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

Zhong, Yang; Zhao, Wei; ZhangSheng, Tang; Huang, Liming; Zhu, Xiao-feng; Liang, Xiang; Yan, Aifen; ZhiFa, Lu; Yu, Yanling; Tang, Dongsheng; Wang, Dapeng; Lu, Zhuan-Ling

doi:10.1186/s12864-021-07537-x

Cited by 9 publications

(7 citation statements)

References 73 publications

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“…This elevation corresponds with the GnRH signaling pathway and ovarian steroidogenesis pathway, suggesting that these pathways may regulate oogenesis and oocyte maturation in S. pharaonis by sensing the levels of growth hormone and vitellogenesis. Similar findings have been reported in transcriptome analyses of different developmental stages of Procambarus clarkii ovaries [ 51 ]. Future studies will involve independent functional analyses of these differentially expressed genes (DEGs) to identify their roles in ovarian maturation and to elucidate the synergistic interactions among these reproductive regulatory genes.…”

Section: Discussionsupporting

confidence: 90%

Comparative transcriptomic analysis of the different developmental stages of ovary in the cuttlefish Sepia pharaonis

Jiang,

Han,

et al. 2024

BMC Genomics

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The cuttlefish, Sepia pharaonis, is characterized by rapid growth and strong disease resistance, making it an important commercially farmed cephalopod species in the southeastern coastal regions of China. However, in the reproductive process of S. pharaonis, there are challenges such as a low output of eggs, poor quality, and low survival rates of newly hatched juveniles. Therefore, there is an urgent need to study the molecular mechanisms underlying ovarian development in this species. In this study, we conducted the first transcriptomic analysis of the ovary at four developmental stages: the undeveloped stage, developing stage, nearly-ripe stage, and ripe stage, and compared the transcriptomics among these four stages using Illumina sequencing technology. The total numbers of clean reads of the four stages ranged from 40,890,772 to 52,055,714 reads. A total of 136,829 DEGs were obtained, GC base ratios of raw data were between 38.44 and 44.59%, and the number of uniquely mapped reads spanned from 88.08 to 95.90%. The Pearson correlation coefficient demonstrated a strong correlation among different samples within the same group, PCA and Anosim analysis also revealed that the grouping of these four stages was feasible, and each stage could be distinguished from the others. GO enrichment analysis demonstrated that ovarian follicle growth, sex differentiation, and transforming growth factor beta receptor, played a foreshadowing role at the early ovarian development stage, and the terms of small molecule metabolic process, peptide metabolic process, and catalytic activity were prominent at the mature stage. Meanwhile, KEGG analysis showed that the early ovarian development of S. pharaonis was mainly associated with the cell cycle, DNA replication, and carbon metabolism, while the mid-late ovarian development was involved with the signal transduction, endocrine system, and reproduction pathway. RT-qPCR further confirmed the consistent expression patterns of genes such as 17β-HSD, GH, VGS, NFR, and NYR in the ovaries of S. pharaonis, exhibiting elevated levels of expression during the maturation stage. Conversely, ER and OM exhibited high expression levels during the early stages of ovarian development. These transcriptomic data provide insights into the molecular mechanisms of S. pharaonis ovarian development. The findings of this study will contribute to improving the reproduction and development of cuttlefish and enriching the bioinformatics knowledge of cephalopods.

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Section: Discussionsupporting

confidence: 90%

Comparative transcriptomic analysis of the different developmental stages of ovary in the cuttlefish Sepia pharaonis

Jiang,

Han,

et al. 2024

BMC Genomics

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“…For example, on Day 80, the alpha diversity of the Chinese giant salamander decreased as the temperature rose. This pattern was, to some extent, inverse on Day 30 (Zhu et al, 2021). The test results manifested that P. clarkii had the highest diversity in the ZJ group, the most suitable temperature.…”

Section: Discussionmentioning

confidence: 83%

“…Red swamp crayfish, Procambarus clarkii, belongs to an important group of crustaceans, characterized by its fast growth rate and strong adaptability (Zhong et al, 2021). P. clarkii is a popular freshwater economic species.…”

Section: Introductionmentioning

confidence: 99%

Comparison of the gut microbiota and metabolism in different regions of Red Swamp Crayfish (Procambarus clarkii)

Liu,

Wang,

Wang

et al. 2023

Front. Microbiol.

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BackgroundThe gut microbiota is very important for maintaining the homeostasis and health of crustaceans. Many factors affect the gut microbiota of crustaceans, one of which is temperature. However, it is currently unclear how temperature affects the gut microbiota and metabolites of Procambarus clarkii.MethodsUsing metagenomic sequencing and gas chromatography–mass spectrometry (GC–MS) techniques, the gut microbiota and metabolites of P. clarkii from Hubei (HB), Jiangsu (JS), Shandong (SD), and Zhejiang (ZJ) in China were investigated.ResultsUnder the impact of temperature, the gut microbiota and metabolites of P. clarkii exhibit a specific trend of change. The primary pathogenic bacteria affecting P. clarkii are Citrobacter, Enterobacterium, and Aeromonas, which are affected by temperature. Two metabolites, namely, sugars and amino acids, are regulated by temperature.ImplicationThis study demonstrated that the gut microbiota and gut metabolites of P. clarkii were considerably affected by temperature. It provides a theoretical basis for the systematic study of P. clarkii and provides a basis for a healthy culture of P. clarkii.

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“…Recent studies demonstrated that downregulation of the wnt signaling pathway was associated with delayed maturation of porcine oocytes and cell cycle arrest of mice granulosa cells [37]. In red swamp crayfish Procambarus clarkia, the p53 signaling pathway was independent for cell proliferation in late ovarian development [38]. The Jak-STAT signaling pathway was pivotal in regulating cell fate and necessary in germ cell proliferation of spotted knifejaw [39].…”

Section: Discussionmentioning

confidence: 99%

Transcription Analysis for Core Networks of lncRNAs–mRNAs: Implication for Potential Role in Sterility of Crassostrea gigas

Liu

2022

Biology

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Long noncoding RNA (lncRNA), a type of non-protein-coding transcript, is emerging as a crucial regulator of gene expression. However, few roles of lncRNA in the reproductive process of the Pacific oyster (Crassostrea gigas) have been defined, especially in the regulatory mechanism of sterile triploids gametogenesis. To uncover the potential role of lncRNA, the gonads of diploids, sterile triploids, and partially sterile triploids underwent RNA sequencing. A total of 9618 reliable lncRNAs were identified. The target relationship between lncRNA and mRNA was predicted based on cis, trans, and antisense regulation with bioinformatic software. We chose differentially expressed lncRNAs and mRNAs when sterile triploids were compared to partially sterile triploids and diploids for subsequent functional enrichment analysis. Findings revealed that trans-regulatory lncRNAs might play a significant role in the gametogenesis of C. gigas. Combining pathway results, we constructed core networks of lncRNAs–mRNAs for triploid sterile females and hermaphrodites. Fifty-four genes related to cell division, germline-cell maintenance, and glycogen metabolism were found to be associated with sterility. A total of 28 candidate lncRNAs were predicted to trans-regulate these genes. We speculated that MSTRG.79882.3 and MSTRG.79882.4 for triploid sterile females and MSTRG.33704.1, MSTRG.63844.1, and MSTRG.5675.1 for hermaphrodites were highly important as they were predicted to regulate more sterility-specific genes than others. Our work collectively identified sterility-related lncRNAs and implicated the potential mechanism of lncRNA-mediated regulation in the gametogenesis of sterile triploid oysters.

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

Cited by 9 publications

References 73 publications

Comparative transcriptomic analysis of the different developmental stages of ovary in the cuttlefish Sepia pharaonis

Comparative transcriptomic analysis of the different developmental stages of ovary in the cuttlefish Sepia pharaonis

Comparison of the gut microbiota and metabolism in different regions of Red Swamp Crayfish (Procambarus clarkii)

Transcription Analysis for Core Networks of lncRNAs–mRNAs: Implication for Potential Role in Sterility of Crassostrea gigas

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