Comp. Biochem. Physiol. Part D Genomics Proteomics [JOURNAL]
Sun
200 papers
Comparative analysis of histological and transcriptomic characteristics in caudal muscles of nile crocodiles (Crocodylus niloticus), siamese crocodiles (Crocodylus siamensis), and their hybrids.
Wu Y, Nong Y, Zheng Y … +10 more , Fu S, Liu J, Ma F, Wang Y, Liu X, Ouyang B, Liu Q, Huang H, Guo Z, Wang M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 42242154 · Publisher ↗
Crocodylus niloticus and Crocodylus siamensis are high-value aquaculture species. C. niloticus is large-bodied but less abundant, while C. siamensis grows fast but is small-sized. Their hybrids combine parental advantage...
Crocodylus niloticus and Crocodylus siamensis are high-value aquaculture species. C. niloticus is large-bodied but less abundant, while C. siamensis grows fast but is small-sized. Their hybrids combine parental advantages, yet relevant research is scarce. This study compared the histological and transcriptomic characteristics of the caudal muscle across the three taxa. HE staining indicated that C. niloticus had significantly larger myofiber diameters (p < 0.05); C. siamensis had the smallest, and the myofiber density of hybrids was much closer to that of C. siamensis. Masson's trichrome staining indicated that C. niloticus had the thickest collagen fibers (p < 0.05), C. siamensis the thinnest, and hybrids exhibited highly similar histological traits to C. siamensis. C. niloticus had higher LDH and SDH activities in caudal muscles, whereas the hybrid crocodile indicated the highest CK activity. Transcriptomic analysis identified numerous differentially expressed genes (DEGs), which were enriched in growth, muscle metabolism, and energy allocation pathways via GO/KEGG annotations. PPI analysis screened 24 hub genes related to energy metabolism. This study systematically reveals caudal muscle differences, providing insights into growth-related molecular mechanisms and theoretical support for crocodile artificial breeding.
Genome-wide identification of the HSP70 superfamily in tropical sea cucumber Stichopus monotuberculatus and their expression analysis under low-salinity stress.
Chen Y, Yang X, Ye Y … +2 more , Zeng Y, Wang H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 42235441 · Publisher ↗
Heat shock proteins (HSPs) are a group of evolutionarily conserved molecular chaperones that serve as indispensable core regulators in preserving cellular homeostasis and orchestrating organismal stress responses. The tr...
Heat shock proteins (HSPs) are a group of evolutionarily conserved molecular chaperones that serve as indispensable core regulators in preserving cellular homeostasis and orchestrating organismal stress responses. The tropical sea cucumber Stichopus monotuberculatus, a high-value aquaculture species, is sensitive to fluctuations in environmental salinity-a challenge that has emerged as a critical bottleneck limiting its large-scale commercial cultivation. However, no systematic investigation has been conducted to characterize the HSP70 superfamily in S. monotuberculatus and elucidate its functional roles in salinity adaptation. In the present study, we performed a comprehensive genome-wide scan and identified 19 HSP70 superfamily genes in the S. monotuberculatus genome, with the HSP70IV subfamily showing remarkable gene expansion, containing 8 distinct copies. Phylogenetic analysis, conserved motif identification, and gene structure characterization demonstrated high evolutionary conservation within each HSP subfamily. These genes were unevenly distributed across the chromosomes of S. monotuberculatus, and prediction of cis-acting elements revealed that their upstream regulatory regions were enriched with numerous functional elements associated with stress response and immune regulation. Salinity stress experiments revealed that under severe low-salinity conditions (18‰), the expression levels of SmHSPA14L and multiple HSP70IV subfamily members were significantly elevated, while SmHYOU1D was significantly downregulated; in contrast, only subtle changes were detected in the expression of most HSP70 genes under moderate low-salinity stress (24‰). These findings strongly suggest that HSP70 genes, particularly the expanded HSP70IV subfamily, may act as key modulators in the low-salinity stress response. This work provides valuable insight into the molecular mechanisms underlying salinity adaptation in tropical sea cucumbers.
Genome-wide characterization of the TGF-β superfamily identifies bmp15, gdf9, and gsdf as sex-biased candidate regulators of gonadal differentiation in the synchronous hermaphrodite Plectropomus leopardus.
Li J, Liu M, Jin C … +6 more , Zheng D, Tang H, Zhai Z, Wang B, Bao Z, Hu J
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 42235440 · Publisher ↗
The transforming growth factor-β (TGF-β) superfamily plays conserved roles in vertebrate reproduction and gonadal sex differentiation. However, its genomic repertoire and sex-biased expression patterns remain unclear in...
The transforming growth factor-β (TGF-β) superfamily plays conserved roles in vertebrate reproduction and gonadal sex differentiation. However, its genomic repertoire and sex-biased expression patterns remain unclear in the leopard coral grouper (Plectropomus leopardus), a species with synchronous hermaphroditism. Here, we performed a genome-wide identification of the TGF-β superfamily, identifying 42 genes from the chromosome-level genome. Phylogenetic and synteny analyses indicated that segmental duplication under purifying selection contributed to family expansion. Expression profiling across multiple tissues and four gonadal developmental stages (undifferentiated, 120 dph; early differentiated, 15 months; mature testis, 3 years; mature ovary, 3 years) identified eight gonad-enriched genes, among which bmp15 and gdf9 exhibited pronounced female-biased expression, with transcripts localized exclusively to the oocyte cytoplasm, particularly in stage II-III oocytes. In contrast, gsdf showed male-biased expression and was localized in spermatogenic cells of the testis. These reciprocal expression patterns indicate that bmp15/gdf9 and gsdf are candidate factors associated with gonadal sex differentiation. Our study provides the first comprehensive characterization of the TGF-β superfamily in P. leopardus and highlights bmp15, gdf9, and gsdf as candidate sex-differentiation factors in this hermaphroditic species.
Construction of circRNA-miRNA-mRNA regulatory networks in the intestine of turbot (Scophthalmus maximus) following Vibrio anguillarum infection.
Liu Y, Zhang P, Chen C … +5 more , Zhang X, Cao M, Yang N, Li C, Fu Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 42235439 · Publisher ↗
Circular RNAs (circRNAs) play pivotal roles in post-transcriptional regulation by acting as molecular sponges for microRNAs (miRNAs) within the competitive endogenous RNA (ceRNA) network. However, the regulatory mechanis...
Circular RNAs (circRNAs) play pivotal roles in post-transcriptional regulation by acting as molecular sponges for microRNAs (miRNAs) within the competitive endogenous RNA (ceRNA) network. However, the regulatory mechanisms in teleost immune responses remain poorly understood. In this study, circRNA-miRNA-mRNA networks were investigated in turbot (Scophthalmus maximus) following Vibrio anguillarum infection to elucidate host-pathogen interactions. Through high-throughput sequencing of intestinal tissues, a total of 50 differentially expressed circRNAs (DE-circRNAs) (18 at 2 hpi, 16 at 12 hpi, 16 at 48 hpi), 212 DE-miRNAs (11 at 2 hpi, 70 at 12 hpi, 15 at 48 hpi), and 1774 DE-mRNAs were identified. Functional enrichment analyses (GO/KEGG) revealed significant associations with immune pathways, including the MAPK signaling pathway and gap junction. An integrated circRNA-miRNA-mRNA regulatory network was constructed, highlighting key interactions including novel_circ_0002573/DE-miR-27a-3p/FGB and novel_circ_0002423/novel_347/GNE, which may regulate inflammatory and antibacterial responses. The expression patterns of selected circRNAs, miRNAs and mRNAs were validated using qRT-PCR, confirming the reliability of the sequencing results. Importantly, fibrinogen beta chain (FGB) and CXCR4/CXCL12 signaling were identified as critical immune modulators. These findings provide insights of the ceRNA regulatory networks involved in teleost intestinal immunity and provide potential molecular targets for selective breeding of disease resistance in this species.
Evolutionary conservation of heat shock proteins in Blattodea and their roles in wing morphogenesis and ovarian development of Blattella germanica.
Shi Z, Zhang K, Cao Z … +2 more , Che Y, Wang Z
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Jun · PMID 42229281 · Publisher ↗
Heat shock proteins (Hsps) are essential molecular chaperones for protein homeostasis and stress responses. However, the Hsp repertoires and functions in Blattodea remain underexplored. Our genome-scale survey of nine Bl...
Heat shock proteins (Hsps) are essential molecular chaperones for protein homeostasis and stress responses. However, the Hsp repertoires and functions in Blattodea remain underexplored. Our genome-scale survey of nine Blattodea species revealed 37-46 conserved Hsp90, Hsp70, and DNAJ (Hsp40) genes, with DNAJ the most abundant and Hsp90 the least. Phylogenetic analysis confirmed the evolutionary conservation of three Hsp90, seven Hsp70, and 29 DNAJ subclades in Blattodea. Selection pressure analysis revealed predominant purifying selection (dN/dS ≪ 1) across lineages, strongest in DNAJ and highest in Hsp90 conservation. In Blattella germanica, expression of six representative BgHsp genes progressively increased during development, peaking in fifth-instar nymphs. Tissue expression profiling revealed that BgHspA1-2/3/4 were predominantly expressed in legs, BgDNAJB5 and BgHsp90AB1-2 were enriched in the fat body, and BgHsp90AB1 was highly expressed in the head. dsRNA injection targeting conserved Hsp gene regions achieved 61.9-94.1% knockdown of all six target genes. RNAi knockdown of six BgHsp genes disrupted wing morphogenesis, causing distinct phenotypes: wing whitening (56.7%, dsBgHspA1-4), unequal length (66.7%, dsBgHspA1-3; 76.7%, dsBgDNAJB5), and wing wrinkling (70%, dsBgHspA1-2; 63.3%, dsBgHsp90AB1; 76.7%, dsBgHsp90AB1-2). During ovarian formation, the developmental delay was most severe in the dsBgHsp90AB1 group, moderate in the dsBgHsp90AB1-2 and dsBgHspA1-2/3/4 groups, and weakest in the dsBgDNAJB5 group. Besides, knockdown significantly downregulated key developmental genes (apterous-a, nubbin, scalloped, ultrabithorax, wingless, and vitellogenin). These findings provide a reference for understanding the evolutionary patterns of Hsps in Blattodea, and offer mechanistic insights into the developmental regulation mediated by Hsps in this important public-health pest.
Comparative genomic and proteomic analysis reveals orthogroup structured evolution of tick protease inhibitors.
Mohankumar K, Rajitha M, Vijay M … +1 more , Srivastava A
Comp Biochem Physiol Part D Genomics Proteomics · 2026 May · PMID 42224754 · Publisher ↗
Protease inhibitors (PIs) play central roles in regulating endogenous proteolysis and host-parasite interactions in ticks. However, the evolutionary architecture underlying their diversification across tick lineages rema...
Protease inhibitors (PIs) play central roles in regulating endogenous proteolysis and host-parasite interactions in ticks. However, the evolutionary architecture underlying their diversification across tick lineages remains insufficiently resolved. Here, we performed a genome-wide comparative analysis of predicted proteomes from 14 tick species to systematically characterize PI repertoires. In total, 4931 putative PIs were identified and grouped into 20 families using the MEROPS classification system. Further, PI families such as Antistasin, WAP-type, and Pacifastin, which have not previously been systematically reported in tick genomes, were classified. Orthogroup inference demonstrated that PI expansion is structured at the level of evolutionary lineages rather than uniformly across families. By stratifying orthogroups according to duplication burden and taxonomic conservation, we identified a broadly conserved single-copy core under strong purifying selection. Motif level analysis of serpin reactive center loops further revealed conservation of inhibitory specificity within single copy orthogroups and diversification of key functional residues in duplication-associated lineages. Integration of secretion prediction and tissue-resolved proteomics from Hyalomma anatolicum and Rhipicephalus microplus demonstrated that evolutionary stratification is reflected at the protein level. Together, these findings provide an orthogroup-resolved evolutionary framework linking duplication dynamics, molecular evolution, and tissue-level protein deployment. This integrative approach offers a systematic basis for prioritizing conserved and diversified PI lineages for future functional and anti-tick intervention studies.
Molecular adaptation of caspase genes to salinity stress in the tropical sea cucumber Stichopus monotuberculatus: A comparative analysis across echinoderms.
Yang X, Ye Y, Qin LZ … +2 more , Zeng Y, Wang H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 May · PMID 42224753 · Publisher ↗
Apoptosis is an essential physiological process that plays a critical role in development and tissue homeostasis. Caspases, as central regulators of apoptosis, are crucial in controlling inflammation and cell death. In t...
Apoptosis is an essential physiological process that plays a critical role in development and tissue homeostasis. Caspases, as central regulators of apoptosis, are crucial in controlling inflammation and cell death. In this study, we investigated the caspase gene family in Stichopus monotuberculatus to explore their potential roles in salinity stress adaptation. Five caspase genes were identified from the genome of S. monotuberculatus, including Smcaspase3, Smcaspase6, Smcaspase8a, Smcaspase8b, and Smcaspase8c. Phylogenetic analysis revealed that these Smcaspase genes clustered into distinct caspase subfamilies and showed high conservation with homologs from other echinoderms and representative vertebrates. Conserved motif and gene structure analyses showed relatively similar structural patterns within each clade, whereas divergence was observed among different subfamilies. Promoter analysis identified numerous cis-acting elements related to gene regulation, immune response, and growth and development. Expression profiling under salinity stress showed that Smcaspase8a was significantly upregulated, particularly under prolonged stress, whereas the other genes exhibited limited transcriptional responses. Our findings highlight caspase function in salinity stress and provide the foundation of molecular salinity adaptation mechanisms in S. monotuberculatus.
Corrigendum to "Characteristics of the long non-coding RNA-mRNA regulatory network in American eel (Anguilla rostrata) during Vibrio harveyi infection" [Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics 59 (2026) 101871].
Sun G, Wu L, Tang Y … +2 more , Hong S, Guo S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 May · PMID 42215347 · Publisher ↗
Abstract loading — click title to view on PubMed.
Comparative analysis of gut microbiota in yaks under different feeding management strategies during cold seasons.
Zhang Z, Cao Q, Chen Y … +6 more , Yu Y, Yang X, Zhang Z, Liu Y, Lv W, Dong Q
Comp Biochem Physiol Part D Genomics Proteomics · 2026 May · PMID 42214847 · Publisher ↗
Yaks (Bos grunniens) are crucial for the livelihoods of pastoral communities in cold regions, where feed scarcity during the cold season poses challenges to their health and productivity, underscoring the necessity of un...
Yaks (Bos grunniens) are crucial for the livelihoods of pastoral communities in cold regions, where feed scarcity during the cold season poses challenges to their health and productivity, underscoring the necessity of understanding how dietary management influences the gut microbiota. In this study, 24 yak steers matched for body weight and health status were randomly allocated to four groups: natural grazing or indoor feeding with roughage-to-concentrate ratios of 50:50, 70:30, or 90:10. Fecal samples were collected for 16S rDNA sequencing and subsequent functional prediction of the microbiota. The results showed that Firmicutes and Bacteroidetes were the dominant phyla across all groups, and UCG-005 and Rikenellaceae_RC9_gut_group were the predominant genera. Concentrate supplementation during the cold season significantly enhanced microbial richness and diversity, with the 70:30 ratio exerting the most pronounced beneficial effects on microbiota structure and key taxa enrichment. These findings highlight the critical role of dietary management in shaping the yak gut microbiota during cold seasons and suggest that the 70:30 ratio optimally improves microbial community structure, thereby promoting yak health and productivity under harsh climatic conditions. Future research should explore the long-term implications of such dietary strategies.
Cloning of two Hsp70 genes and association analysis between SNP haplotypes and high temperature tolerance trait in red swamp crayfish (Procambarus clarkii).
Zhang S, Tan Y, Peng B … +2 more , Feng Z, Bai X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 May · PMID 42202727 · Publisher ↗
Aquaculture is suffering the challenge from high temperature climate. Two Hsp70 genes, PcHsp70-1 and PcHsp70-2, as key genes involved in the high temperature tolerance of red swamp crayfish (Procambarus clarkii) were ide...
Aquaculture is suffering the challenge from high temperature climate. Two Hsp70 genes, PcHsp70-1 and PcHsp70-2, as key genes involved in the high temperature tolerance of red swamp crayfish (Procambarus clarkii) were identified and cloned in this study. Their molecular features and expression patterns were characterized, revealing the distinct tissue-specific upregulation expression under high temperature stress (33 °C). Two SNPs, PcHsp70-1 (SNP258) and PcHsp70-2 (SNP555) were examined to associate with high temperature tolerance in three populations (n = 675). The genotypes of PcHsp70-1-SNP258 (GA) and PcHsp70-2-SNP555 (TT) were significantly associated with stronger high temperature tolerance. Notably, individuals carrying the haplotype of Hap I (GG + TT) showed a survival rate exceeding 70% under high temperature stress, whereas, the Hap VIII (AA + CT) showed it at 5.2%. RNA interference of PcHsp70-1 resulted in a significant decrease expression of the gene GSH-Px and its encoding protein (glutathione peroxidase) activity, and damage in intestinal tissue under high temperature stress. The transcriptome result revealed that PcHsp70-1 participates in regulation of the pathways related to cytoskeletal construction, immune response, apoptosis, and antioxidant defense. These findings indicate that PcHsp70 genes are crucial for the cellular stress response under high temperature stress. The developed Kompetitive Allele Specific PCR (KASP) markers provide valuable tools for the marker-assisted selection of high temperature tolerant crayfish varieties, supporting the sustainable development of aquaculture under the challenge of global warming.
Characteristics of the long non-coding RNA-mRNA regulatory network in American eel (Anguilla rostrata) during Vibrio harveyi infection.
Sun G, Wu L, Tang Y … +2 more , Hong S, Guo S
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42172972 · Publisher ↗
Vibrio harveyi is a highly pathogenic bacterium causing severe septicemia in American eel (Anguilla rostrata), yet the regulatory roles of long non-coding RNAs (lncRNAs) in the host immune response remain largely unexplo...
Vibrio harveyi is a highly pathogenic bacterium causing severe septicemia in American eel (Anguilla rostrata), yet the regulatory roles of long non-coding RNAs (lncRNAs) in the host immune response remain largely unexplored. In this study, American eels were challenged with V. harveyi, and kidney tissues were collected at 0-, 12-, 24-, 36-, 48 and 60-h post-infection (hpi) for bacterial load detection. Histopathological lesions and transcriptomic profiles (strand-specific RNA sequencing) were systematically analyzed at 0-, 24-, 36 and 48 hpi. Co-expression and co-location networks were constructed to identify interactions between differentially expressed (DE) lncRNAs and their target mRNAs. Bacterial load increased progressively, peaking at 48 hpi with a 100-fold higher load than at 12 hpi, accompanied by severe renal damage including tubular vacuolation and glomerular disintegration. Transcriptome analysis identified 76 shared DE-lncRNAs and 2230 shared DE-mRNAs across three infected time points from 24 to 48 hpi. Among these, 673 shared DE-mRNAs targeted by 60 shared DE-lncRNAs were significantly enriched in seven immune-related Gene Ontology (GO) terms and 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including complement activation, TNF signaling, and pathogen defense. Network analysis further revealed 24 key DE-lncRNAs that potentially regulate 600 DE-mRNAs via trans-acting mechanisms and 11 via cis-acting mechanisms. This study presents the first systematic characterization of lncRNA-mRNA regulatory networks in American eel during V. harveyi infection. The identified DE-lncRNAs and their target genes provide new insights into the molecular basis of host immune defense and offer potential targets for disease control in eel aquaculture.
Transcriptome reveals key genes involved in oxidative stress, lipid metabolism and signal transduction in response to low temperature in hybrid puffer (Takifugu obscurus ♀ × Takifugu rubripes ♂).
Gao Y, Wang C, Wang Y … +6 more , Zhao X, Yao Y, Wu J, Wang Y, Zhao Z, Shi Y
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42167052 · Publisher ↗
Pufferfish is an economically important aquaculture species in Asia, yet cold stress during overwintering can markedly increase risks and costs. Hybrid puffer (Takifugu obscurus ♀ × Takifugu rubripes ♂) was bred integrat...
Pufferfish is an economically important aquaculture species in Asia, yet cold stress during overwintering can markedly increase risks and costs. Hybrid puffer (Takifugu obscurus ♀ × Takifugu rubripes ♂) was bred integrating growth advantage and freshwater acclimation traits of its parents. To gain further insight into the physiological and molecular responses to cold tolerance in hybrid puffer, adult fish were exposed to two cold stress endpoints during a stepped cooling treatment (CS13 and CS8), with 25 °C as the control (CK). Oxidative stress indicators and liver transcriptomes were analyzed. Antioxidant enzyme activities generally increased under cold stress in a tissue-dependent manner. RNA-seq identified 6732, 6127, and 2504 differentially expressed genes (DEGs) in CS13 vs. CK, CS8 vs. CK, and CS8 vs. CS13, respectively. Functional enrichment highlighted metabolic pathways, metal ion binding, cytokine-cytokine receptor interaction, arachidonic acid metabolism, ECM-receptor interaction, and TGF-β-related signaling. Integrated DEG, weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI), and Venn analyses identified 25 candidate cold-responsive genes (CRGs), and qRT-PCR validation of 12 DEGs supported the transcriptomic results. These findings suggest that hybrid puffer responds to cold stress by coordinating lipid metabolism, antioxidant defense, immune regulation, and FoxO, Hedgehog, PPAR, and TGF-β signaling pathways. This study advances the understanding of molecular mechanisms of thermal adaptation in fish and supports the breeding of cold-tolerant pufferfish to alleviate risks and costs in overwintering aquaculture.
Phenotypic characterization and hepatopancreatic transcriptomics reveal the regulatory mechanisms of precocious maturation in Macrobrachium nipponense.
Zhu JP, Cao XD, Luo ZQ
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42150459 · Publisher ↗
Precocious maturation is a challenge in Macrobrachium nipponense culture, leading to reduced yields and germplasm degradation. However, the regulatory mechanisms underlying this phenomenon remain uncharacterized. In this...
Precocious maturation is a challenge in Macrobrachium nipponense culture, leading to reduced yields and germplasm degradation. However, the regulatory mechanisms underlying this phenomenon remain uncharacterized. In this study, precocious individuals were identified during a five-month culture encompassing broodstock selection and larval rearing. The precocious group exhibited significantly lower body length, body weight, and fecundity (P < 0.05), with the precocious individuals accounting for approximately 13.56% of the population. Comparative transcriptomic analysis of the hepatopancreas identified 373 differentially expressed genes (DEGs), comprising 201 upregulated and 172 downregulated genes. Functional enrichment analysis highlighted three key reproductive development-related pathways: MAPK, estrogen, and Wnt signaling. Within these pathways, AP-1 was consistently downregulated, while MKNK1-like and HSP70-like exhibited pathway-specific expression patterns (downregulated and upregulated, respectively). These findings, validated by qRT-PCR, suggest a cross-pathway "transcription-translation dual-gate" suppression mechanism. This mechanism likely facilitates the physiological transition from a high-biosynthesis state before precocity to a state of homeostatic maintenance. The results provide a valuable reference for future research on the reproductive regulation of M. nipponense.
Microbial community and water quality changes associated with the disease occurrence in northern snakehead (Channa argus) aquaculture ponds.
Liu Z, Chen Z, Sun R … +7 more , Liu D, Wang Z, Yu Y, Li J, Sun C, Li B, Li W
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42150458 · Publisher ↗
Prokaryotic and eukaryotic communities in aquaculture water play critical roles in fish health, yet their relationships with water quality during disease outbreaks remain poorly understood. Addressing this critical knowl...
Prokaryotic and eukaryotic communities in aquaculture water play critical roles in fish health, yet their relationships with water quality during disease outbreaks remain poorly understood. Addressing this critical knowledge gap, this study provides novel insights by systematically profiling the concurrent shifts in both prokaryotic and eukaryotic microbiomes and their specific associations with water quality variations in intensive northern snakehead (Channa argus) ponds. In this study, water quality parameters and microbial community were compared between healthy and diseased C. argus aquaculture ponds. The results showed that diseased ponds exhibited higher NH-N concentrations and lower bacterial richness compared to healthy ponds. Microcystis and other potentially harmful cyanobacteria were markedly enriched in diseased ponds, while certain taxa such as unclassified_Synechococcaceae and CL500_29_marine_group were reduced. In eukaryotic communities, an increased relative abundance of specific bloom-forming algae and opportunistic protozoa was observed in diseased ponds. Correlation analysis revealed strong positive associations between NH-N levels and harmful cyanobacterial abundance, suggesting that nitrogen enrichment was associated with microecological imbalance during disease outbreaks. These findings offer insights into the role of water quality management, particularly NH-N control, which may be key to maintaining a stable microbial community and preventing disease in intensive C. argus aquaculture.
Proteomic insights into larval stages of coffee leaf miner (Leucoptera coffeella): A step towards the development of pest management strategies.
Nascimento BO, Palhares ARM, Santos IR … +6 more , Mendes PDN, Ribeiro DG, Togawa RC, Albuquerque E, Fontes W, Mehta A
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42142440 · Publisher ↗
Coffee, one of the most popular beverages worldwide, is among the main commodities driving the economy, not only in Brazil but in the entire world.Leucoptera coffeella, also known as Coffee Leaf Miner (CLM), is considere...
Coffee, one of the most popular beverages worldwide, is among the main commodities driving the economy, not only in Brazil but in the entire world.Leucoptera coffeella, also known as Coffee Leaf Miner (CLM), is considered one of the most significant coffee pests, responsible for yield losses of up to 70% in production. In this context, this work aimed to identify the protein profiles in the different stages of CLM larvae life cycle, generating valuable and innovative information for this organism. Proteins were identified in two analyses with different approaches, one homology-based and the other draft genome-based. Among the differentially abundant proteins (DAPs), 141 were characterized using the data from Plutella xylostella, and 324 were identified using the data from L.coffeella itself. Both proteomic analyses resulted in the discovery of important proteins associated with fundamental functions for the organism and with high potential for use in pest control. Seven proteins were subjected to analysis via RT-qPCR to confirm their relative abundance, identifying proteins that play important roles in CLM adaptation to environmental conditions. The results obtained provide important information in the pursuit of biocontrol strategies aiming at the reduction of pesticide use in crop production.
Seasonal metabolite profiling of Thyone aurea from Saldanha Bay, South Africa.
Upton C, Prinsloo G, Steenkamp PA … +1 more , Okpeku M
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42140138 · Publisher ↗
The pursuit of natural therapeutic drugs has fuelled interest in metabolomics, particularly marine metabolomics, with sea cucumbers standing out for their high nutritional value and potential for bioactive metabolites. H...
The pursuit of natural therapeutic drugs has fuelled interest in metabolomics, particularly marine metabolomics, with sea cucumbers standing out for their high nutritional value and potential for bioactive metabolites. However, limited research, especially in Southern Africa, has resulted in significant knowledge gaps regarding the value of lesser-known species, contributing to the exploitation of select high-value species due to rising market demand for holothurian products. This study aimed to address these gaps by characterising the metabolic profile of three body tissue extracts-body wall, gonad, and gut/mesentery-from Thyone aurea, an endemic species found along the Western Coast of Southern Africa, using untargeted H NMR metabolomics and full-scan UPLC-QTOF-MS/MS. The results revealed a diverse array of amino acids, sugars, and organic acids, with the gut/mesentery tissue and spring-summer extracts exhibiting the highest potential for variable metabolites. However, these patterns represent relative signatures requiring further validation with fresh tissues. While some compounds may be integral to sea cucumber physiology, the origin of others remains unclear, warranting further research into holothurian metabolic pathways and the potential impact of dietary sources and microbial activity on the metabolome. Therefore, this study emphasises the importance of expanding research to understand the metabolic responses to environmental changes, which could offer valuable insights to support conservation and sustainable cultivation strategies. Moreover, these findings underscore the need to explore lesser-known species as alternative resources in cultivation strategies to promote sustainable holothurian resources for commercial, pharmaceutical, and nutritional applications. Overall, this research enhances our understanding of sea cucumber biology and underscores the importance of incorporating a broader range of species in scientific research.
Ionomic, metabolomic, and enzymatic responses of the sea cucumber Apostichopus japonicus to single and combined salinity and metal stress.
Wang D, Du X, You L … +5 more , Zhan J, Ji C, Sun J, Li S, Wu H
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42140137 · Publisher ↗
Desalination brine discharge poses emerging threats to benthic marine organisms through combined salinity stress and metal contamination. This study investigated the individual and combined effects of salinity (35 ppt) a...
Desalination brine discharge poses emerging threats to benthic marine organisms through combined salinity stress and metal contamination. This study investigated the individual and combined effects of salinity (35 ppt) and metal exposure (Cu, Fe, and Cd) on the sea cucumber Apostichopus japonicus by integrating ionomics, enzymatic biomarkers, and LC-MS/MS-based metabolomics. After 16 days of exposure, only Cd and Cu significantly accumulated in body wall tissues. Combined high salinity and metals contributed to a slight increase in Fe accumulation and a decrease in Cu accumulation. Metal exposure disrupted the balance of metal elements (e.g., Mn, Zn, Co, Ni), with interactive effects modulated by salinity. Antioxidants and immune-related enzymes (SOD, CAT, ACP, ALP, Na/K-ATPase) responded distinctly to metal and salinity stress, with salinity often dominating the combined stress response. Metabolomic profiling revealed that Cd and Cu under ambient salinity induced widespread metabolic perturbations, altering metabolites related to lipid metabolism, glutathione metabolism, and saponin biosynthesis. Notably, high salinity (35 ppt) alleviated some metal-specific metabolic effects, while salinity alone caused significant downregulation of bioactive saponins and flavonoids. These findings demonstrate that salinity modulates metal toxicity in sea cucumbers, with potential consequences for immune function, oxidative defense, and nutritional value. This study provides novel insights into the ecological risks of desalination brine discharge on benthic ecosystems.
Genome-wide identification and expression analysis of calmodulin and calmodulin-like (CaM and CML) gene family in Magallana gigas.
Zhang Z, Liu C, Lu H … +4 more , Wang J, Shan W, Wang L, Song L
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42134298 · Publisher ↗
Ca is a multifunctional second messenger that can regulate the activities of hormones and environmental signals related to biotic and abiotic stresses, playing a role in a wide range of cellular processes and influencing...
Ca is a multifunctional second messenger that can regulate the activities of hormones and environmental signals related to biotic and abiotic stresses, playing a role in a wide range of cellular processes and influencing almost all aspects of life. In organisms, calmodulin (CaM) and calmodulin-like proteins (CML) can sense and decode the regulatory signals of Ca through the EF-hand (a helix-loop-helix structure) domain. In this study, 7 CaM family members and 55 CML family members were identified in Magallana gigas. All MgCaM and MgCML genes distributed unevenly on 7 chromosomes, with 90% of the genes located on chromosomes 6 and 5. Furthermore, the expression of MgCaMs and MgCMLs was tissue-specific in M. gigas, and most of the genes expressed highly in gill, labial palp, adductor muscle and female gonad. Through the analysis of transcriptome data, it was found that the MgCaM and MgCML genes showed specific expression patterns in response to abiotic stress. When encountering heat-shock stress, different genes responded at different time points. In response to acidification stimulation, genes in the outer edge of mantle could respond to the stimulus obviously. The expression patterns of five representative genes were validated by RT-qPCR under acidification. This study systematically analyzed the characteristics of oyster CaM and CML gene families, revealing their crucial roles in the environmental adaptation mechanisms of M. gigas.
Investigating the influence of lncRNA-mRNA interactions on Mytilus coruscus growth using transcriptome data.
Zhao X, Dong X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42127708 · Publisher ↗
Mytilus coruscus (M. coruscus) is a high-value marine aquaculture species with significant economic importance. Traditional semi-artificial seed collection methods in coastal waters are insufficient to meet current deman...
Mytilus coruscus (M. coruscus) is a high-value marine aquaculture species with significant economic importance. Traditional semi-artificial seed collection methods in coastal waters are insufficient to meet current demands for improved M. coruscus varieties exhibiting desirable traits such as enhanced growth rates and larger body size. Long non-coding RNAs (lncRNAs) are known to regulate critical cellular processes, including proliferation, development, and the cell cycle. To investigate potential regulatory influences on M. coruscus growth, comparative transcriptomic analyses were performed on specimens exhibiting divergent growth phenotypes (fast-growing and slow-growing) reared under identical conditions. Foot tissue samples were aseptically collected from each group for full transcriptome sequencing. Sequencing analysis identified 91 differentially expressed long non-coding RNAs (DE-lncRNAs), comprising 55 upregulated and 36 downregulated transcripts. GO analysis showed that the target or source genes of these differentially expressed RNAs were mainly enriched in the categories of biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed several signaling pathways potentially involved in growth regulation, notably TGF-beta, VEGF, Wnt, and mTOR signaling pathways. Among the identified DE-lncRNAs, MSTRG.10759.1 exhibited the highest expression levels and is predicted to regulate the BVES and RASV genes, as well as the ST13/HIP protein. Interaction network analysis of lncRNA-mRNA pairs highlighted two core target genes, PLOD1 and ANK, suggesting their potential regulatory roles in mussel growth. These findings offer new perspectives on the molecular mechanisms underlying growth in mytilids and provide foundational data for the development of molecular marker-assisted breeding strategies to produce fast-growing mussel strains.
Population genomics and GWAS reveal genetic basis of shell traits in Manila clam (Ruditapes philippinarum).
Wang J, Wei D, Liu Z … +3 more , Zhou L, Wu B, Sun X
Comp Biochem Physiol Part D Genomics Proteomics · 2026 Sep · PMID 42114498 · Publisher ↗
The Manila clam (Ruditapes philippinarum) is a key aquaculture species in China's intertidal zones, where body size and growth rates strongly influence market preference and commercial value. Nevertheless, the genetic ba...
The Manila clam (Ruditapes philippinarum) is a key aquaculture species in China's intertidal zones, where body size and growth rates strongly influence market preference and commercial value. Nevertheless, the genetic basis of shell traits and population structure of coastal stocks remain poorly understood. Here, we performed RAD-seq sequencing of 301 individuals from 10 populations along the Chinese coast to analyze population genetics and conduct a genome-wide association study (GWAS). Population genetic analyses revealed nucleotide diversity (π) ranging from 0.259 to 0.273, with the Haiyang population showing the highest diversity. The Hongdao population exhibited the highest inbreeding coefficient (F = 0.469) and lowest observed heterozygosity (H = 0.144), whereas the Sanya population had the lowest inbreeding (F = 0.235) and highest heterozygosity (H = 0.199). Genetic differentiation (F) was greatest between the Rizhao and Donggang populations (F = 0.0484). In contrast, unexpectedly low differentiation between the geographically distant Donggang and Beihai populations (F = 0.0122) suggests the possible anthropogenic translocation and gene flow. Using a mixed linear model (MLM) for GWAS, we identified 142 significant SNPs associated with shell traits after Bonferroni correction. Notably, 139 SNPs distributed across chromosomes from 1 to 19 were linked to shell thickness, while only three SNPs on chromosome 13 were associated with shell width. Within 50 kb flanking regions of these loci, 453 candidate genes were annotated. Functional enrichment analyses (GO and KEGG) highlighted seven candidate genes (e.g., Calml3, MC1R, and TBXT) that may be associated with biomineralization, calcium signaling, and shell-related trait variation. Additionally, a selective sweep analysis comparing Beihai and Hongdao populations identified 118 candidate genes located in putative outlier regions (top 1% of F and π ratio). Enrichment of these regions revealed three candidate genes (Acp5, SLC6A1, and FNTA) related to metabolism and cellular transport, potentially reflecting local adaptation or artificial selection. Together, these findings provide important insights into the germplasm resources of R. philippinarum and offer valuable genomic targets for marker-assisted selection to improve shell traits in aquaculture breeding programs.
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