Pub Date : 2025-09-17DOI: 10.1016/j.cbd.2025.101635
Xuan Zhang , Mengfei Yi , Yongliang Fan , Yiping Li , Xiangqun Yuan
ATP-binding cassette (ABC) transporter family, is one of the largest and most ancient classes of transmembrane protein. Rice skipper, Parnara guttata, is a major rice pest distributed across China, Japan, and South Korea, and damages rice crop by rolling leaves into shelters, resulting in complicated pest control efforts. In this study, we performed genome-wide identification, docking and expression analysis of ABC transporters in P. guttata, and identified 47 ABC transporter genes. Phylogenetic analysis classified these genes into eight subfamilies (ABCA-H). Molecular docking revealed that transporters with the strongest binding affinities for Bt toxin Cry1Ac and chemical pesticides (cypermethrin, imidacloprid, malathion) predominantly belonged to the ABCC and ABCG subfamilies, suggesting these as potential pesticide targets. Transcriptomic data showed that all ABCD, ABCE, and ABCF genes were highly expressed in larval midguts, while other subfamilies exhibited partial high expression. These findings provide critical insights for toxicological studies and evolutionary analyses of ABC transporters in invertebrates.
{"title":"Genome-wide identification, docking and expression analysis of ATP-binding cassette gene family of Parnara guttata, a major rice pest (Insecta: Lepidoptera: Hesperiidae)","authors":"Xuan Zhang , Mengfei Yi , Yongliang Fan , Yiping Li , Xiangqun Yuan","doi":"10.1016/j.cbd.2025.101635","DOIUrl":"10.1016/j.cbd.2025.101635","url":null,"abstract":"<div><div>ATP-binding cassette (ABC) transporter family, is one of the largest and most ancient classes of transmembrane protein. Rice skipper, <em>Parnara guttata</em>, is a major rice pest distributed across China, Japan, and South Korea, and damages rice crop by rolling leaves into shelters, resulting in complicated pest control efforts. In this study, we performed genome-wide identification, docking and expression analysis of ABC transporters in <em>P. guttata</em>, and identified 47 ABC transporter genes. Phylogenetic analysis classified these genes into eight subfamilies (ABCA-H). Molecular docking revealed that transporters with the strongest binding affinities for <em>Bt</em> toxin Cry1Ac and chemical pesticides (cypermethrin, imidacloprid, malathion) predominantly belonged to the ABCC and ABCG subfamilies, suggesting these as potential pesticide targets. Transcriptomic data showed that all ABCD, ABCE, and ABCF genes were highly expressed in larval midguts, while other subfamilies exhibited partial high expression. These findings provide critical insights for toxicological studies and evolutionary analyses of ABC transporters in invertebrates.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101635"},"PeriodicalIF":2.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145108770","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}
Pub Date : 2025-09-17DOI: 10.1016/j.cbd.2025.101639
Yeyu Chen , Hua Li , Qinyao Wei , Guiliang Liu , Zhao Liu , Xiaoyun Wu , Yanling Chen , Yi Yu , Quanyu Tu , Huanchao Yang
Hucho bleekeri is a Class I protected species in China. In recent years, very few records of wild H. bleekeri have been documented. Therefore, artificial breeding has become the last resort to protect this species. However, during the larvae cultivation phase, a large number of individuals exhibit abnormal morphology, which constitute the majority of dead larvae. In this study, we conducted transcriptome sequencing on normal and malformed fish at three distinct developmental stages: 4 days post-hatching (dph), 15 dph, and 31 dph, and explored the expression patterns of key differentially expressed genes (DEGs) associated with skeletal development. Transcriptomic sequencing identified a total of 3024, 2678, and 7088 DEGs in the control versus malformed groups at 4 dph, 15 dph, and 31 dph, respectively. Gene Set Enrichment Analysis showed that cell development, regulation of cytoskeleton organization, TGF-β signaling pathway, and Wnt signaling pathway, had relatively high enrichment scores. Genes involved in skeletal development, including shh, daam1, osteonectin, twist1, osteocalcin, col1a1, myod, and hox3, were significantly down-regulated in malformed fish, while mmp13 and TGFβ were significantly up-regulated. Notably, key genes in the Hedgehog signaling pathway were all inhibited in the malformed groups, indicating their crucial roles in the normal skeletal development of H. bleekeri. This study enhances our understanding of the underlying mechanisms of skeletal regulation in fish and may help reduce the incidence of malformations in H. bleekeri.
{"title":"Transcriptome sequencing reveals the molecular mechanisms of early malformations in the critically endangered Sichuan taimen (Hucho bleekeri)","authors":"Yeyu Chen , Hua Li , Qinyao Wei , Guiliang Liu , Zhao Liu , Xiaoyun Wu , Yanling Chen , Yi Yu , Quanyu Tu , Huanchao Yang","doi":"10.1016/j.cbd.2025.101639","DOIUrl":"10.1016/j.cbd.2025.101639","url":null,"abstract":"<div><div><em>Hucho bleekeri</em> is a Class I protected species in China. In recent years, very few records of wild <em>H. bleekeri</em> have been documented. Therefore, artificial breeding has become the last resort to protect this species. However, during the larvae cultivation phase, a large number of individuals exhibit abnormal morphology, which constitute the majority of dead larvae. In this study, we conducted transcriptome sequencing on normal and malformed fish at three distinct developmental stages: 4 days post-hatching (dph), 15 dph, and 31 dph, and explored the expression patterns of key differentially expressed genes (DEGs) associated with skeletal development. Transcriptomic sequencing identified a total of 3024, 2678, and 7088 DEGs in the control versus malformed groups at 4 dph, 15 dph, and 31 dph, respectively. Gene Set Enrichment Analysis showed that cell development, regulation of cytoskeleton organization, TGF-β signaling pathway, and Wnt signaling pathway, had relatively high enrichment scores. Genes involved in skeletal development, including <em>shh</em>, <em>daam1</em>, <em>osteonectin</em>, <em>twist1</em>, <em>osteocalcin</em>, <em>col1a1</em>, <em>myod</em>, and <em>hox3</em>, were significantly down-regulated in malformed fish, while <em>mmp13</em> and <em>TGFβ</em> were significantly up-regulated. Notably, key genes in the Hedgehog signaling pathway were all inhibited in the malformed groups, indicating their crucial roles in the normal skeletal development of <em>H. bleekeri</em>. This study enhances our understanding of the underlying mechanisms of skeletal regulation in fish and may help reduce the incidence of malformations in <em>H. bleekeri</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101639"},"PeriodicalIF":2.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145104356","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}
Characterization of reproduction-related genes is crucial for comprehending molecular mechanisms involved in ovarian development of banana shrimp (Penaeus merguiensis). Here, genes expressed in different ovarian (immature, vitellogenic and mature) stages were characterized by RNA-Seq. In total, 12 libraries were established and 88.56 Gb (6.91–8.04 Gb/sample) clean data were obtained for overall samples. The Q30 values were between 94.14 and 94.86 %. The N50 values were 2763 bp for transcripts and 2536 bp for unigenes. A total of 2208 differentially expressed genes (DEGs) were identified, comprising 1203 up-regulated and 1005 down-regulated genes. Identified genes were annotated and functionally categorized. DEGs in protein synthesis, metabolism and biogenesis levels were abundant suggested that the development of immature ovaries to further stages requires energy and nutrient accumulation. Expression of DEGs in Cellular process, Environmental information processing, Genetic information processing, and Metabolism in immature ovaries increased in vitellogenic ovaries and decreased in mature ovaries. This reflects the rapid accumulation of various proteins during the vitellogenic stage. The identified DEGs in mature ovaries suggest that signal transduction pathways are crucial during the final ovarian maturation of P. merguiensis. Gene expression was further analyzed by qRT-PCR. PmMknk1, PmTtc3 and PmSult1C4 were upregulated in vitellogenic and mature ovaries (P < 0.05). In addition, PmCcnF, PmBmp2, PmFoxA1, PmChst5 and PmVtg were upregulated in mature ovaries (P < 0.05). This suggested their important role in ovarian development and maturation. The information is crucial for further studies on reproductive maturation of P. merguiensis.
{"title":"Comparative transcriptome analysis for identifying genes involved in reproduction of banana shrimp (Penaeus merguiensis)","authors":"Phimsucha Bunphimpapha , Premruethai Supungul , Sureerat Tang , Kittanasan Inbumrung , Sirawut Klinbunga","doi":"10.1016/j.cbd.2025.101637","DOIUrl":"10.1016/j.cbd.2025.101637","url":null,"abstract":"<div><div>Characterization of reproduction-related genes is crucial for comprehending molecular mechanisms involved in ovarian development of banana shrimp (<em>Penaeus merguiensis</em>). Here, genes expressed in different ovarian (immature, vitellogenic and mature) stages were characterized by RNA-Seq. In total, 12 libraries were established and 88.56 Gb (6.91–8.04 Gb/sample) clean data were obtained for overall samples. The Q30 values were between 94.14 and 94.86 %. The N50 values were 2763 bp for transcripts and 2536 bp for unigenes. A total of 2208 differentially expressed genes (DEGs) were identified, comprising 1203 up-regulated and 1005 down-regulated genes. Identified genes were annotated and functionally categorized. DEGs in protein synthesis, metabolism and biogenesis levels were abundant suggested that the development of immature ovaries to further stages requires energy and nutrient accumulation. Expression of DEGs in Cellular process, Environmental information processing, Genetic information processing, and Metabolism in immature ovaries increased in vitellogenic ovaries and decreased in mature ovaries. This reflects the rapid accumulation of various proteins during the vitellogenic stage. The identified DEGs in mature ovaries suggest that signal transduction pathways are crucial during the final ovarian maturation of <em>P. merguiensis</em>. Gene expression was further analyzed by qRT-PCR. <em>PmMknk1</em>, <em>PmTtc3</em> and <em>PmSult1C4</em> were upregulated in vitellogenic and mature ovaries (<em>P</em> < 0.05). In addition, <em>PmCcnF</em>, <em>PmBmp2</em>, <em>PmFoxA1</em>, <em>PmChst5</em> and <em>PmVtg</em> were upregulated in mature ovaries (<em>P</em> < 0.05). This suggested their important role in ovarian development and maturation. The information is crucial for further studies on reproductive maturation of <em>P. merguiensis</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101637"},"PeriodicalIF":2.2,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145104348","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}
Pub Date : 2025-09-13DOI: 10.1016/j.cbd.2025.101636
Kejie Ou , Kang An , Biaobiao Hao , Jia Kang , Junhu Su
Seasonal reproduction in animals is characterized by programmed activation, dormancy of reproductive activities, and precise regulation of hormone levels. Androgens secreted by Leydig cells are essential for testicular development and spermatogenesis. To explore the mechanism of androgen in spermatogenesis in seasonal breeding animals, this study used the plateau zokor (Eospalax baileyi) as a model and, during the breeding season, treated it with the androgen receptor antagonist, flutamide, to analyze its effect on the microRNA (miRNA) expression profile in testicular tissue. Flutamide treatment resulted in marked changes in the expression of 91 miRNAs in the testes (28 upregulated and 63 downregulated), including 44 known and 47 newly predicted miRNAs. Functional enrichment analysis of the target genes of differentially expressed miRNAs demonstrated significantly enriched cell adhesion, hypoxia response, apoptosis process, inflammatory response， lipid metabolism (Gene Ontology analysis, P < 0.05) and ferroptosis, fatty acid metabolism and other signaling pathways (Kyoto Encyclopedia of Genes and Genomes analysis, P < 0.05). Based on this, an interaction network of miRNA–mRNA in the spermatogenesis and ferroptosis pathways was constructed. Dual-luciferase reporter gene assay confirmed that ACSL4 was a direct target gene of miR-486-y. The expression of miR-486-y was inhibited by an antagomir, which verified its involvement in the regulation of spermatogenesis in the plateau zokor during reproduction. Androgens regulate spermatogenesis in plateau zokors by inhibiting specific miRNAs (such as miR-486-y). This study provides molecular evidence and new perspectives on the regulatory network of seasonal reproduction in animals.
{"title":"Analysis of miRNA expression profiles during spermatogenesis of plateau zokor (Eospalax baileyi) under androgen antagonism treatment","authors":"Kejie Ou , Kang An , Biaobiao Hao , Jia Kang , Junhu Su","doi":"10.1016/j.cbd.2025.101636","DOIUrl":"10.1016/j.cbd.2025.101636","url":null,"abstract":"<div><div>Seasonal reproduction in animals is characterized by programmed activation, dormancy of reproductive activities, and precise regulation of hormone levels. Androgens secreted by Leydig cells are essential for testicular development and spermatogenesis. To explore the mechanism of androgen in spermatogenesis in seasonal breeding animals, this study used the plateau zokor (<em>Eospalax baileyi</em>) as a model and, during the breeding season, treated it with the androgen receptor antagonist, flutamide, to analyze its effect on the microRNA (miRNA) expression profile in testicular tissue. Flutamide treatment resulted in marked changes in the expression of 91 miRNAs in the testes (28 upregulated and 63 downregulated), including 44 known and 47 newly predicted miRNAs. Functional enrichment analysis of the target genes of differentially expressed miRNAs demonstrated significantly enriched cell adhesion, hypoxia response, apoptosis process, inflammatory response， lipid metabolism (Gene Ontology analysis, <em>P</em> < 0.05) and ferroptosis, fatty acid metabolism and other signaling pathways (Kyoto Encyclopedia of Genes and Genomes analysis, <em>P</em> < 0.05). Based on this, an interaction network of miRNA–mRNA in the spermatogenesis and ferroptosis pathways was constructed. Dual-luciferase reporter gene assay confirmed that <em>ACSL4</em> was a direct target gene of miR-486-y. The expression of miR-486-y was inhibited by an antagomir, which verified its involvement in the regulation of spermatogenesis in the plateau zokor during reproduction. Androgens regulate spermatogenesis in plateau zokors by inhibiting specific miRNAs (such as miR-486-y). This study provides molecular evidence and new perspectives on the regulatory network of seasonal reproduction in animals.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101636"},"PeriodicalIF":2.2,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145082732","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}
Pub Date : 2025-09-11DOI: 10.1016/j.cbd.2025.101633
Waraphorn Sihamok , Sk Injamamul Islam , Luu Tang Phuc Khang , Orathai Dangsawat , Papungkorn Sangsawad , Truong Anh Tu , Cao Phuong Thao , Nguyen Dinh-Hung , Patima Permpoonpattana , Nguyen Vu Linh
In the context of sustainable aquaculture, probiotics represent a promising alternative to antibiotics for promoting shrimp health and disease resistance. In this study, Bacillus sp. KNSH11, a Gram-positive, rod-shaped bacterium isolated from the intestine of whiteleg shrimp (Litopenaeus vannamei), was characterized to assess its probiotic potential. The strain exhibited excellent sporulation efficiency (> 99 %), supporting its resilience under harsh environmental conditions. Functional assays demonstrated that KNSH11 retained high viability under various stressors, including acidic pH (2–4), bile salts, elevated temperatures (up to 95 °C), and lysozyme exposure, indicating robust tolerance to gastrointestinal and processing challenges. Metabolic profiling revealed substantial lactic acid production with minimal levels of acetate and propionate, distinguishing it from conventional lactic acid bacteria. The strain also exhibited strong antioxidant activity and moderate antibiofilm effects against pathogenic bacteria. Antibiotic susceptibility testing showed sensitivity to amoxicillin, chloramphenicol, kanamycin, and tetracycline (all at 30 μg/disc), while resistance was observed against ampicillin and penicillin (10 μg/disc each). Whole genome sequencing confirmed the absence of virulence genes and identified the presence of mobile genetic elements, a CRISPR/Cas system, and gene clusters potentially responsible for bacteriocin production. Collectively, these results indicate that Bacillus sp. KNSH11 exhibits key probiotic characteristics and genomic features consistent with a safe profile, supporting its potential application in sustainable shrimp aquaculture, pending further in vitro and in vivo validation.
{"title":"Genomic insights into Bacillus sp. KNSH11 from Litopenaeus vannamei intestine: Probiotic potential, safety, and aquaculture applications","authors":"Waraphorn Sihamok , Sk Injamamul Islam , Luu Tang Phuc Khang , Orathai Dangsawat , Papungkorn Sangsawad , Truong Anh Tu , Cao Phuong Thao , Nguyen Dinh-Hung , Patima Permpoonpattana , Nguyen Vu Linh","doi":"10.1016/j.cbd.2025.101633","DOIUrl":"10.1016/j.cbd.2025.101633","url":null,"abstract":"<div><div>In the context of sustainable aquaculture, probiotics represent a promising alternative to antibiotics for promoting shrimp health and disease resistance. In this study, <em>Bacillus</em> sp. KNSH11, a Gram-positive, rod-shaped bacterium isolated from the intestine of whiteleg shrimp (<em>Litopenaeus vannamei</em>), was characterized to assess its probiotic potential. The strain exhibited excellent sporulation efficiency (> 99 %), supporting its resilience under harsh environmental conditions. Functional assays demonstrated that KNSH11 retained high viability under various stressors, including acidic pH (2–4), bile salts, elevated temperatures (up to 95 °C), and lysozyme exposure, indicating robust tolerance to gastrointestinal and processing challenges. Metabolic profiling revealed substantial lactic acid production with minimal levels of acetate and propionate, distinguishing it from conventional lactic acid bacteria. The strain also exhibited strong antioxidant activity and moderate antibiofilm effects against pathogenic bacteria. Antibiotic susceptibility testing showed sensitivity to amoxicillin, chloramphenicol, kanamycin, and tetracycline (all at 30 μg/disc), while resistance was observed against ampicillin and penicillin (10 μg/disc each). Whole genome sequencing confirmed the absence of virulence genes and identified the presence of mobile genetic elements, a CRISPR/Cas system, and gene clusters potentially responsible for bacteriocin production. Collectively, these results indicate that <em>Bacillus</em> sp. KNSH11 exhibits key probiotic characteristics and genomic features consistent with a safe profile, supporting its potential application in sustainable shrimp aquaculture, pending further in vitro and in vivo validation.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101633"},"PeriodicalIF":2.2,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145088570","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}
Pub Date : 2025-09-11DOI: 10.1016/j.cbd.2025.101632
Yongshuang Xiao , Pingrui Xu , Jun Li , Zhizhong Xiao
Oplegnathus fasciatus is a commercially important marine fish species, valued both in wild fisheries and aquaculture. It possesses a multivalent sex-determination system (X1X1X2X2/X1X2Y) and exhibits marked sexual growth dimorphism, with males demonstrating significantly faster growth rates. Sex-specific molecular markers are instrumental in advancing selective breeding strategies. In this study, whole-genome screening of O. fasciatus revealed a male-specific structural variant within an intronic region of ndc80: two insertions of 3 bp and 538 bp (totaling 541 bp), which were consistently absent in females. To facilitate practical application, we developed a PCR-based assay using a single primer pair that amplifies a conserved region flanking the insertion site. This assay reproducibly generates distinct banding patterns: males yield two fragments (208 bp and 749 bp), consistent with the 541 bp male-specific insertion, whereas females yield only the 208 bp amplicon. This method enables efficient, high-throughput sex identification in O. fasciatus without the need for sequencing. Using standard agarose gel electrophoresis, the assay reliably distinguishes sexes through clearly divergent banding patterns. Beyond applications in selective breeding, these sex-specific markers provide critical molecular insights into the sex determination mechanisms and the genetic basis of sexual dimorphism in O. fasciatus.
{"title":"A novel indel-based molecular sex identification system for oplegnathus fasciatus: Insights from ndc80 gene polymorphisms and aquaculture applications","authors":"Yongshuang Xiao , Pingrui Xu , Jun Li , Zhizhong Xiao","doi":"10.1016/j.cbd.2025.101632","DOIUrl":"10.1016/j.cbd.2025.101632","url":null,"abstract":"<div><div><em>Oplegnathus fasciatus</em> is a commercially important marine fish species, valued both in wild fisheries and aquaculture. It possesses a multivalent sex-determination system (X<sub>1</sub>X<sub>1</sub>X<sub>2</sub>X<sub>2</sub>/X<sub>1</sub>X<sub>2</sub>Y) and exhibits marked sexual growth dimorphism, with males demonstrating significantly faster growth rates. Sex-specific molecular markers are instrumental in advancing selective breeding strategies. In this study, whole-genome screening of <em>O. fasciatus</em> revealed a male-specific structural variant within an intronic region of <em>ndc80</em>: two insertions of 3<!--> <!-->bp and 538<!--> <!-->bp (totaling 541<!--> <!-->bp), which were consistently absent in females. To facilitate practical application, we developed a PCR-based assay using a single primer pair that amplifies a conserved region flanking the insertion site. This assay reproducibly generates distinct banding patterns: males yield two fragments (208<!--> <!-->bp and 749<!--> <!-->bp), consistent with the 541<!--> <!-->bp male-specific insertion, whereas females yield only the 208<!--> <!-->bp amplicon. This method enables efficient, high-throughput sex identification in <em>O. fasciatus</em> without the need for sequencing. Using standard agarose gel electrophoresis, the assay reliably distinguishes sexes through clearly divergent banding patterns. Beyond applications in selective breeding, these sex-specific markers provide critical molecular insights into the sex determination mechanisms and the genetic basis of sexual dimorphism in <em>O. fasciatus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101632"},"PeriodicalIF":2.2,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145076745","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}
Pub Date : 2025-09-10DOI: 10.1016/j.cbd.2025.101634
Lina Yang , Dun Jiang , Weichao Ma , Shanchun Yan
Lymantria dispar, a destructive forest pest, poses a significant threat to forest ecosystems. Olfaction plays a pivotal role in mate finding, host location, and oviposition site selection in insects. This study aimed to systematically characterize olfactory-related genes in adult L. dispar and examine sex-specific expression profiles, shedding light on the molecular mechanisms of olfactory perception in this species. Antennal transcriptomes of male and female L. dispar were sequenced, generating 36.61 Gb of high-quality clean data. A total of 134 olfactory-related genes were identified, including 40 odorant receptors (ORs), 12 gustatory receptors (GRs), 20 ionotropic receptors (IRs), 17 chemosensory proteins (CSPs), 38 odorant-binding proteins (OBPs), 3 odorant-degrading enzymes (ODEs), and 4 sensory neuron membrane proteins (SNMPs). Relative expression levels of these genes were validated by qRT-PCR, revealing that 28 genes were significantly upregulated in female antennae, while 32 genes exhibited higher expression in males. These findings aligned closely with the transcriptome data. This study provides a comprehensive characterization of olfactory-related genes in L. dispar antennae and uncovers their sex-biased expression, offering valuable insights into the molecular mechanisms of pheromone detection and other olfactory-driven behaviors in this pest species.
{"title":"Identification and sex-biased expression analysis of olfactory-related genes in Lymantria dispar based on transcriptome and qRT-PCR","authors":"Lina Yang , Dun Jiang , Weichao Ma , Shanchun Yan","doi":"10.1016/j.cbd.2025.101634","DOIUrl":"10.1016/j.cbd.2025.101634","url":null,"abstract":"<div><div><em>Lymantria dispar</em>, a destructive forest pest, poses a significant threat to forest ecosystems. Olfaction plays a pivotal role in mate finding, host location, and oviposition site selection in insects. This study aimed to systematically characterize olfactory-related genes in adult <em>L. dispar</em> and examine sex-specific expression profiles, shedding light on the molecular mechanisms of olfactory perception in this species. Antennal transcriptomes of male and female <em>L. dispar</em> were sequenced, generating 36.61 Gb of high-quality clean data. A total of 134 olfactory-related genes were identified, including 40 odorant receptors (ORs), 12 gustatory receptors (GRs), 20 ionotropic receptors (IRs), 17 chemosensory proteins (CSPs), 38 odorant-binding proteins (OBPs), 3 odorant-degrading enzymes (ODEs), and 4 sensory neuron membrane proteins (SNMPs). Relative expression levels of these genes were validated by qRT-PCR, revealing that 28 genes were significantly upregulated in female antennae, while 32 genes exhibited higher expression in males. These findings aligned closely with the transcriptome data. This study provides a comprehensive characterization of olfactory-related genes in <em>L. dispar</em> antennae and uncovers their sex-biased expression, offering valuable insights into the molecular mechanisms of pheromone detection and other olfactory-driven behaviors in this pest species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101634"},"PeriodicalIF":2.2,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093130","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}
Pub Date : 2025-09-09DOI: 10.1016/j.cbd.2025.101629
Gaoyuan Yuan , Meihui Huo , Boyi Zheng , Zhichao Wang , Xugan Wu , Meimei Liu , Zhiguo Dong
Photoperiod is a critical environmental cue that orchestrates reproductive physiology and circadian biology in crustaceans, yet the neural gene networks linking photoperiod to ovarian maturation and clock regulation remain largely unknown. To elucidate the molecular mechanisms underlying photoperiod regulation of ovarian development and associated circadian rhythmicity, the eyestalk (SG) and brain ganglion (BG) of female Chinese mitten crab (Eriocheir sinensis) from two photoperiod groups (Light (L): Dark (D) = 0 h: 24 h (L0) and L: D = 18 h: 6 h (L18)) were used for transcriptome analysis. The analysis identified 298 differentially expressed genes (DEGs) in the brain and 109 DEGs in the eyestalk. KEGG enrichment analysis indicated these DEGs were primarily associated with ovarian development and circadian rhythm-related signaling pathways. Key ovarian development-related genes, including E3 ubiquitin-protein ligase lubel-like isoform X6, 5-hydroxytryptamine receptor-like, serine/threonine-protein phosphatase alpha-2, estrogen sulfotransferase, cytochrome P450 2 L1-like, follicle-stimulating hormone receptor-like isoform X1 and E3 ubiquitin-protein ligase CHIP (EULCHIP), exhibited significant upregulation or downregulation in the L18-BG group. Meanwhile, genes such as EULCHIP, E3 ubiquitin-protein ligase TRIM71-like, CREB-binding protein-like isoform X2, serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit C, collagen alpha-5(IV) chain, integrin beta 1, ecdysone-induced protein 74EF-like, and insulin-like growth factor-binding protein complex acid labile subunit showed significant upregulation or downregulation in the L18-SG group. These findings suggest that prolonged photoperiods enhance ovarian development and modulate reproductive endocrine activity during ovarian maturation. Furthermore, circadian rhythm-related genes such as period circadian protein-like isoform X1, prostaglandin D synthase, and acetylcholine receptor subunit alpha-type acr-16 displayed marked differential expression between photoperiod groups, indicating disrupted molecular oscillations and gradual desynchronization of circadian rhythmicity under extended light exposure. This study provides critical, systems-level insights into the photoperiod-driven regulatory networks of ovarian development and endocrine dynamics in crustaceans, offering a molecular basis for optimizing aquaculture practices and advancing our understanding of crustacean reproductive physiology.
光周期是协调甲壳类动物生殖生理和昼夜节律生物学的关键环境线索，但将光周期与卵巢成熟和生物钟调节联系起来的神经基因网络在很大程度上仍然未知。为了阐明光周期调控卵巢发育及其昼夜节律的分子机制，对中华绒螯蟹（Eriocheir sinensis）雌性绒螯蟹（Eriocheir sinensis）的眼柄（SG）和脑神经节（BG）进行了转录组分析，分析了两个光周期组(Light (L): Dark （D) = 0 h: 24 h （L0）和L: D = 18 h: 6 h (L18)）的眼柄（SG）和脑神经节（BG）。该分析在大脑中鉴定出298个差异表达基因（DEGs），在眼柄中鉴定出109个差异表达基因（DEGs）。KEGG富集分析表明，这些deg主要与卵巢发育和昼夜节律相关的信号通路有关。卵巢发育相关的关键基因，包括E3泛素蛋白连接酶lubel样异构体X6、5-羟色胺受体样异构体、丝氨酸/苏氨酸蛋白磷酸酶α -2、雌激素硫转移酶、细胞色素P450 2 l1样、促卵泡激素受体样异构体X1和E3泛素蛋白连接酶CHIP (EULCHIP)，在L18-BG组均出现显著上调或下调。同时，EULCHIP、E3泛素蛋白连接酶trim71样、creb结合蛋白样异构体X2、丝氨酸/苏氨酸蛋白磷酸酶6调节锚蛋白重复亚基C、胶原α -5（IV）链、整合素β 1、外皮激素诱导蛋白74ef样、胰岛素样生长因子结合蛋白复合体酸不稳定亚基等基因在L18-SG组均出现显著上调或下调。这些结果表明，延长光周期可以促进卵巢发育，调节卵巢成熟过程中的生殖内分泌活动。此外，昼夜节律相关基因，如周期昼夜节律蛋白样异构体X1、前列腺素D合成酶和乙酰胆碱受体亚基α型acr-16在光周期组之间表现出明显的差异表达，表明在长时间光照下，分子振荡被破坏，昼夜节律逐渐去同步。该研究为甲壳类动物卵巢发育和内分泌动力学的光周期驱动调控网络提供了关键的系统级见解，为优化水产养殖实践提供了分子基础，并促进了我们对甲壳类动物生殖生理学的理解。
{"title":"Neuroendocrine transcriptomics in Eriocheir sinensis: Photoperiod-induced modulation of gonadal development and circadian clock genes in neural tissues","authors":"Gaoyuan Yuan , Meihui Huo , Boyi Zheng , Zhichao Wang , Xugan Wu , Meimei Liu , Zhiguo Dong","doi":"10.1016/j.cbd.2025.101629","DOIUrl":"10.1016/j.cbd.2025.101629","url":null,"abstract":"<div><div>Photoperiod is a critical environmental cue that orchestrates reproductive physiology and circadian biology in crustaceans, yet the neural gene networks linking photoperiod to ovarian maturation and clock regulation remain largely unknown. To elucidate the molecular mechanisms underlying photoperiod regulation of ovarian development and associated circadian rhythmicity, the eyestalk (SG) and brain ganglion (BG) of female Chinese mitten crab (<em>Eriocheir sinensis</em>) from two photoperiod groups (Light (L): Dark (D) = 0 h: 24 h (L0) and L: D = 18 h: 6 h (L18)) were used for transcriptome analysis. The analysis identified 298 differentially expressed genes (DEGs) in the brain and 109 DEGs in the eyestalk. KEGG enrichment analysis indicated these DEGs were primarily associated with ovarian development and circadian rhythm-related signaling pathways. Key ovarian development-related genes, including E3 ubiquitin-protein ligase lubel-like isoform X6, 5-hydroxytryptamine receptor-like, serine/threonine-protein phosphatase alpha-2, estrogen sulfotransferase, cytochrome P450 2 L1-like, follicle-stimulating hormone receptor-like isoform X1 and E3 ubiquitin-protein ligase CHIP (EULCHIP), exhibited significant upregulation or downregulation in the L18-BG group. Meanwhile, genes such as EULCHIP, E3 ubiquitin-protein ligase TRIM71-like, CREB-binding protein-like isoform X2, serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit C, collagen alpha-5(IV) chain, integrin beta 1, ecdysone-induced protein 74EF-like, and insulin-like growth factor-binding protein complex acid labile subunit showed significant upregulation or downregulation in the L18-SG group. These findings suggest that prolonged photoperiods enhance ovarian development and modulate reproductive endocrine activity during ovarian maturation. Furthermore, circadian rhythm-related genes such as period circadian protein-like isoform X1, prostaglandin D synthase, and acetylcholine receptor subunit alpha-type acr-16 displayed marked differential expression between photoperiod groups, indicating disrupted molecular oscillations and gradual desynchronization of circadian rhythmicity under extended light exposure. This study provides critical, systems-level insights into the photoperiod-driven regulatory networks of ovarian development and endocrine dynamics in crustaceans, offering a molecular basis for optimizing aquaculture practices and advancing our understanding of crustacean reproductive physiology.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101629"},"PeriodicalIF":2.2,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145048557","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}
The increasing challenge in agricultural insect pest management is the rapid development of insecticide resistance. Amrasca biguttula biguttula, a significant sap-sucking pest of cotton and other crops, causes severe damage through feeding and toxin injection while exhibiting resistance to multiple insecticides, including Imidacloprid. Understanding the genetic factors and mechanisms driving resistance in A. biguttula biguttula is crucial for effective pest control. This study utilized Illumina HiSeq sequencing to generate a transcriptome assembly and analyze differential gene expression in response to Imidacloprid. Differential expression analysis using DESeq2 identified 177 significantly expressed transcripts, with 67 upregulated and 110 downregulated. To validate these findings, the gene expression of selected genes in response to Imidacloprid exposure at LC50 concentration (24.91 ppm) was tested at different time points (6 h, 12 h, and 24 h) relative to 0 h (control). The significant upregulation of detoxification-related genes such as cytochrome P450 monooxygenase (CYP303A1, CYP4DE1, CYP3184-fragment1 and CYP3939A2), three carboxylesterases (CE-1, CE-2, and CE-3), and one ABC transporter (ABC), highlights its potential role in Imidacloprid resistance. This study is the first to explore the molecular mechanisms underlying Imidacloprid resistance in A. biguttula biguttula and offers valuable insights for improving current pest management strategies.
{"title":"Investigating imidacloprid resistance in Amrasca biguttula biguttula (Ishida) (Hemiptera: Cicadellidae): Insights from RNA-Seq and functional validation using RT-qPCR","authors":"Muthugounder Mohan , B.R. Basavaarya , Karuppannasamy Ashok , Sathasivam Malarvizhi , P.J. Aneesha , Gandhi R. Gracy , Thiruvengadam Venkatesan , R.S. Ramya , S.N. Sushil","doi":"10.1016/j.cbd.2025.101630","DOIUrl":"10.1016/j.cbd.2025.101630","url":null,"abstract":"<div><div>The increasing challenge in agricultural insect pest management is the rapid development of insecticide resistance. <em>Amrasca biguttula biguttula</em>, a significant sap-sucking pest of cotton and other crops, causes severe damage through feeding and toxin injection while exhibiting resistance to multiple insecticides, including Imidacloprid. Understanding the genetic factors and mechanisms driving resistance in <em>A. biguttula biguttula</em> is crucial for effective pest control. This study utilized Illumina HiSeq sequencing to generate a transcriptome assembly and analyze differential gene expression in response to Imidacloprid. Differential expression analysis using DESeq2 identified 177 significantly expressed transcripts, with 67 upregulated and 110 downregulated. To validate these findings, the gene expression of selected genes in response to Imidacloprid exposure at LC<sub>50</sub> concentration (24.91 ppm) was tested at different time points (6 h, 12 h, and 24 h) relative to 0 h (control). The significant upregulation of detoxification-related genes such as cytochrome P450 monooxygenase (CYP303A1, CYP4DE1, CYP3184-fragment1 and CYP3939A2), three carboxylesterases (CE-1, CE-2, and CE-3), and one ABC transporter (ABC), highlights its potential role in Imidacloprid resistance. This study is the first to explore the molecular mechanisms underlying Imidacloprid resistance in <em>A. biguttula biguttula</em> and offers valuable insights for improving current pest management strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101630"},"PeriodicalIF":2.2,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145048556","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}
Pub Date : 2025-09-06DOI: 10.1016/j.cbd.2025.101628
Xiao Wei , Xiangna Zhao
The transmission of mosquito-borne diseases is intrinsically linked to mosquito blood-feeding behavior, yet the metabolic adaptations of the midgut microbiota in response to blood meals remain poorly understood. This study aimed to characterize the structural and functional changes in the midgut microbiota of Aedes albopictus following blood feeding and to elucidate their potential physiological implications. In this study, we employed 16S rRNA gene amplification coupled with PacBio Sequel II sequencing to characterize shifts in the midgut microbiota of Aedes albopictus before and after blood feeding on mice. Following blood feeding, we observed a significant restructuring of the microbial composition. This shift was characterized by a marked enrichment of Acinetobacter and Wolbachia, with Wolbachia displacing Flavisolibacter as the dominant taxon. Functionally, blood feeding promoted the upregulation of pathways related to mobile genetic elements and stress tolerance, largely driven by Lactobacillaceae. Furthermore, we presented the first comprehensive analysis of blood meal-induced metabolic network remodeling in the mosquito midgut microbiota. Post-prandial microbiota exhibited enhanced metabolic capacity for pyruvate and glycine catabolism. These findings reveal that blood meals induce rapid microbial metabolic adaptation aimed at nutrient utilization and oxidative management. This study provides insight into how microbiota dynamics support mosquito host adaptation under nutritional stress and offers potential targets for microbiome-based strategies to interfere with vector competence.
{"title":"Blood meal modulates midgut bacterial community structure and metabolic function in Aedes albopictus","authors":"Xiao Wei , Xiangna Zhao","doi":"10.1016/j.cbd.2025.101628","DOIUrl":"10.1016/j.cbd.2025.101628","url":null,"abstract":"<div><div>The transmission of mosquito-borne diseases is intrinsically linked to mosquito blood-feeding behavior, yet the metabolic adaptations of the midgut microbiota in response to blood meals remain poorly understood. This study aimed to characterize the structural and functional changes in the midgut microbiota of <em>Aedes albopictus</em> following blood feeding and to elucidate their potential physiological implications. In this study, we employed 16S rRNA gene amplification coupled with PacBio Sequel II sequencing to characterize shifts in the midgut microbiota of <em>Aedes albopictus</em> before and after blood feeding on mice. Following blood feeding, we observed a significant restructuring of the microbial composition. This shift was characterized by a marked enrichment of <em>Acinetobacter</em> and <em>Wolbachia</em>, with <em>Wolbachia</em> displacing <em>Flavisolibacter</em> as the dominant taxon. Functionally, blood feeding promoted the upregulation of pathways related to mobile genetic elements and stress tolerance, largely driven by <em>Lactobacillaceae</em>. Furthermore, we presented the first comprehensive analysis of blood meal-induced metabolic network remodeling in the mosquito midgut microbiota. Post-prandial microbiota exhibited enhanced metabolic capacity for pyruvate and glycine catabolism. These findings reveal that blood meals induce rapid microbial metabolic adaptation aimed at nutrient utilization and oxidative management. This study provides insight into how microbiota dynamics support mosquito host adaptation under nutritional stress and offers potential targets for microbiome-based strategies to interfere with vector competence.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101628"},"PeriodicalIF":2.2,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018705","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}
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