Integrated microRNA study and pathological analysis provides new insights into the immune response of Ruditapes philippinarum under Vibrio anguillarum challenge.

Manila clam (Ruditapes philippenarum) is an important shellfish aquaculture product. The large-scale breeding of clams is often affected by V. anguillarum and causes large-scale death.

Characterization and expression patterns of the Fox gene family under heat and cold stress in Manila clam Ruditapes philippinarum based on genome-wide identification.

In this study, the Fox gene family of Ruditapes philippinarum was identified by bioinformatics analysis and genome data. The results showed that a total of 21 Fox genes were identified in R. philippinarum, which were divided into 16 subfamilies, including two members of Foxa subfamily (Foxa1, Foxa2), three members of Foxl subfamily (Foxl1b, Foxl1a, FOXL2), three members of Foxn subfamily (FOXN3, FOX4A, Foxn4b) and one member of other families.

Exploring the Heat-Responsive miRNAs and their Target Gene Regulation in Ruditapes philippinarum Under Acute Heat Stress.

This study aimed to investigate the inherent molecular regulatory mechanisms of Ruditapes philippinarum in response to extremely high-temperature environments and to enhance the sustainable development of the R. philippinarum aquaculture industry. In this study, we established a differential expression profile of miRNA under acute heat stress and identified a total of 46 known miRNAs and 80 novel miRNAs, three of which were detected to be significantly differentially expressed.

The energy metabolism and transcriptomic responses of the Manila clam (Ruditapes philippinarum) under the low-temperature stress.

Low temperature in winter poses a threat to the Manila clam Ruditapes philippinarum in North China. However, a number of low-temperature-tolerant clams could survive such condition. It is therefore of interest to explore the survival mechanisms underlying the cold tolerance of R.

Physiological and transcriptomic analysis provides new insights into osmoregulation mechanism of Ruditapes philippinarum under low and high salinity stress.

The Manila clam (Ruditapes philippinarum) is a commercially important marine bivalve, which inhabits the estuarine and mudflat areas. The osmoregulation is of great significance for molluscs adaptation to salinity fluctuations. In this study, we investigated the effects of low salinity (10 psu) and high salinity (40 psu) stress on survival and osmoregulation of the R.

Genome-wide identification and expression analysis of Sox gene family in the Manila clam (Ruditapes philippinarum).

Sox transcription factors are vital in numerous fundamental biological processes. In this study, nine Sox gene family members were discovered in the Ruditapes philippinarum genome, classified into the SoxB1, SoxB2, SoxC, SoxD, SoxE, and SoxF groups, marking the first genome-wide identification of this gene family in R. philippinarum.

The lgi-miR-2d is Potentially Involved in Shell Melanin Synthesis by Targeting mitf in Manila Clam Ruditapes philippinarum.

Shell color as an important economic trait is also the crucial target trait for breeding and production. MicroRNA (miRNA) is an endogenous small non-coding RNA that can post-transcriptionally regulate the expression of target genes, it plays important roles in many life activities and physiological processes, such as shell color, stress response, and disease traits. In this study, we investigated the function of lgi-miR-2d in shell melanin formation and the expression patterns of lgi-miR-2d and target gene Rpmitf in Manila clam Ruditapes philippinarum.

Metabolic adaptation of the clam during air exposure and the positive effects of sodium nitroprusside pretreatment.

The Manila clam (), as one of the shellfish living in the intertidal zone, is known for its strong ability to withstand air exposure. Sodium nitroprusside (SNP), a donor of nitric oxide (NO), has been shown to be useful for antioxidant and immune regulation in aquatic animals. In this study, an untargeted metabolomics (LC-MS/MS) technique was employed for the first time in Manila clam to analyze the metabolic and histological impacts after air exposure and the positive effects of SNP pretreatment.

iTRAQ-based proteomic analysis reveals proteins associated with cold stress response in two different populations of Manila clam (Ruditapes philippinarum).

Water temperature is one of the key environmental factors for marine ectotherms and a change in temperature beyond and organism's capacity limits can cause a series of changes to physiological state and damage to the organism. Understanding how organisms adapt to complex environments is a central goal of evolutionary biology and ecology. Ruditapes philippinarum is an ecologically and scientifically important marine bivalve species.

Genome-wide investigation and expression analysis of TLR gene family reveals its immune role in tolerance challenge of Manila clam.

Toll-like receptors (TLRs) play key roles in activating immune responses during infection. In this study, we identified TLR genes in Manila clam at the genome-wide level and characterized it into 9 types according to the genome annotation, including TLR1 (1-10), TLR2 (1-10), TLR2-2 (1-5), TLR3 (1-3), TLR4 (1-9), TLR5, TLR6 (1-5), TLR7 (1-2), and TLR13 (1-4). The length of TLR proteins varied from 128 to 1257 amino acids.

Metabolomic analysis provides new insights into the heat-hardening response of Manila clam (Ruditapes philippinarum) to high temperature stress.

The temperature has always been a key environmental factor in Manila clam (Ruditapes philippinarum) culture. In this study, the Manila clam was treated to different temperature pre-heat (28 °C, 30 °C) and gained heat tolerance after recover of 12 h, and a survival rate (14.7 %-49.

Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Ruditapes philippinarum and their involvement in the response to heat stress and Vibrio anguillarum infection.

E3 ubiquitin ligase (E3s) plays an important role in ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains. However, the role of HECT E3 ubiquitin ligase in mollusk was rarely explored. In this study, we performed a genome-wide analysis of the HECT domain-containing gene in Ruditapes philippinarum to identify and predict the structural and functional characterization of HECT genes in response to abiotic and biotic stress.

Molecular Mechanisms Underlying Tolerance in Revealed by Comparative Transcriptome Profiling.

The clam is an important species in the marine aquaculture industry in China. However, in recent years, the aquaculture of has been negatively impacted by various bacterial pathogens. In this study, the transcriptome libraries of showing different levels of resistance to challenge with were constructed and RNA-seq was performed using the Illumina sequencing platform.

Gene Co-Expression Network Analysis Reveals the Correlation Patterns Among Genes in Different Temperature Stress Adaptation of Manila Clam.

The Manila clam (Ruditapes philippinarum) is one of the most important aquaculture species and widely distributed along the coasts of China, Japan, and Korea. Due to its wide distribution, it can tolerate a wide range of temperature. Studying the gene expression profiles of clam gills had found differentially expressed genes (DEGs) and pathway involved in temperature stress tolerance.

MiRNA-mRNA Integration Analysis Reveals the Regulatory Roles of MiRNAs in Shell Pigmentation of the Manila clam (Ruditapes philippinarum).

The shell color of the Manila clam (Ruditapes philippinarum) is an economically important trait. We used high-throughput sequencing and transcriptome analysis to study the molecular mechanisms that underlie shell color formation and regulation in this species. We constructed small RNA libraries from mantle tissues from four shell color strains of Manila clam, subjected them to high-throughput sequencing.

Transcriptomic analysis of Manila clam Ruditapes philippinarum under lipopolysaccharide challenge provides molecular insights into immune response.

The Manila clam, Ruditapes philippinarum, is an economically important shellfish in marine aquaculture. A better understanding of the immune system in R. philippinarum will provide the basis for the development of strategies to mitigate the impact of infectious diseases affecting this species but can also be of relevance for other bivalves of commercial interest.

Modulated Expression and Activities of Enzymes After Oxidative Stress Induced by Aerial Exposure and Reimmersion.

, is an economically and scientifically important bivalve mollusk. Its tolerance of aerial exposure has long been considered an important trait for its survival under acute environmental stress. In this study, the effects of air exposure at high and low temperatures (28 and 4°C) on the survival, antioxidant and metabolic enzyme activities, and the expression of antioxidant and immune-related genes in were investigated.

Molecular cloning and expression analysis of tyrosinases () in four shell-color strains of Manila clam .

The Manila clam () is an economically important molluscan bivalve with variation in pigmentation frequently observed in the shell. In nature, tyrosinase is widely distributed in invertebrates and vertebrates, and plays a crucial role in a variety of physiological activities. In this study, a tyrosinase gene ( 9) was cloned and the expression level of genes ( 6, 9, 10, and 11) were investigated in different shell colors.

Expression analyses of C-type lectins (CTLs) in Manila clam under cold stress provide insights for its potential function in cold resistance of Ruditapes philippinarum.

Manila clam Ruditapes philippinarum is an economically and scientifically important marine bivalve species. C-type lectin acts as a pattern-recognition receptor (PPR), plays a crucial role in the innate immunity of invertebrates, and involves in pathogen recognition, and cell-cell interaction. In this study, six different types of C-type lectin genes, CTL-1, CTL-2, CTL-3, CTL-4, CTL-5, and CTL-6, were identified from the R.

Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity.

Ruditapes philippinarum is an economically important bivalve with remarkable diversity in its shell coloration patterns. In this study, we sequenced the whole genome of the Manila clam and investigated the molecular basis of its adaptation to hypoxia, acidification, and parasite stress with transcriptome sequencing and an RNA sequence analysis of different tissues and developmental stages to clarify these major issues. A number of immune-related gene families are expanded in the R.

Genetic variation and population structure of different geographical populations of based on mitochondrial gene COI.

The hard clam () is a commercially important shellfish in China. To provide valuable insights into management and conservation of , we investigated the genetic variation and population structure of by analysing samples from nine geographical populations. In this study, the genetic diversity and differentiation of nine populations of were assessed using the mitochondrial cytochrome oxidase subunit I (mtCOI) gene.

Analysis of differential gene expression by SRAP-cDNA in mantle tissue of with different external shell color.

Gene expression of two shell colors in were analyzed by sequence related amplified polymorphism-cDNA to screen the associated molecular markers. The two shell color genomes of were amplified using combinations of 30 primers; 11 pairs of primers showed differential fragments, and by recovery, cloning and sequencing, 18 different differential sequences were obtained. The sequencing results were analyzed by BlastX.

Molecular cloning and expression analysis of C-type lectin (RpCTL) in Manila clam Ruditapes philippinarum after lipopolysaccharide challenge.

The Manila clam, Ruditapes philippinarum, is one of the most commercially important marine bivalves. C-type lectins (CTLs) are pattern recognition receptors (PRRs) that play important roles in the identification and elimination of pathogens by the innate immune system. In this study, a new CTL (RpCTL) was identified in the Manila clam, R.

Publisher Correction: Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

RNA-Seq analysis of differentially expressed genes in the grand jackknife clam Solen grandis under aerial exposure.

Aerial exposure tolerance has been long considered as an important trait for the life survival under acute environmental stress. In this study, we utilized RNA-seq-based transcriptomic profiling to characterize the molecular responses of grand jackknife clam in response to aerial exposure. This assembly yielded 190,856 unigenes with an average length of 1147 bp, a minimum length of 201 bp, and a maximum length of 51,869 bp, with an N50 length of 1875 bp.