Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples

Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant non-target species mackerel tuna (Euthynnus affinis), showing a clear relation between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrie..., This data is the raw sequencing output for a mitochondrial capture and a nuclear capture using custom-made myBaits target capture. Both captures are based on a single sample (two one-liter eDNA samples combined after extraction) collected in Qatari waters in the middle of a whale shark aggregation, in an area with an expected high abundance of Euthynnus affinis. There is thus no need for demultiplexing. 

The sequencing was performed on a MiSeq with 301 bp PE sequencing. 
, The mitochondrial target capture data consists of two zipped fastq-files (paired-end sequencing):
\"MKRJ_S3_L001_R1_001.fastq.gz\" and \"MKRJ_S3_L001_R2_001.fastq.gz\"


The nuclear target capture data consists of two zipped fastq-files (paired-end sequencing):
\"M6_S1_L001_R1_001.fastq.gz\" and \"M6_S1_L001_R2_001.fastq.gz\"

环境DNA（eDNA）是传统采样方法在群体遗传推断领域极具应用前景的补充手段，但当前相关研究几乎完全聚焦于短片段线粒体标记物。本研究针对鲸鲨（Rhincodon typus）开发了一套线粒体靶标捕获探针与一套核基因组靶标捕获探针，并将其应用于卡塔尔海域采集的海水样本，以验证靶标捕获技术在基于eDNA的群体研究中的应用潜力。线粒体靶标捕获成功获取了鲸鲨线粒体基因组约235倍的测序覆盖度（单碱基覆盖度区间为90倍至352倍）。以5%的次要等位基因频率为阈值，我们在线粒体基因组中共发现29个变异位点，表明样本中至少有5个贡献个体。此外，我们还从丰度较高的非靶标物种鲣鱼（Euthynnus affinis）中获取了大量线粒体测序读段，这表明序列与捕获探针的相似性与捕获读段数量之间存在显著相关性。核基因组靶标捕获探针的捕获结果……本数据集为使用定制myBaits靶标捕获试剂盒完成的线粒体捕获与核捕获的原始测序产出数据。两次捕获均基于单一样本（提取后将两份1升体积的eDNA样本合并），该样本采集于卡塔尔海域一处鲸鲨聚集的中心区域，且该区域预期存在较高丰度的鲣鱼种群，因此无需进行解多重（demultiplexing）操作。

测序在Illumina MiSeq测序仪上完成，采用301碱基对双端测序模式。

线粒体靶标捕获数据包含两个压缩FASTQ文件（双端测序）："MKRJ_S3_L001_R1_001.fastq.gz"与"MKRJ_S3_L001_R2_001.fastq.gz"

核基因组靶标捕获数据包含两个压缩FASTQ文件（双端测序）："M6_S1_L001_R1_001.fastq.gz"与"M6_S1_L001_R2_001.fastq.gz"