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

{"title":"PvGeneExpDB: An integrative gene expression database for in-depth understanding on the Pacific white shrimp (Litopenaeus vannamei)","authors":"Xi Xiong ,&nbsp;Chun Xie ,&nbsp;Sijun Li ,&nbsp;Yanzhi Wang ,&nbsp;Junyang Jiang ,&nbsp;Dizhi Xie ,&nbsp;Shijun Chen ,&nbsp;Yuanyan Xiong ,&nbsp;Lian Gan","doi":"10.1016/j.cbd.2024.101227","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101227","url":null,"abstract":"<div><p>The Pacific white shrimp (<em>Litopenaeus vannamei</em>) is a high-valued economic farming species. With the development of high-throughput sequencing technology, cumulative large-scale transcriptomic studies have been revealing molecular landscape of various biological conditions including genetic selection, breeding, evolution, disease landscape, etc. However, no single experiment or databases allow thorough investigations of transcriptomic dynamics for these progressions. Meanwhile, the available datasets are often scattered and lack management. Here, we have established PvGeneExpDB, the first gene expression database for L. <em>vannamei</em> (<span>www.bio-marine-scau.com/pv_ex/</span><svg><path></path></svg>), which encompasses gene expression profiles, differential expression, and co-expression analyses under various biological conditions. Based on the analyses of 7 datasets, which include 53 samples with accurate and detailed records, PvGeneExpDB identifies 20,599 novel transcripts, shows expression profiles of a total of 20,817 genes, and implements Gene Ontology (GO) reconstruction of 76.7 % of these genes. Besides, 26 co-expressed groups were first identified by large-scale, cross-sample Weighted Gene Co-expression Network Analysis (WGCNA). By integrating the gene expression data in the database, our goal is to deepen the biological understanding of L. <em>vannamei</em>.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140188242","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 insights into vibrio-induced mortality in the clam Meretrix petechialis under high temperature","authors":"Li Dong ,&nbsp;Jiajia Yu ,&nbsp;Hongxia Wang ,&nbsp;Xin Yue ,&nbsp;Baozhong Liu","doi":"10.1016/j.cbd.2024.101226","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101226","url":null,"abstract":"<div><p>In this study, we investigate the mortality of the clam <em>Meretrix petechialis</em> facing a vibrio challenge under different temperatures and the underlying molecular mechanisms. Our experiment distinctly revealed that clam mortality was predominantly observed under high temperature, highlighting the critical impact of thermal stress on clam susceptibility to infection. Using RNA-seq, we further compared the global transcriptional response to vibrio in clam gills between high and low temperatures. Compared to other groups, the differentially expressed genes in vibrio-challenged group at high temperature associated with immunity, oxidative stress, and membrane transport. Key results show a weakened immune response in clams at high temperature, especially in the TNF signaling pathway, and a decrease in membrane transport efficiency, notably in SLC proteins. Additionally, high temperature enhanced pro-inflammatory related unsaturated fatty acid metabolism, leading to increased oxidative damage. This was further evidenced by our biochemical assays, which showed significantly higher levels of lipid peroxidation and protein carbonylation in clams at high temperature, indicating heightened oxidative damage. RT-PCR validation of selected DEGs corroborated the RNA-seq findings. Our findings contribute to the understanding of more frequent shellfish mortality in summer, emphasizing the role of temperature in pathogen response, elucidating the molecular mechanisms underlying the synergistic effect of pathogen and high temperature stresses. The key genes identified provide potential targets for resistance-assisted breeding. This research has significant implications for bivalve aquaculture and their physiology, particularly in light of global climate changes affecting marine ecosystems.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140191851","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 cold stress on tissue structure, antioxidant response, and key gene expression in the warm-water bivalve Chlamys nobilis","authors":"Chuanxu Zhang,&nbsp;Yizhou Sun,&nbsp;Jiahua Wen,&nbsp;Boya Xu,&nbsp;Wenlu Zhu,&nbsp;Hongkuan Zhang,&nbsp;Xiaodong Liu,&nbsp;Lingshan LiChu,&nbsp;Huaiping Zheng","doi":"10.1016/j.cbd.2024.101225","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101225","url":null,"abstract":"<div><p>As ectothermic invertebrates, mollusks are regarded as good environmental indicator species for determining the adverse effects of climate change on marine organisms. In the present study, the effects of cold stress on the tissue structure, antioxidant activity, and expression levels of genes were evaluated in the warm-water noble scallop <em>Chlamys nobilis</em> by simulating natural seawater cooled down during winter from 17 °C to 14 °C, 12 °C, 10 °C, and 9 °C. Firstly, the gill was severely damaged at 10 °C and 9 °C, indicating that it could be used as a visually indicative organ for monitoring cold stress. The methylenedioxyamphetamine (MDA) content significantly increased with the temperatures decreasing, meanwhile, the antioxidant enzyme activities superoxide dismutase (SOD) and catalase (CAT) showed a similar pattern, suggesting that the scallop made a positive response. More importantly, 6179 genes related to low temperatures were constructed in a module-gene clustering heat map including 10 modules. Furthermore, three gene modules about membrane lipid metabolism, amino acid metabolism, and molecular defense were identified. Finally, six key genes were verified, and <em>HEATR1</em>, <em>HSP70B2</em>, <em>PI3K</em>, and <em>ATP6V1B</em> were significantly upregulated, while <em>WNT6</em> and <em>SHMT</em> were significantly downregulated under cold stress. This study provides a dynamic demonstration of the major gene pathways' response to various low-temperature stresses from a transcriptomic perspective. The findings shed light on how warm-water bivalves can tolerate cold stress and can help in breeding new strains of aquatic organisms with low-temperature resistance.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140113369","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":"Identification and characterization of circadian clock genes in the head transcriptome of Conopomorpha sinensis Bradley","authors":"Lin-fa Quan,&nbsp;Yan-yan Chi,&nbsp;Yi-Zhi Dong,&nbsp;Shu Xu,&nbsp;Bing-xu Chen,&nbsp;Wen-jing Li","doi":"10.1016/j.cbd.2024.101223","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101223","url":null,"abstract":"<div><p><em>Conopomorpha sinensis</em> Bradley is the most detrimental pest to litchi and longan in China. Adult eclosion, locomotion, mating and oviposition of <em>C. sinensis</em> usually occur at night, regulated by a circadian rhythm. Nevertheless, our understanding of the linkages between adult circadian rhythms and clock genes remains inadequate. To address this gap, transcriptomic analysis was conducted on female and male heads (including antennae) of <em>C. sinensis</em> using the Illumina HiSeq 6000 platform to identify major circadian clock-related genes. The annotated sequences were analyzed by BLASTx, and candidate clock genes were classified based on conservation, predicted domain architectures, and phylogenetic analysis. The analysis revealed a higher conservation of these genes among the compared moths. Further, the expression profile analysis showed a significant spatiotemporal and circadian rhythmic accumulation of some clock genes during development. The candidate clock genes were predominantly expressed in the head, highlighting their crucial function in circadian rhythm regulation. Moreover, <em>CsinPer</em>, <em>CsinTim</em>1, and <em>CsinCry</em>1 displayed similar dynamic expressions with a peak expression level in the 4th age adults, suggesting their involvement in regulation of courtship and mating behaviors. The <em>CsinPer</em> and <em>CsinTim</em>1 mRNA oscillated strongly with a similar phase, containing a peak expression just before the female mating peak. This work will greatly contribute to understanding the circadian clock system of <em>C. sinensis</em> and provide valuable information for further studies of the molecular mechanisms involved in rhythmicity in fruit-boring pests.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140014521","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":"Preliminary analysis of pathways and their implications during salinity stress in abalone","authors":"Grace Afumwaa Boamah ,&nbsp;Zekun Huang ,&nbsp;Caihuan Ke ,&nbsp;Weiwei You ,&nbsp;Christian Larbi Ayisi ,&nbsp;Eric Amenyobge ,&nbsp;Eric Dropenu","doi":"10.1016/j.cbd.2024.101224","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101224","url":null,"abstract":"<div><p>Transcriptome sequencing has offered immense opportunities to study non-model organisms. Abalone is an important marine mollusk that encounters harsh environmental conditions in its natural habitat and under aquaculture conditions; hence, research that increases molecular information to understand abalone physiology and stress response is noteworthy. Accordingly, the study used transcriptome sequencing of the gill tissues of abalone exposed to low salinity stress. The aim is to explore some enriched pathways during salinity stress and the crosstalk and functions of the genes involved in the candidate biological processes for future further analysis of their expression patterns.</p><p>The data suggest that abalone genes such as YAP/TAZ, Myc, Nkd, and Axin (involved in the Hippo signaling pathway) and PI3K/Akt, SHC, and RTK (involved in the Ras signaling pathways) might mediate growth and development. Thus, deregulation of the Hippo and Ras pathways by salinity stress could be a possible mechanism by which unfavorable salinities influence growth in abalone. Furthermore, PEPCK, GYS, and PLC genes (mediating the Glucagon signaling pathway) might be necessary for glucose homeostasis, reproduction, and abalone meat sensory qualities; hence, a need to investigate how they might be influenced by environmental stress. Genes such as MYD88, IRAK1/4, JNK, AP-1, and TRAF6 (mediating the MAPK signaling pathway) could be useful in understanding abalone's innate immune response to environmental stresses. Finally, the aminoacyl-tRNA biosynthesis pathway hints at the mechanism by which new raw materials for protein biosynthesis are mobilized for physiological processes and how abalone might respond to this process during salinity stress. Low salinity clearly regulated genes in these pathways in a time-dependent manner, as hinted by the heat maps. In the future, qRT-PCR verification and in-depth study of the various genes and proteins discussed would provide enormous molecular information resources for the abalone biology.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139999493","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":"Methylosome protein 50 is necessary for oogenesis in medaka","authors":"Qiting Yao ,&nbsp;Qing Yang ,&nbsp;Zhenyu Li ,&nbsp;Fan Wu ,&nbsp;Shi Duan ,&nbsp;Mengxi Cao ,&nbsp;Xinhua Chen ,&nbsp;Xueping Zhong ,&nbsp;Qingchun Zhou ,&nbsp;Haobin Zhao","doi":"10.1016/j.cbd.2024.101220","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101220","url":null,"abstract":"<div><p>Methylosome protein 50 (Mep50) functions as a partner to protein arginine methyltransferase 5. MEP50 serves as a coactivator for both the androgen receptor and estrogen receptor in humans. Mep50 plays a crucial role in the development of germ cells in <em>Drosophila</em>. The precise role of Mep50 in oogenesis remains unclear in vertebrates. The objective of this study was to investigate the role of Mep50 in oogenesis in medaka fish. Disruption of Mep50 resulted in impaired oogenesis and the formation of multiple oocyte follicles in medaka. RNA-seq analysis revealed significant differential gene expression in the mutant ovary, with 4542 genes up-regulated and 1264 genes down-regulated. The regulated genes were found to be enriched in cellular matrices and ECM-receptor interaction, the Notch signaling pathway, the PI3K-Akt signaling pathway, the MAPK signaling pathway, the Hippo signaling pathway, and the Jak-Stat pathway, among others. In addition, the genes related to the hypothalamus-pituitary-gonad axis, steroid metabolism, and IGF system were impacted. Furthermore, the mutation of mep50 caused significant alterations in alternative splicing of pre-mRNA in ovarian cells. Quantitative RT-PCR results validated the findings from RNA-seq analysis in the specific genes, including <em>akt2</em>, <em>map3k5</em>, <em>yap1</em>, <em>fshr</em>, <em>cyp17a</em>, <em>igf1</em>, <em>ythdc2</em>, <em>cdk6</em>, and <em>col1</em>, among others. The findings of this study demonstrate that Mep50 plays a crucial role in oogenesis, participating in a diverse range of biological processes such as steroid metabolism, cell matrix regulation, and signal pathways. This may be achieved through the regulation of gene expression via mRNA splicing in medaka ovarian cells.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140014520","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":"Identification and sex expression profiles of candidate chemosensory genes from Atherigona orientalis via the antennae and leg transcriptome analysis","authors":"Zihao Zhou,&nbsp;Yujie Luo,&nbsp;Xintong Wang,&nbsp;Jing He,&nbsp;Qiong Zhou","doi":"10.1016/j.cbd.2024.101222","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101222","url":null,"abstract":"<div><p><em>Atherigona orientalis</em> Schiner (1868) is an acknowledged agricultural pest owing to its feeding habits and breeding locations. This insect is a tropical and subtropical pest in fruits and vegetables, in which &gt;50 varieties of fruits and vegetables in 26 families, such as <em>Capsicum annuum</em>, <em>Lycopersicon esculentum</em>, and <em>Cucumis melo</em> have been attacked. Moreover, <em>A. orientalis</em> may also develop in rotten crops and feces or insect carcasses, which are also considered one kind of sanitary pest and medical insect. At present, the invasion ranges of <em>A. orientalis</em> are still increasing and more preventive and management measures are to be processed. To gain a better understanding of the molecular mechanisms involved in olfactory reception in <em>A. orientalis</em>, the transcriptome of male and female antennae and legs was systematically analyzed. In total, 131 chemosensory-related genes, including 63 odorant receptors (ORs), 20 gustatory receptors (GRs), 18 ionotropic receptors (IRs), 27 odorant binding proteins (OBPs), 1 chemosensory protein (CSP), and 2 sensory neuron membrane proteins (SNMPs), were identified. The analysis focused on obtaining expression information of candidate olfactory genes at the transcriptomic level by examining the differentially expressed genes (DEGs) in all samples. Totally, 41 DEGs were identified between male antennae (MA) and female antennae (FA), including 32 ORs, 5 OBPs, 1 IR, 2 GRs and 1 SNMP. In MA versus male legs (ML), 78 DEGs were identified (45 ORs, 18 OBPs, 6 GRs, 6 IRs, 1 CSP and 2 SNMPs). In FA and female legs (FL), 96 DEGs were identified (51 ORs, 21 OBPs, 9 GRs, 12 IRs, 1 CSP and 2 SNMPs). For ML and FL, 3 DEGs were identified, including 2 ORs and 1 SNMP. Our results supplement valuable insights for future research on the chemoreception mechanisms in <em>A. orientalis</em>.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140014518","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":"Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda","authors":"Nevil Pinto ,&nbsp;Mehar Un Nissa ,&nbsp;B.S. Yashwanth ,&nbsp;A. Sathiyanarayanan ,&nbsp;Medha Gayathri J. Pai ,&nbsp;Sanjeeva Srivastava ,&nbsp;Mukunda Goswami","doi":"10.1016/j.cbd.2024.101221","DOIUrl":"https://doi.org/10.1016/j.cbd.2024.101221","url":null,"abstract":"<div><p><em>Edwardsiella tarda</em> (<em>Et</em>) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of <em>Labeo rohita</em> (rohu) kidney to <em>Et</em> are poorly understood. A proteomic and histopathological analysis was performed for the rohu kidney after <em>Et</em> infection. The histopathology of the infected rohu kidney showed vacuolation and necrosis. After LC-MS/MS analysis, ~1240 proteins were identified with ≥2 unique peptides. A total of 96 differentially abundant proteins (DAPs) were observed between the control and <em>Et</em> infected group (ET). Metascape and STRING analysis were used for the gene ontology (GO), and protein-protein interaction network (PPI) for the significant pathways of DAPs. In PPI, low-abundant proteins were mapped to metabolic pathways and oxidative phosphorylation (cox5ab, uqcrfs1). High-abundance proteins were mapped to ribosomes (rplp2), protein process in the ER (hspa8), and immune system (ptgdsb.1, muc2). Our label-free proteomic approach in the rohu kidney revealed abundant enriched proteins involved in vesicle coat (ehd4), complement activation (c3a.1, c9, c7a), phagosome (thbs4, mapk1), metabolic reprogramming (hao1, glud1a), wound healing (vim, alox5), and the immune system (psap) after <em>Et</em> infection. A targeted proteomics approach of multiple reaction monitoring (MRM) validated the DAPs (nprl3, ambp, vmo1a, hspg2, muc2, hao1 and glud1a) between control and ET. Overall, the current analysis of histology and proteome in the rohu kidney provides comprehensive data on pathogenicity and the potential immune proteins against <em>Et</em>.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140014519","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 hypoxia response pathway in the Antarctic fish Notothenia coriiceps is functional despite a poly Q/E insertion mutation in HIF-1α","authors":"K.M. O'Brien ,&nbsp;A.S. Rix ,&nbsp;A. Jasmin ,&nbsp;E. Lavelle","doi":"10.1016/j.cbd.2024.101218","DOIUrl":"10.1016/j.cbd.2024.101218","url":null,"abstract":"<div><p>Antarctic notothenioid fishes, inhabiting the oxygen-rich Southern Ocean, possess a polyglutamine and glutamic acid (poly Q/E) insertion mutation in the master transcriptional regulator of oxygen homeostasis, hypoxia- inducible factor-1α (HIF-1α). To determine if this mutation impairs the ability of HIF-1 to regulate gene expression in response to hypoxia, we exposed <em>Notothenia coriiceps</em>, with a poly Q/E insertion mutation in HIF-1α that is 9 amino acids long, to hypoxia (2.3 mg L⁻¹ O₂) or normoxia (10 mg L ⁻¹ O₂) for 12 h. Heart ventricles, brain, liver, and gill tissue were harvested and changes in gene expression quantified using RNA sequencing. Levels of glycogen and lactate were also quantified to determine if anaerobic metabolism increases in response to hypoxia. Exposure to hypoxia resulted in 818 unique differentially expressed genes (DEGs) in liver tissue of <em>N. coriiceps</em>. Many hypoxic genes were induced, including ones involved in the MAP kinase and FoxO pathways, glycolytic metabolism, and vascular remodeling. In contrast, there were fewer than 104 unique DEGs in each of the other tissues sampled. Lactate levels significantly increased in liver in response to hypoxia, indicating that anaerobic metabolism increases in response to hypoxia in this tissue. Overall, our results indicate that the hypoxia response pathway is functional in <em>N. coriiceps</em> despite a poly Q/E mutation in HIF-1α, and confirm that Antarctic fishes are capable of altering gene expression in response to hypoxia.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139927246","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":"Comparative skin histological and transcriptomic analysis of Rana kukunoris with two different skin colors","authors":"Xu-Ze Zhang ,&nbsp;Xiao-Dong Ma ,&nbsp;Wan-Ting Wang ,&nbsp;Fei Peng ,&nbsp;Ye-Mao Hou ,&nbsp;Yue-Xia Shen ,&nbsp;Yu-Qi Sun ,&nbsp;Jin-Fang Chen ,&nbsp;Yi-Jin Yin ,&nbsp;Yu-Ye Zeng ,&nbsp;Yi Yu ,&nbsp;Peng Zhou ,&nbsp;Fu-Hao Zhang ,&nbsp;Yan-Feng He ,&nbsp;Ying-Fang Shen","doi":"10.1016/j.cbd.2024.101217","DOIUrl":"10.1016/j.cbd.2024.101217","url":null,"abstract":"<div><p>This study compares the skin structures of <em>Rana kukunoris</em> with two different skin colors living in the same area of Haibei in the Northeastern Qinghai-Tibet Plateau. The skin thickness of the khaki <em>R. kukunoris</em> was significantly greater than that of the brown <em>R. kukunoris</em> (<em>P</em> &lt; 0.01), and significantly more mucous and granular glands were present on the dorsal skin of the khaki frog (<em>P</em> &lt; 0.05). Meanwhile, the melanocytes on the dorsal skin of the brown frog were significantly larger than those on the khaki one (<em>P</em> &lt; 0.05). Morphological changes in the expansion and aggregation of melanocytes seemed to deepen the skin color of <em>R. kukunoris</em>. Moreover, transcriptome sequencing identified tyrosine metabolism, melanogenesis, and riboflavin metabolism as the main pathways involved in melanin formation and metabolism in brown <em>R. kukunoris</em>. <em>TYR, MC1R</em> was upregulated as the skin color of <em>R. kukunoris</em> was deepened and contributed to melanin production and metabolism<em>.</em> In contrast, the khaki frog had significantly more upregulated genes and metabolic pathways related to autoimmunity. The khaki frog appeared to defend against ultraviolet (UV) radiation-induced damage by secreting mucus and small molecular peptides, whereas the brown frog protected itself by distributing a large amount of melanin. Hence, the different skin colors of <em>R. kukunoris</em> might represent different adaptation strategies for survival in the intense UV radiation environment of the Qinghai-Tibet Plateau.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139927400","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}