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Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii

BACKGROUND: The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, the molecular mechanisms of ovarian development in P. clarkii remain largely...

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Autores principales: Zhong, Yizhi, Zhao, Wenbin, Tang, Zhangsheng, Huang, Liming, Zhu, Xiangxing, Liang, Xiang, Yan, Aifen, Lu, Zhifa, Yu, Yanling, Tang, Dongsheng, Wang, Dapeng, Lu, Zhuanling
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7981885/
https://www.ncbi.nlm.nih.gov/pubmed/33745451
http://dx.doi.org/10.1186/s12864-021-07537-x
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author Zhong, Yizhi
Zhao, Wenbin
Tang, Zhangsheng
Huang, Liming
Zhu, Xiangxing
Liang, Xiang
Yan, Aifen
Lu, Zhifa
Yu, Yanling
Tang, Dongsheng
Wang, Dapeng
Lu, Zhuanling
author_facet Zhong, Yizhi
Zhao, Wenbin
Tang, Zhangsheng
Huang, Liming
Zhu, Xiangxing
Liang, Xiang
Yan, Aifen
Lu, Zhifa
Yu, Yanling
Tang, Dongsheng
Wang, Dapeng
Lu, Zhuanling
author_sort Zhong, Yizhi
collection PubMed
description BACKGROUND: The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, the molecular mechanisms of ovarian development in P. clarkii remain largely unknown. In this study, we identified four stages of P. clarkii ovary development, the previtellogenic stage (stage I), early vitellogenic stage (stage II), middle vitellogenic stage (stage III), and mature stage (stage IV) and compared the transcriptomics among these four stages through next-generation sequencing (NGS). RESULTS: The total numbers of clean reads of the four stages ranged from 42,013,648 to 62,220,956. A total of 216,444 unigenes were obtained, and the GC content of most unigenes was slightly less than the AT content. Principal Component Analysis (PCA) and Anosim analysis demonstrated that the grouping of these four stages was feasible, and each stage could be distinguished from the others. In the expression pattern analysis, 2301 genes were continuously increase from stage I to stage IV, and 2660 genes were sharply decrease at stage IV compared to stages I-III. By comparing each of the stages at the same time, four clusters of differentially expressed genes (DEGs) were found to be uniquely highly expressed in stage I (136 genes), stage II (43 genes), stage III-IV (49 genes), and stage IV (22 genes), thus exhibiting developmental stage specificity. Moreover, in comparisons between adjacent stages, the number of DEGs between stage III and IV was the highest. GO enrichment analysis demonstrated that nutrient reservoir activity was highest at stage II and that this played a foreshadowing role in ovarian development, and the GO terms of cell, intracellular and organelle participated in the ovary maturation during later stages. In addition, KEGG pathway analysis revealed that the early development of the ovary was mainly associated with the PI3K-Akt signaling pathway and focal adhesion; the middle developmental period was related to apoptosis, lysine biosynthesis, and the NF-kappa B signaling pathway; the late developmental period was involved with the cell cycle and the p53 signaling pathway. CONCLUSION: These transcriptomic data provide insights into the molecular mechanisms of ovarian development in P. clarkii. The results will be helpful for improving the reproduction and development of this aquatic species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07537-x.
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spelling pubmed-79818852021-03-22 Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii Zhong, Yizhi Zhao, Wenbin Tang, Zhangsheng Huang, Liming Zhu, Xiangxing Liang, Xiang Yan, Aifen Lu, Zhifa Yu, Yanling Tang, Dongsheng Wang, Dapeng Lu, Zhuanling BMC Genomics Research Article BACKGROUND: The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, the molecular mechanisms of ovarian development in P. clarkii remain largely unknown. In this study, we identified four stages of P. clarkii ovary development, the previtellogenic stage (stage I), early vitellogenic stage (stage II), middle vitellogenic stage (stage III), and mature stage (stage IV) and compared the transcriptomics among these four stages through next-generation sequencing (NGS). RESULTS: The total numbers of clean reads of the four stages ranged from 42,013,648 to 62,220,956. A total of 216,444 unigenes were obtained, and the GC content of most unigenes was slightly less than the AT content. Principal Component Analysis (PCA) and Anosim analysis demonstrated that the grouping of these four stages was feasible, and each stage could be distinguished from the others. In the expression pattern analysis, 2301 genes were continuously increase from stage I to stage IV, and 2660 genes were sharply decrease at stage IV compared to stages I-III. By comparing each of the stages at the same time, four clusters of differentially expressed genes (DEGs) were found to be uniquely highly expressed in stage I (136 genes), stage II (43 genes), stage III-IV (49 genes), and stage IV (22 genes), thus exhibiting developmental stage specificity. Moreover, in comparisons between adjacent stages, the number of DEGs between stage III and IV was the highest. GO enrichment analysis demonstrated that nutrient reservoir activity was highest at stage II and that this played a foreshadowing role in ovarian development, and the GO terms of cell, intracellular and organelle participated in the ovary maturation during later stages. In addition, KEGG pathway analysis revealed that the early development of the ovary was mainly associated with the PI3K-Akt signaling pathway and focal adhesion; the middle developmental period was related to apoptosis, lysine biosynthesis, and the NF-kappa B signaling pathway; the late developmental period was involved with the cell cycle and the p53 signaling pathway. CONCLUSION: These transcriptomic data provide insights into the molecular mechanisms of ovarian development in P. clarkii. The results will be helpful for improving the reproduction and development of this aquatic species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07537-x. BioMed Central 2021-03-21 /pmc/articles/PMC7981885/ /pubmed/33745451 http://dx.doi.org/10.1186/s12864-021-07537-x Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Zhong, Yizhi
Zhao, Wenbin
Tang, Zhangsheng
Huang, Liming
Zhu, Xiangxing
Liang, Xiang
Yan, Aifen
Lu, Zhifa
Yu, Yanling
Tang, Dongsheng
Wang, Dapeng
Lu, Zhuanling
Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
title Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
title_full Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
title_fullStr Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
title_full_unstemmed Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
title_short Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii
title_sort comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish procambarus clarkii
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7981885/
https://www.ncbi.nlm.nih.gov/pubmed/33745451
http://dx.doi.org/10.1186/s12864-021-07537-x
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