{"title":"通过基因表达模式识别用于半翅栉水母(鞘翅目:镍蝶科)表达分析的稳定参考基因","authors":"Raman Bansal, Charles S. Burks, Spencer S. Walse","doi":"10.1016/j.genrep.2024.101982","DOIUrl":null,"url":null,"abstract":"<div><p>Dried fruit beetle, <em>Carpophilus hemipterus</em>, (Linnaeus, 1758) (Coleoptera: Nitidulidae) is a serious pest of ripened fresh fruit in the orchard and dried fruit in post-processing storage. Despite the economic significance and widespread distribution of <em>C. hemipterus</em>, there is a lack of functional genomics research seeking to elucidate features of developmental biology and molecular physiology for improved pest management. Performing such functional genomics studies requires validated, stably expressed reference genes for accurate normalization of real-time quantitative reverse transcription-PCR (qRT-PCR) data. Here, we identified and validated 12 common insect reference genes (<em>RPL6</em>, <em>RPL4</em>, <em>RPL9</em>, <em>RPS13</em>, <em>RPS18</em>, <em>RPSA</em>, <em>TUB</em>, <em>UBE3A</em>, <em>RPS23</em>, <em>GLU</em>, <em>EF1A</em>, and <em>RBP</em>) for expression stability in <em>C. hemipterus</em>. These genes were assessed across developmental stages and sexes (egg, three larval instars, prepupa, pupa, adult male, and adult female) as well as thermal stress conditions. Stability of candidate genes was estimated using software algorithms geNorm, NormFinder, BestKeeper, comparative delta-Ct, and RefFinder. Two genes <em>UBE3A</em> and <em>RPL9</em> showed the highest stability across the treatments, and thus were proposed for normalizing the qRT-PCR raw data. Results of this study will strengthen the application of genomics to reveal the fundamental and applied biological aspects in this important beetle species.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0000,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Gene expression patterns to identify stable reference genes for expression analyses in Carpophilus hemipterus (L.) (Coleoptera: Nitidulidae)\",\"authors\":\"Raman Bansal, Charles S. Burks, Spencer S. Walse\",\"doi\":\"10.1016/j.genrep.2024.101982\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Dried fruit beetle, <em>Carpophilus hemipterus</em>, (Linnaeus, 1758) (Coleoptera: Nitidulidae) is a serious pest of ripened fresh fruit in the orchard and dried fruit in post-processing storage. Despite the economic significance and widespread distribution of <em>C. hemipterus</em>, there is a lack of functional genomics research seeking to elucidate features of developmental biology and molecular physiology for improved pest management. Performing such functional genomics studies requires validated, stably expressed reference genes for accurate normalization of real-time quantitative reverse transcription-PCR (qRT-PCR) data. Here, we identified and validated 12 common insect reference genes (<em>RPL6</em>, <em>RPL4</em>, <em>RPL9</em>, <em>RPS13</em>, <em>RPS18</em>, <em>RPSA</em>, <em>TUB</em>, <em>UBE3A</em>, <em>RPS23</em>, <em>GLU</em>, <em>EF1A</em>, and <em>RBP</em>) for expression stability in <em>C. hemipterus</em>. These genes were assessed across developmental stages and sexes (egg, three larval instars, prepupa, pupa, adult male, and adult female) as well as thermal stress conditions. Stability of candidate genes was estimated using software algorithms geNorm, NormFinder, BestKeeper, comparative delta-Ct, and RefFinder. Two genes <em>UBE3A</em> and <em>RPL9</em> showed the highest stability across the treatments, and thus were proposed for normalizing the qRT-PCR raw data. Results of this study will strengthen the application of genomics to reveal the fundamental and applied biological aspects in this important beetle species.</p></div>\",\"PeriodicalId\":12673,\"journal\":{\"name\":\"Gene Reports\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.0000,\"publicationDate\":\"2024-07-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Gene Reports\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2452014424001055\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Gene Reports","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2452014424001055","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Gene expression patterns to identify stable reference genes for expression analyses in Carpophilus hemipterus (L.) (Coleoptera: Nitidulidae)
Dried fruit beetle, Carpophilus hemipterus, (Linnaeus, 1758) (Coleoptera: Nitidulidae) is a serious pest of ripened fresh fruit in the orchard and dried fruit in post-processing storage. Despite the economic significance and widespread distribution of C. hemipterus, there is a lack of functional genomics research seeking to elucidate features of developmental biology and molecular physiology for improved pest management. Performing such functional genomics studies requires validated, stably expressed reference genes for accurate normalization of real-time quantitative reverse transcription-PCR (qRT-PCR) data. Here, we identified and validated 12 common insect reference genes (RPL6, RPL4, RPL9, RPS13, RPS18, RPSA, TUB, UBE3A, RPS23, GLU, EF1A, and RBP) for expression stability in C. hemipterus. These genes were assessed across developmental stages and sexes (egg, three larval instars, prepupa, pupa, adult male, and adult female) as well as thermal stress conditions. Stability of candidate genes was estimated using software algorithms geNorm, NormFinder, BestKeeper, comparative delta-Ct, and RefFinder. Two genes UBE3A and RPL9 showed the highest stability across the treatments, and thus were proposed for normalizing the qRT-PCR raw data. Results of this study will strengthen the application of genomics to reveal the fundamental and applied biological aspects in this important beetle species.
Gene ReportsBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
3.30
自引率
7.70%
发文量
246
审稿时长
49 days
期刊介绍:
Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.