Satya Prakash, Adrian Racovita, Teresa Petrucci, Roberto Galizi, Alfonso Jaramillo
{"title":"qSanger:通过Sanger测序对细菌培养物中的遗传变异进行量化。","authors":"Satya Prakash, Adrian Racovita, Teresa Petrucci, Roberto Galizi, Alfonso Jaramillo","doi":"10.34133/bdr.0007","DOIUrl":null,"url":null,"abstract":"<p><p>Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed <i>Escherichia coli</i> via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.</p>","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"5 ","pages":"0007"},"PeriodicalIF":0.0000,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521659/pdf/","citationCount":"1","resultStr":"{\"title\":\"qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing.\",\"authors\":\"Satya Prakash, Adrian Racovita, Teresa Petrucci, Roberto Galizi, Alfonso Jaramillo\",\"doi\":\"10.34133/bdr.0007\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed <i>Escherichia coli</i> via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.</p>\",\"PeriodicalId\":56832,\"journal\":{\"name\":\"生物设计研究(英文)\",\"volume\":\"5 \",\"pages\":\"0007\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2023-02-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521659/pdf/\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"生物设计研究(英文)\",\"FirstCategoryId\":\"1087\",\"ListUrlMain\":\"https://doi.org/10.34133/bdr.0007\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2023/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"生物设计研究(英文)","FirstCategoryId":"1087","ListUrlMain":"https://doi.org/10.34133/bdr.0007","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing.
Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed Escherichia coli via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.