Transcriptional profiling of pigmentation-regulated long non-coding RNAs in the mantle of Manila clam (Ruditapes philippinarum)

Chen, Sitong; Nie, Hongtao; Huo, Zhongming; Yan, Xiwu

doi:10.1016/j.aquaculture.2023.739889

Cited by 5 publications

(2 citation statements)

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“…In the Pacific oyster, two members of Tyrs were differentially expressed between different shell color individuals, which were associated with melanin biosynthesis, and they were the target genes of nine cis-acting lncRNAs [ 42 ]. Similarly, four Tyrs with their eleven corresponding cis -acting lncRNAs were detected modulating melanin biosynthesis in R. philippinarum [ 45 ]. In this study, a total of eight Tyrs showed significantly higher expression levels in diseased P. yessoensis , indicating their important roles in P. yessoensis to defend against Polydora infestation.…”

Section: Discussionmentioning

confidence: 99%

“…Emerging evidence has also revealed that lncRNAs are involved in the modulation of shell biomineralization and pigmentation in molluscs [ 42 – 46 ]. For example, chorions peroxidase and its cis -acting lncRNA TCONS_00951105 were predicted to exhibit a key function in melanin biosynthesis in Pacific oysters ( Crassostrea gigas ) by RNA-seq [ 42 ]; in manila clam ( Ruditapes philippinarum ), 14 differential expressed mRNAs and their interactive 77 lncRNAs were thought to be involved in the pathways of melanin synthesis and porphyrin metabolic [ 45 ]; besides, a lncRNA named LncMSEN2 were identified functioning in exoskeleton formation in the pearl oyster ( Pinctada fucuta martensii ) [ 47 ]. However, most reports focused on species of oysters, clams and abalones, especially oysters, and almost no relevant research has been conducted in scallops, limiting our comprehensive understanding of the regulatory mechanisms of lncRNAs in molluscs.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora

Wang,

Mao,

Fan

et al. 2023

BMC Genomics

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Background Patinopecten yessoensis, a large and old molluscan group, has been one of the most important aquaculture shellfish in Asian countries because of its high economic value. However, the aquaculture of the species has recently been seriously affected by the frequent outbreaks of Polydora disease, causing great economic losses. Long non-coding RNAs (lncRNAs) exhibit exhibit crucial effects on diverse biological processes, but still remain poorly studied in scallops, limiting our understanding of the molecular regulatory mechanism of P. yessoensis in response to Polydora infestation. Results In this study, a high-throughput transcriptome analysis was conducted in the mantles of healthy and Polydora-infected P. yessoensis by RNA sequencing. A total of 19,133 lncRNAs with 2,203 known and 16,930 novel were identified. The genomic characterizations of lncRNAs showed shorter sequence and open reading frame (ORF) length, fewer number of exons and lower expression levels in comparison with mRNAs. There were separately 2280 and 1636 differentially expressed mRNAs and lncRNAs (DEGs and DELs) detected in diseased individuals. The target genes of DELs were determined by both co-location and co-expression analyses. Functional enrichment analysis revealed that DEGs involved in melanization and biomineralization were significantly upregulated; further, obviously increased melanin granules were observed in epithelial cells of the edge mantle in diseased scallops by histological and TEM study, indicating the crucial role of melanizaiton and biomineralization in P. yessoensis to resist against Polydora infestation. Moreover, many key genes, such as Tyrs, Frizzled, Wnts, calmodulins, Pifs, perlucin, laccase, shell matrix protein, mucins and chitins, were targeted by DELs. Finally, a core lncRNA-mRNA interactive network involved in melanization and biomineralization was constructed and validated by qRT-PCR. Conclusions This work provides valuable resources for studies of lncRNAs in scallops, and adds a new insight into the molecular regulatory mechanisms of P. yessoensis defending against Polydora infestation, which will contribute to Polydora disease control and breeding of disease-resistant varieties in molluscs.

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Section: Discussionmentioning

confidence: 99%