons are considered living fossils, and have a very high conservation and economic value. Studies on the molecular mechanism of sturgeon gonadal development and sex differentiation would not only aid in understanding vertebrate sex determination but also benefit sturgeon aquaculture. Piwi-interacting RNAs (piRNAs) have been shown to function in germline or gonadal development. In this study, we performed small RNA deep sequencing and microarray hybridization to identify potential sturgeon piRNAs. Methods Male and female sturgeon gonads were collected and used for small RNA sequencing on an Illumina HiSeq platform with the validation of piRNA expression by microarray chip. The program Bowtie and k-mer scheme were performed to filter small RNA reads and discover potential sturgeon piRNAs. A known piRNA database, the coding sequence (CDS), 5′ and 3′ untranslated region (UTR) database of the A. Schrenckii transcriptome, Gene Ontology (GO) database and KEGG pathway database were searched subsequently to analyze the potential bio-function of sturgeon piRNAs. Results A total of 875,679 putative sturgeon piRNAs were obtained, including 93 homologous to known piRNAs and hundreds showing sex-specific and sex-biased expression. Further analysis showed that they are predominant in both the ovaries and testes and those with a sex-specific expression pattern are nearly equally distribution between sexes. This may imply a relevant role in sturgeon gonadal development. KEGG pathway and GO annotation analyses indicated that they may be related to sturgeon reproductive processes. Conclusion Our study provides the first insights into the gonadal piRNAs in a sturgeon species and should serve as a useful resource for further elucidation of the gene regulation involved in the sex differentiation of vertebrates. These results should also facilitate the technological development of early sex identification in sturgeon aquaculture.https://peerj.com/articles/6709.pdfpiRNASturgeonGonadal development |
| spellingShingle | Lihong Yuan Linmiao Li Xiujuan Zhang Haiying Jiang Jinping Chen Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii) PeerJ piRNA Sturgeon Gonadal development |
| title | Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii) |
| title_full | Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii) |
| title_fullStr | Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii) |
| title_full_unstemmed | Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii) |
| title_short | Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii) |
| title_sort | identification and differential expression of pirnas in the gonads of amur sturgeon acipenser schrenckii |
| topic | piRNA Sturgeon Gonadal development |
| url | https://peerj.com/articles/6709.pdf |
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