Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp (Cyprinus carpio)

The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio.

近年来新兴的环境DNA（environmental DNA, eDNA）分析技术，常以线粒体DNA（mitochondrial DNA, mtDNA）作为遗传标记，用于估算水生脊椎动物的分布范围。然而，mtDNA标记存在拷贝数可变、母系遗传等固有缺陷。本研究以鲤（Cyprinus carpio）为研究对象，探究核DNA（nuclear DNA, ncDNA）作为更可靠的eDNA分析遗传标记的潜力。我们测定了鲤不同组织中mtDNA细胞色素b（cytochrome b, CytB）基因区域与ncDNA核糖体DNA内部转录间隔区1（internal transcribed spacer 1, ITS1）的拷贝数，并对比了两类标记在eDNA样本中的检出效能。在脑组织、鳃组织及肠道内容物的提取DNA中，CytB的拷贝数分别为每细胞95.1±10.7（平均值±标准误）、29.7±1.59及24.0±4.33个，而ITS1的拷贝数则分别为每细胞1760±343、2880±503及1910±352个。在中型水生生态系统、池塘及湖泊水体的eDNA样本中，ITS1的拷贝数分别较CytB高出约160倍、300倍及150倍。用于定量检测的最小池塘水体体积，ITS1为33mL，CytB为100mL。上述结果表明，ITS1可作为鲤eDNA研究中灵敏度更优的遗传标记。