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 mL 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.近年来发展起来的环境DNA（environmental DNA, eDNA）分析技术，已被用于以线粒体DNA（mitochondrial DNA, mtDNA）作为遗传标记来估算水生脊椎动物的分布范围。然而，线粒体DNA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，探讨了核DNA（nuclear DNA, ncDNA）作为更可靠的eDNA分析遗传标记的潜力。我们分别测定了鲤不同组织中线粒体DNA的细胞色素b（cytochrome b, CytB）基因区域，以及核DNA中核糖体DNA的内转录间隔区1（internal transcribed spacer 1, ITS1）区域的拷贝数，并对比了这两种标记在eDNA样本中的检出能力。在从脑组织、鳃组织以及肠道内容物中提取的DNA样本内，每细胞的CytB拷贝数分别为95.1±10.7（平均值±标准误）、29.7±1.59及24.0±4.33；而ITS1的每细胞拷贝数则分别为1760±343、2880±503及1910±352。在中宇宙（mesocosm）、池塘及湖水的eDNA样本中，ITS1的拷贝数分别约为CytB的160倍、300倍和150倍。用于定量检测所需的最小水样体积方面，ITS1仅需33 mL，而CytB则需要100 mL。上述结果表明，ITS1可作为鲤eDNA研究中更为灵敏的遗传标记。