Transcriptome analysis provides insights into the molecular mechanisms responsible for evisceration behavior in the sea cucumber Apostichopus japonicus

2019 ◽  
Vol 30 ◽  
pp. 143-157 ◽  
Author(s):  
Kui Ding ◽  
Libin Zhang ◽  
Lina Sun ◽  
Chenggang Lin ◽  
Qiming Feng ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Sea Cucumber ◽  
Molecular Mechanisms ◽  
Apostichopus Japonicus

scholarly journals Comparative transcriptome analysis of papilla and skin in the sea cucumber,Apostichopus japonicus

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1779 ◽  
Author(s):  
Xiaoxu Zhou ◽  
Jun Cui ◽  
Shikai Liu ◽  
Derong Kong ◽  
He Sun ◽  
...  
Keyword(s):  
Growth Factor ◽  
Transcriptome Analysis ◽  
Sea Cucumber ◽  
Molecular Mechanisms ◽  
Transforming Growth Factor ◽  
Apostichopus Japonicus ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such asfibroblast growth factor,transforming growth factor-β,collagen-α2andIntegrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber.

scholarly journals Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0181471 ◽  
Author(s):  
Lei Gao ◽  
Chongbo He ◽  
Xiangbo Bao ◽  
Meilin Tian ◽  
Zhen Ma
Keyword(s):  
Transcriptome Analysis ◽  
Sea Cucumber ◽  
Apostichopus Japonicus ◽  
Individual Growth

Transcriptome analysis of sea cucumber (Apostichopus japonicus) polian vesicles in response to evisceration

2020 ◽  
Vol 97 ◽  
pp. 108-113
Author(s):  
Weibo Shi ◽  
Jialin Zhang ◽  
Yinan Wang ◽  
Jinlin Ji ◽  
Liyuan Guo ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Sea Cucumber ◽  
Apostichopus Japonicus

scholarly journals RNA Sequencing Analysis to Capture the Transcriptome Landscape during Tenderization in Sea Cucumber Apostichopus japonicus

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 998 ◽  
Author(s):  
Xiufang Dong ◽  
Hang Qi ◽  
Baoyu He ◽  
Di Jiang ◽  
Beiwei Zhu
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Sea Cucumber ◽  
Molecular Mechanisms ◽  
Apostichopus Japonicus ◽  
Expression Profiles ◽  
Textural Properties ◽  
Sequencing Analysis ◽  
Type Iv Collagenase ◽  
Illumina Hiseq

Sea cucumber (Apostichopus japonicus) is an economically significant species in China having great commercial value. It is challenging to maintain the textural properties during thermal processing due to the distinctive physiochemical structure of the A. japonicus body wall (AJBW). In this study, the gene expression profiles associated with tenderization in AJBW were determined at 0 h (CON), 1 h (T_1h), and 3 h (T_3h) after treatment at 37 °C using Illumina HiSeq™ 4000 platform. Seven-hundred-and-twenty-one and 806 differentially expressed genes (DEGs) were identified in comparisons of T_1h vs. CON and T_3h vs. CON, respectively. Among these DEGs, we found that two endogenous proteases—72 kDa type IV collagenase and matrix metalloproteinase 16 precursor—were significantly upregulated that could directly affect the tenderness of AJBW. In addition, 92 genes controlled four types of physiological and biochemical processes such as oxidative stress response (3), immune system process (55), apoptosis (4), and reorganization of the cytoskeleton and extracellular matrix (30). Further, the RT-qPCR results confirmed the accuracy of RNA-sequencing analysis. Our results showed the dynamic changes in global gene expression during tenderization and provided a series of candidate genes that contributed to tenderization in AJBW. This can help further studies on the genetics/molecular mechanisms associated with tenderization.

Comparative transcriptome analysis of three color variants of the sea cucumber Apostichopus japonicus

2016 ◽  
Vol 28 ◽  
pp. 21-24 ◽  
Author(s):  
Jihoon Jo ◽  
Jongsun Park ◽  
Hyun-Gwan Lee ◽  
Elizabeth M.A. Kern ◽  
Seongmin Cheon ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Sea Cucumber ◽  
Apostichopus Japonicus ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Color Variants
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