Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput Sequencing
Although the expression of miRNAs has been widely applied to investigate on gonads, the role of miRNAs in the gonadal development of white Pacific shrimp (<i>Litopenaeus vannamei</i>) remains unknown. In this study, we performed high-throughput sequencing to identify the sex-related micr...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Fishes |
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| Online Access: | https://www.mdpi.com/2410-3888/7/6/308 |
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| author | Wei Li Pingping He Xingzhi Zhang Junliang Guan Yongxian Chen Li Zhang Bin Zhang Yusi Zheng Xin Li Qingsong He Longcheng Liu Chang Yuan Pinyuan Wei Jinxia Peng |
| author_facet | Wei Li Pingping He Xingzhi Zhang Junliang Guan Yongxian Chen Li Zhang Bin Zhang Yusi Zheng Xin Li Qingsong He Longcheng Liu Chang Yuan Pinyuan Wei Jinxia Peng |
| author_sort | Wei Li |
| collection | DOAJ |
| description | Although the expression of miRNAs has been widely applied to investigate on gonads, the role of miRNAs in the gonadal development of white Pacific shrimp (<i>Litopenaeus vannamei</i>) remains unknown. In this study, we performed high-throughput sequencing to identify the sex-related microRNAs (miRNAs) that elucidated the regulatory mechanisms on the gonadal differentiation of <i>L. vannamei</i>. We obtained a total of 29,671,557 and 28,526,942 raw reads from the ovaries and testes library, respectively. We then mapped 26,365,828 (92.73%) of the ovarian clean sequences and 23,694,294 (85.65%) of the testicular clean sequences for a transcriptome reference sequence of <i>L. vannamei</i>. After blasting the miRNA sequences against the miRBase database, we identified 153 significantly differentially expressed miRNAs between the ovaries and testes. To confirm the high-throughput sequencing results, we used a reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) to verify the expression patterns of the seven most differentially expressed miRNAs (i.e., novel_mir23, miR-92b-3p_3, miR-12-5p_2, novel_mir67, miR-279_1, let-7-5p_6, miR-263a-5p_1). According to the results of RT-qPCR, most of the miRNAs were expressed consistently with the high-throughput sequencing results. In addition, the target genes significantly enriched several Kyoto Encyclopedia of Genes and Genome (KEGG) pathways that were closely related to gonadal differentiation and development, including extracellular matrix–receptor interaction, Hedgehog signaling pathway, protein digestion and absorption and cell adhesion molecules (CAMs). This study revealed the first miRNAs sequencing of <i>L. vannamei</i> gonads. We identified sex-related differentially expressed miRNAs and KEGG pathways, which will be helpful to facilitate future research into the regulatory mechanism on the gonadal differentiation of <i>L. vannamei</i>. |
| first_indexed | 2024-03-09T16:44:40Z |
| format | Article |
| id | doaj.art-16a6ab19e36441b8a9934befd2bdb19a |
| institution | Directory Open Access Journal |
| issn | 2410-3888 |
| language | English |
| last_indexed | 2024-03-09T16:44:40Z |
| publishDate | 2022-10-01 |
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| record_format | Article |
| series | Fishes |
| spelling | doaj.art-16a6ab19e36441b8a9934befd2bdb19a2023-11-24T14:47:26ZengMDPI AGFishes2410-38882022-10-017630810.3390/fishes7060308Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput SequencingWei Li0Pingping He1Xingzhi Zhang2Junliang Guan3Yongxian Chen4Li Zhang5Bin Zhang6Yusi Zheng7Xin Li8Qingsong He9Longcheng Liu10Chang Yuan11Pinyuan Wei12Jinxia Peng13Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaGuangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, ChinaAlthough the expression of miRNAs has been widely applied to investigate on gonads, the role of miRNAs in the gonadal development of white Pacific shrimp (<i>Litopenaeus vannamei</i>) remains unknown. In this study, we performed high-throughput sequencing to identify the sex-related microRNAs (miRNAs) that elucidated the regulatory mechanisms on the gonadal differentiation of <i>L. vannamei</i>. We obtained a total of 29,671,557 and 28,526,942 raw reads from the ovaries and testes library, respectively. We then mapped 26,365,828 (92.73%) of the ovarian clean sequences and 23,694,294 (85.65%) of the testicular clean sequences for a transcriptome reference sequence of <i>L. vannamei</i>. After blasting the miRNA sequences against the miRBase database, we identified 153 significantly differentially expressed miRNAs between the ovaries and testes. To confirm the high-throughput sequencing results, we used a reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) to verify the expression patterns of the seven most differentially expressed miRNAs (i.e., novel_mir23, miR-92b-3p_3, miR-12-5p_2, novel_mir67, miR-279_1, let-7-5p_6, miR-263a-5p_1). According to the results of RT-qPCR, most of the miRNAs were expressed consistently with the high-throughput sequencing results. In addition, the target genes significantly enriched several Kyoto Encyclopedia of Genes and Genome (KEGG) pathways that were closely related to gonadal differentiation and development, including extracellular matrix–receptor interaction, Hedgehog signaling pathway, protein digestion and absorption and cell adhesion molecules (CAMs). This study revealed the first miRNAs sequencing of <i>L. vannamei</i> gonads. We identified sex-related differentially expressed miRNAs and KEGG pathways, which will be helpful to facilitate future research into the regulatory mechanism on the gonadal differentiation of <i>L. vannamei</i>.https://www.mdpi.com/2410-3888/7/6/308<i>Litopenaeus vannamei</i>miRNAsgonadhigh-throughput sequencingRT-qPCR |
| spellingShingle | Wei Li Pingping He Xingzhi Zhang Junliang Guan Yongxian Chen Li Zhang Bin Zhang Yusi Zheng Xin Li Qingsong He Longcheng Liu Chang Yuan Pinyuan Wei Jinxia Peng Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput Sequencing Fishes <i>Litopenaeus vannamei</i> miRNAs gonad high-throughput sequencing RT-qPCR |
| title | Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput Sequencing |
| title_full | Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput Sequencing |
| title_fullStr | Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput Sequencing |
| title_full_unstemmed | Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput Sequencing |
| title_short | Identification and Characterization of microRNAs in the Gonads of <i>Litopenaeus vannamei</i> Using High-Throughput Sequencing |
| title_sort | identification and characterization of micrornas in the gonads of i litopenaeus vannamei i using high throughput sequencing |
| topic | <i>Litopenaeus vannamei</i> miRNAs gonad high-throughput sequencing RT-qPCR |
| url | https://www.mdpi.com/2410-3888/7/6/308 |
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