Genome-wide identification and characterization of Pif genes in the Yesso scallop (Patinopecten yessoensis), and their expression patterns in response to Polydora shell infestation

Yuan, Changzi; Mao, Junxia; Sun, Hongyan; Wang, Xubo; Tian, Ying; Jiang, Song; Yin, Donghong; Hao, Zhenlin; Ding, Jun; Chang, Yaqing

doi:10.1016/j.aquaculture.2021.737223

Cited by 5 publications

(3 citation statements)

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“…Pif is deemed to participate in the initiation of aragonite crystallization and subsequently stack aragonite tablets in the nacreous layer [ 85 – 88 ]. In our previous study, 8 Pif homologs in total were identified in the genome of P. yessoensis , and most of these genes represented dramatically increased expression levels in the edge mantle tissues of scallops infected by Polydora , indicating their important function in shell formation [ 65 ]. In this study, two of the Pifs ( Pif1 and Pif7 ) were detected significantly upregulated in the mantle transcriptome of diseased individuals, consistent with the expression trends in our previous study.…”

Section: Discussionmentioning

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%

“…Expression levels of lcnRNAs and genes participating in melanization and biomineralization were validated by qRT-PCR following the way mentioned in [ 65 ]. In brief, total RNAs were first isolated utilizing an RNAprep pure tissue kit (Tiangen, China).…”

Section: Methodsmentioning

confidence: 99%

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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“…Next‐generation sequencing and systems biology are powerful approaches enabling elucidation of molecular mechanisms engaged in the cellular stress response of non‐model systems (Fan et al., 2024 ; Jia et al., 2021 ). For example, transcriptome sequencing of the massive starlet coral, Siderastrea siderea , revealed activation of biocalcification‐related processes under high p CO2 and repression of functions related to environmental sensing under thermal stress (Davies et al., 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Gene networks governing the response of a calcareous sponge to future ocean conditions reveal lineage‐specific XBP1 regulation of the unfolded protein response

Posadas,

Conaco

2024

Ecology and Evolution

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Marine sponges are predicted to be winners in the future ocean due to their exemplary adaptive capacity. However, while many sponge groups exhibit tolerance to a wide range of environmental insults, calcifying sponges may be more susceptible to thermo‐acidic stress. To describe the gene regulatory networks that govern the stress response of the calcareous sponge, Leucetta chagosensis (class Calcarea, order Clathrinida), individuals were subjected to warming and acidification conditions based on the climate models for 2100. Transcriptome analysis and gene co‐expression network reconstruction revealed that the unfolded protein response (UPR) was activated under thermo‐acidic stress. Among the upregulated genes were two lineage‐specific homologs of X‐box binding protein 1 (XBP1), a transcription factor that activates the UPR. Alternative dimerization between these XBP1 gene products suggests a clathrinid‐specific mechanism to reversibly sequester the transcription factor into an inactive form, enabling the rapid regulation of pathways linked to the UPR in clathrinid calcareous sponges. Our findings support the idea that transcription factor duplication events may refine evolutionarily conserved molecular pathways and contribute to ecological success.

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First insight on the genetic base of the heritable variation of Pacific abalone (Haliotis discus hannai) resistance to Polydora hoplura infestation

Winkler,

Díaz-González,

Valdivia

et al. 2024

Aquaculture Reports

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Genome-wide identification and characterization of Pif genes in the Yesso scallop (Patinopecten yessoensis), and their expression patterns in response to Polydora shell infestation

Cited by 5 publications

References 50 publications

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

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

Gene networks governing the response of a calcareous sponge to future ocean conditions reveal lineage‐specific XBP1 regulation of the unfolded protein response

First insight on the genetic base of the heritable variation of Pacific abalone (Haliotis discus hannai) resistance to Polydora hoplura infestation

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