Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Identification of sex-related genes across bivalves reveals key genes in gonad development and sex reversal","authors":"Yifan Li,&nbsp;Huiqi Li,&nbsp;Meizheng Chen,&nbsp;Yetao Zeng,&nbsp;Jianming Ye,&nbsp;Xixi Duan,&nbsp;Weili Wang,&nbsp;Hongkuan Zhang,&nbsp;Huaiping Zheng","doi":"10.1016/j.cbd.2025.101506","DOIUrl":"10.1016/j.cbd.2025.101506","url":null,"abstract":"<div><div>The complex and diverse sexual reproduction patterns and multiple sex types of mollusks make it important to elucidate their sex mechanisms. Recent studies have demonstrated the crucial roles of <em>Dmrt</em>, <em>STAT</em>, and <em>Sox</em> genes in animal sex determination/differentiation. However, the comprehensive comparison of these genes in different bivalves is limited. In this study, 33 bivalves were analyzed to investigate the sequence characteristics, phylogenetic relationships, and expression profiles of these genes. Total of 112 Dmrt genes, 88 STAT genes and 229 Sox genes were identified in 33 bivalves. Phylogenetic analysis grouped the <em>Dmrt</em>, <em>STAT</em>, and <em>Sox</em> genes into 4, 3, and 7 groups, respectively. By comparing gene family number and sequence differences, we observed expansion and contraction in the <em>Dmrt</em> and <em>STAT</em> family genes, as well as sequence variations in <em>Dmrt-01</em> and <em>SoxH</em> among different bivalves, suggesting their molecular adaptations to diverse sexual mechanisms. Expression profiles of these genes in noble scallop <em>Chlamys nobilis</em> revealed that <em>CnDmrt-01</em> and <em>CnSox-07</em> (<em>SoxH</em>) is predominantly expressed in testis, suggesting their male-specific role in gonad development and maturation. A higher expression level of <em>CnSox-01/03</em> (<em>Sox-B1/C</em>) in ovary suggest their essential role in ovary development<em>.</em> These genes also showed significantly higher expression level during sex reversal, suggesting their crucial roles in this process. Additionally, transcriptome data from other bivalves further support that the sexual expression patterns of <em>Dmrt-01</em> and <em>Sox-B1/C/H</em> are conserved across most bivalves. The results of this study will provide insights into these sex-related genes and useful information to better understand mechanisms of gonad development and sex reversal in mollusc.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101506"},"PeriodicalIF":2.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143783525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic signatures associated with developmental transitions in the gill of lake sturgeon (Acipenser fulvescens)","authors":"William S. Bugg ,&nbsp;Madison L. Earhart ,&nbsp;Matt J. Thorstensen ,&nbsp;Patricia M. Schulte ,&nbsp;W. Gary Anderson ,&nbsp;Ken M. Jeffries","doi":"10.1016/j.cbd.2025.101505","DOIUrl":"10.1016/j.cbd.2025.101505","url":null,"abstract":"<div><div>The developmental transition from the larval to juvenile stage, represents one of the highest periods of mortality for many species of fish. Thus, understanding the factors that may influence susceptibility to environmental stressors at this vulnerable stage is likely to be important for predicting responses to environmental change. Here, we compared gill mRNA transcript abundance during this critical developmental transition in fish from two geographically distinct populations of lake sturgeon (<em>Acipenser fulvescens</em>) that experience highly divergent thermal environments. Throughout the developmental transition from the larval to juvenile stage (30 to 60 days post-fertilization), the ‘colder’ northern population exhibited differential expression of approximately twice as many transcripts as compared to their ‘warmer’ southern counterparts. Transcriptional modifications that were conserved across both populations during the transition from the larva to juvenile stage were involved in histone methylation, protein binding, and apoptotic signaling associated with cell death and turnover. The northern population, specifically, had increased changes associated with GTPase signaling activation, cell surface proteins, mitochondrial and epithelial development which may have contributed to the larger magnitude of transcriptional change in this population, compared to their southern counterparts. Together these findings demonstrate the impacts of transcriptional shifts in the gill during development in lake sturgeon, as well as the potential for population-specific developmental processes.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101505"},"PeriodicalIF":2.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study on the potential impact of sustained high temperatures during non-breeding season on largemouth bass","authors":"Yue Chen ,&nbsp;Jun Wang ,&nbsp;Chun Xiu Jin ,&nbsp;Hao Wu ,&nbsp;Wei He ,&nbsp;Zi Xian Wu ,&nbsp;Zi Tong Wang ,&nbsp;Yi Zhou Hong ,&nbsp;Zi Hang Yang ,&nbsp;Song Yang ,&nbsp;Fei Biao Song ,&nbsp;Jian Luo ,&nbsp;Jun Long Sun","doi":"10.1016/j.cbd.2025.101501","DOIUrl":"10.1016/j.cbd.2025.101501","url":null,"abstract":"<div><div>With the growing scale of largemouth bass breeding, the demand for seedlings is increasing. As global temperatures rise, it is crucial to study the effects of high temperature their regulatory mechanisms in largemouth bass. In this study, we simulated a high water temperature (28 °C) in the non-breeding season in aquaculture ponds for 28 days to examine the growth, reproduction, metabolism, apoptosis, and methylation markers in largemouth bass; transcriptome analysis was also performed. The results showed no significant difference in body weight between male and female largemouth bass. However, the high-temperature exposed females had reduced growth hormone (GH) and estradiol (E2) levels and elevated cortisol levels. They also showed upregulated expression of <em>AR</em>, <em>cyp19a</em>, <em>igf</em>, <em>fshβ</em>, and <em>lhβ</em> in ovarian tissue. Transcriptomic comparisons between temperature treatments revealed 963 differentially expressed genes in females and 700 in males. Both the ECM receptor interaction and PPAR signaling pathways were significantly enriched. High-temperature enhanced the lipid metabolism process through the PPAR signaling pathway. High temperatures increased oxidative stress in females, which corresponded with increases in SOD, CAT, and GSH-Px, likely to counteract the excess reactive oxygen species. Moreover, endoplasmic reticulum stress was activated, indicated by increases in IRE1 and ATF6, leading to the upregulation of apoptosis-related genes and ovarian cell apoptosis. At high temperature, 5-MC%, demethylase, and methyltransferase were not different in females, while 5-MC% and methyltransferase were higher and demethylase was lower in males. In summary, sustained high temperature affected ovarian development by altering the expression of hormone and gonad related genes and inducing endoplasmic reticulum stress leading to ovarian cell apoptosis. However, low demethylase activity and high genome-wide methylation in the test is suggested that high temperatures may affect testis development via methylation, potentially impacting offspring production.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101501"},"PeriodicalIF":2.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143759898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of sulfate on the physiology, biochemistry, and intestinal transcriptome of Scylla paramamosain under low-salinity conditions","authors":"Gao Gao ,&nbsp;Yun Hu ,&nbsp;Kangxiang Qin ,&nbsp;Ziwei Fan ,&nbsp;Chunlin Wang ,&nbsp;Huan Wang","doi":"10.1016/j.cbd.2025.101502","DOIUrl":"10.1016/j.cbd.2025.101502","url":null,"abstract":"<div><div>Sulfate, a key component of seawater and sulfate-saline-alkali soil, critically impacts aquatic species' physiology. The aim of this experiment was to investigate the effects of sulfate concentration on the growth, survival, microstructure of gills and hepatopancreas, as well as the intestinal immune response and molecular mechanisms of <em>Scylla paramamosain</em>. The experimental groups were categorized as S1 (0 g/L sulfate, sulfate-free), S2 (1 g/L sulfate, optimal concentration), and S3 (2 g/L sulfate, high sulfate concentration). The results showed that with the increase of sulfate concentration in the experimental water, Survival and weight growth rates initially increased but declined at higher sulfate concentrations (<em>P</em> &lt; 0.05), while molting rates progressively decreased. The intestinal ACP and AKP levels in S2 were significantly higher than those in S1 and S3 (<em>P</em> &lt; 0.05). AST and ALT in the S2 group showed no significant difference from those in the S3 group (<em>P</em> &gt; 0.05) but were significantly lower than those in the S1 group (<em>P</em> &lt; 0.05). Sulfotransferases in the S2 group were significantly lower than those in the S1 and S3 groups (<em>P</em> &lt; 0.05). Short-term (72 h) microscopic observations of the gills and hepatopancreas revealed that the gills in both the S1 and S3 groups exhibited thickening of the gill filaments and rupture of the cuticle layer, while the hepatopancreatic tissue in the S3 group also showed enlargement of intercellular spaces, fracture of the basement membrane, and blurred boundaries. Transcriptome sequencing of the <em>S. paramamosain</em> intestine revealed significant upregulation of sulfotransferases in both S1 and S3 groups. GO annotation of DEGs indicated similar responses of <em>S. paramamosain</em> to sulfate-free and high-sulfate environments, maintaining physiological stability by activating protein processing pathways, enhancing blood-lymph coagulation, and regulating redox balance. KEGG analysis revealed that sulfate-free environments predominantly enriched lipid metabolism and secondary metabolism pathways. While those enriched in high-sulfate environments were mainly related to amino acid metabolism and secondary metabolism. The results indicate that both sulfate-free and high-sulfate concentrations affect the growth, survival, and molting rates of <em>S. paramamosain</em>, as well as inducing immune responses in the intestine. In the short term, they can cause structural changes in the gills and hepatopancreas. The intestinal transcriptome expression shows a similar response pattern, but the metabolic pathways differ. This study provides theoretical support and technical guidance for the cultivation of <em>S. paramamosain</em> under low-salinity conditions with sulfate-type saline-alkali water.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101502"},"PeriodicalIF":2.2,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143759897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression profiling of the hemoglobin gene family under hypoxia stress in Sillago sihama","authors":"Lingwei Kong ,&nbsp;Minghui Ye ,&nbsp;Jiru Tan ,&nbsp;Wenjing Lai ,&nbsp;Jiaxin Liao ,&nbsp;Yulei Zhang ,&nbsp;Huapu Chen ,&nbsp;Yang Huang ,&nbsp;Guangli Li ,&nbsp;Changxu Tian","doi":"10.1016/j.cbd.2025.101500","DOIUrl":"10.1016/j.cbd.2025.101500","url":null,"abstract":"<div><div>Hemoglobin (Hb) plays a pivotal role in oxygen transport and is essential for the adaptive response to hypoxic stress. Studying the molecular evolution characteristics and expression pattern of <em>S. sihama</em> Hb gene family can provide theoretical basis for further revealing the roles of the <em>Hb</em> genes against hypoxia stress. This study aimed to identify the molecular evolution characteristics and expression patterns of <em>Hb</em> genes in <em>S. sihama</em>. Utilizing bioinformatics methods, we identified ten members of the <em>Hb</em> gene family within the whole genome of <em>S. sihama</em>, located on chromosomes LG16 and LG21 in a tandem repeat pattern. Phylogenetic analysis classified the Hb gene family into two subfamilies (alpha and beta), showing close relationships with the Hb gene family members of the large yellow croaker (<em>Larimichthys crocea</em>). Both phylogenetic and collinearity analysis indicated the conservation of <em>Hb</em> genes throughout evolution. The nonsynonymous substitution rate / synonymous substitution rate (<em>Ka</em>/<em>Ks</em>) results showed that its evolution was purifying selection. RNA-seq and qRT-PCR analyses revealed that five <em>Hb</em> genes were highlighted high expression levels in the heart and liver of <em>S. sihama</em>, with <em>sshba1.4</em>, <em>sshbad</em>, and <em>sshba1</em> showing significant up-regulation in response to hypoxic stress. In summary, this study highlights the vital role of the Hb gene family in the hypoxic stress response of <em>S. sihama</em>, suggesting their potential as crucial candidate genes for regulating environmental stress in this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101500"},"PeriodicalIF":2.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic and proteomic analyses reveal the diverse components in the venom of a recently described spider species Macrothele washanensis","authors":"Mengmeng Zhang ,&nbsp;Wenzheng Cai ,&nbsp;Menghui Yang ,&nbsp;Mengying Zhang ,&nbsp;Luke R. Tembrock ,&nbsp;Zhibin Yang ,&nbsp;Heng Liu ,&nbsp;Zizhong Yang","doi":"10.1016/j.cbd.2025.101491","DOIUrl":"10.1016/j.cbd.2025.101491","url":null,"abstract":"<div><div>Spider venom has been shown to possess a variety of pharmacological activities with promising applications in biomedical and agricultural sciences. However, the molecular structure and functions of these toxins have only been revealed for a few species. In this study, we unveiled the venom composition of <em>Macrothele washanensis</em> venom for the first time using transcriptomics, proteomics, and bioinformatic analyses. A total of 147,492,716 Illumina valid reads were obtained from the transcriptome of the venom glands, and 3,010,024 unigenes were assembled to predict 69 putative toxin sequences, which were classified into 25 toxin superfamilies based on cysteine motifs. Crude venom proteomics analysis identified 43 toxin proteins, including 15 peptide toxins and 28 proteases, including the CAP (CRISP/Allergen/PR) protein family, acetylcholinesterase, metalloproteinases, hyaluronidase, and dermonecrotic toxin. In conclusion, the results of the present study revealed the composition of the venom of <em>M. washanensis</em>, and several peptide toxins with potential medical, such work provides the foundation for further research on the molecular functions of these venom components as well as applied studies for the use of such compounds.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101491"},"PeriodicalIF":2.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of chronic high-temperature stress on muscle tissue integrity and metabolism-related genes in Clarias fuscus","authors":"Xiaolong Li ,&nbsp;Yong Liu ,&nbsp;Cunyu Duan ,&nbsp;Lei Yang ,&nbsp;Dayan Zhou ,&nbsp;Zhixin Zhang ,&nbsp;Huapu Chen ,&nbsp;Guangli Li ,&nbsp;Chunhua Zhu ,&nbsp;Changxu Tian","doi":"10.1016/j.cbd.2025.101497","DOIUrl":"10.1016/j.cbd.2025.101497","url":null,"abstract":"<div><div>The increasing prevalence of high-temperature days due to global warming presents significant challenges for aquatic ecosystems and aquaculture practices. This study investigates the effects of chronic high-temperature stress on <em>Clarias fuscus</em>, a catfish species native to subtropical and tropical regions. The fish were cultured for 90 days under high-temperature conditions (HT, 34 °C) and normal temperature conditions (CT, 26 °C). Histological and transcriptomic analyses were conducted to assess the impact of continuous high-temperature stress on muscle tissue. Histological examination revealed significant damage in the HT group, characterized by irregular tissue arrangement, widened muscle fiber gaps, broken muscle filaments, and cracked nuclei. Transcriptomic analysis identified 975 differentially expressed genes (DEGs) in muscle tissue under high-temperature stress, with 512 genes up-regulated and 463 down-regulated. Notably, heat shock protein (Hsp) family genes, including <em>Hsp40</em>, <em>Hsp70</em> and <em>Hsp90</em>, were significantly up-regulated under heat stress. Enrichment analysis of these DEGs revealed significant alterations in protein processing, the PPAR signaling pathway, and fatty acid oxidation and metabolism within the endoplasmic reticulum. These findings suggest that <em>C. fuscus</em> experiences substantial tissue damage and a reduced metabolic response under high-temperature stress. This study provides a scientific foundation for future research on the adaptability of fish to temperature fluctuations.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101497"},"PeriodicalIF":2.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic response of male Anastrepha fraterculus (Diptera: Tephritidae) to sexual stimulation by host plant volatiles","authors":"Silvina A. Belliard ,&nbsp;Juan Hurtado ,&nbsp;Luciano M. Matzkin ,&nbsp;Santiago Revale ,&nbsp;Diego F. Segura","doi":"10.1016/j.cbd.2025.101495","DOIUrl":"10.1016/j.cbd.2025.101495","url":null,"abstract":"<div><div><em>Anastrepha fraterculus</em> is a major pest of fruits in South America. Previous studies revealed that males exposed to volatiles from guava, a likely ancestral host, intensify courtship behavior and increase mating success. However, the molecular and physiological mechanisms underlying this effect remain unknown. Here, we explore the impact of exposure to guava essential oil volatiles on the gene expression profile of adult male heads through de novo transcriptome assembly and differential expression analysis. We found 678 differentially expressed genes (FDR &lt; 0.05 and |FC| &gt; 2), 308 of which were over-expressed in exposed males and 370 in non-exposed males. The exposure treatment affected the transcription of genes putatively involved in mucus-forming, lipid metabolism and neuropeptide processing. Our findings provide the first insights into the molecular mechanisms underlying sexual stimulation in <em>A. fraterculus</em> males triggered by host fruit volatiles.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101495"},"PeriodicalIF":2.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143734630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of different MT treatment methods on the ovarian transcriptome of Pampus argenteus","authors":"Ruixue Xing ,&nbsp;Zengbing Fang ,&nbsp;Yu Zhou ,&nbsp;Rui Liu ,&nbsp;Yajun Wang ,&nbsp;Danli Wang ,&nbsp;Shanliang Xu ,&nbsp;Xubo Wang ,&nbsp;Chunyang Guo","doi":"10.1016/j.cbd.2025.101496","DOIUrl":"10.1016/j.cbd.2025.101496","url":null,"abstract":"<div><div>17α-methyltestosterone (MT) is a synthetic androgen that is commonly used to induce sex reversal in teleost fish. In this study, MT treatment of <em>Pampus argenteus</em> was carried out by different methods to find the best treatment method and potential mechanism. The results showed that compared with the control group, low concentration of MT (50 mg/kg) could improve the growth performance of <em>P. argenteus</em> in 30 days. Gonadal histology showed that different treatments of MT had different inhibition on the ovarian development, and the number of oocytes decreased in the ovaries. The ovaries of the immersing treatment groups (10 μg/l) showed ovotestis state, but the male germ cells were in the spermatogonia stage. The E2 levels of the mixed feeding and immersing treatment groups was significantly higher than that of the control group (<em>P</em> &lt; 0.05). The 11-KT levels in the 100 mg/kg group was significantly higher than that in the control group (<em>P</em> &lt; 0.05). For the gonadal transcriptome analysis after MT treatment, 460, 568 and 381 DEGs were screened in the 50MT group, 100MT group and MT immersing group, respectively. The DEGs in 50 MT group were enriched in calcium signaling pathway and MAPK signaling pathway affecting gonadal development and differentiation. In 100 MT group, DEGs were mainly enriched in neuroactive ligand-receptor interaction, purine metabolism, vascular smooth muscle contraction and other pathways. The differential gene enrichment p53 signaling pathway and PPAR signaling pathway in the immersing group had an effect on the gonads. In this study, genes showing significant changes in expression after MT treatment were identified. The possible regulatory mechanism of 17α-methyltestosterone on gonadal development of <em>Pampus argenteus</em> was speculated. It provides a theoretical basis for exploring effective ways to improve the fertilization rate of <em>P. argenteus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101496"},"PeriodicalIF":2.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143747679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome resequencing reveals the selection of adaptive evolution during the domestication of pearl oyster Pinctada maxima","authors":"Teng Zhang ,&nbsp;Jiawei Zhang ,&nbsp;Chuangye Yang ,&nbsp;Zhe Zheng ,&nbsp;Yongshan Liao ,&nbsp;Robert Mkuye ,&nbsp;Yongkang Hou ,&nbsp;Minxin Liang ,&nbsp;Shirong Fu ,&nbsp;Ping Wang ,&nbsp;Shijie Zhong ,&nbsp;Qingheng Wang ,&nbsp;Yuewen Deng","doi":"10.1016/j.cbd.2025.101494","DOIUrl":"10.1016/j.cbd.2025.101494","url":null,"abstract":"<div><div>The aquatic environment has a major effect on the domestication of species for aquaculture in nearshore environments. Disruptions in the ion composition of marine ecosystems have a major effect on the growth and development of aquaculture populations. However, research on the adaptation of domesticated bivalves to nearshore environments and the potential underlying regulatory mechanisms is limited. Here, we collected domesticated offspring (F₁ and F₂) and wild individuals (F₀ and P_w) of <em>Pinctada maxima</em> from nearshore areas. We performed a comprehensive genomic data analysis using whole-genome resequencing data. This comprehensive analysis facilitated the identification of signatures of selection on key genes and yielded locus information associated with critical adaptive evolutionary (AE) events during the domestication process. We also evaluated genetic diversity metrics, including observed heterozygosity (<em>H</em>_<em>o</em>), expected heterozygosity (<em>H</em>_<em>e</em>), and the Fixation index (<em>F</em>_<em>is</em>). The findings indicated that domesticated <em>P. maxima</em> may experience balancing selection. In the second-generation domesticated stock, we identified 372 candidate selection regions and 624 genes. Local AE events in the domesticated offspring populations were confirmed via quantitative polymerase chain reaction. We proposed a potential compensatory mechanism in which calcium ions for the main effector genes calmodulin (<em>PmCaM</em>) and catabolite activator protein (<em>PmCAP</em>) are cyclically cached. Our findings enhance our understanding of the mechanisms underlying the regulation of calcium ions, which is essential for the adaptation of species to variation in environmental conditions.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101494"},"PeriodicalIF":2.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}