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

Abstract

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.

Pharmacokinetics and Transport of an Osteogenic Dodecapeptide

“…Amplification reagents used a TB Green Premix Ex Taq II kit (Tli RNase H Plus, TaKaRa, Otsu, Japan). The RT-qPCR amplification conditions used are consistent with previous reports . The results obtained were analyzed and expressed using the 2 –ΔΔCT method.…”

“…The RT-qPCR amplification conditions used are consistent with previous reports. 23 The results obtained were analyzed and expressed using the 2 −ΔΔCT method. Western Blot Analysis.…”

Thermal treatments and their influence on physicochemical properties of sea cucumbers: a comprehensive review

“…The principal approach to controlling sea cucumber textural characteristics is to utilise endogenous enzymes (matrix metalloproteinase, gelatinolytic metalloproteinase, cysteine/cathepsin/caspases/serine protease proteinases) and feasible inhibitors to achieve bidirectional regulation of tenderness or hardness (Dong et al ., 2018; Liu et al ., 2020b). In particular, several matrix metalloproteinases (MMPs) and collagenases play a critical role in the constructive regulation of sea cucumber, which has been verified at the proteomic and genic levels (Dong et al ., 2019a, 2019b; Yan et al ., 2021).…”

A Novel Full-Length Transcriptome Resource for Sea Cucumber Apostichopus japonicus Using Pacbio SMRT Sequencing

“…For instance, transcriptome analysis of sea cucumber during the anti-bacterial process provided a valuable database of the interactions of mRNA-miRNA and gene expression regulatory mechanisms (Zhang et al, 2013). Comparative transcriptome analysis of multiple sea cucumber tissues revealed the molecular mechanisms of larval development (Boyko et al, 2019), growth variation (Gao et al, 2017), color variation (Jo et al, 2016), tissue-specific expression (Zhou et al, 2016a), tissue development (Zhan et al, 2019) and regeneration (Sun et al, 2011), responses to environmental stress (Li et al, 2019), aestivation (Yang et al, 2021), evisceration behavior (Ding et al, 2019), tenderization (Dong et al, 2019), and immune responses (Guo et al, 2021).…”