Amplicon sequencing data of riverine metagenomic samples obtained from Takamigawa River in Nara Prefecture, Japan
Description
The amplicon sequencing data of the partial coding regions of mitochondrial cox1, nuclear histone H3 and 18S rRNA genes were obtained from the bulk community samples. 1. Sampling sites and dates Aridoshi (ARD) on 17-March-2017, 34°23′23″N 135°59′17″E, Shisetsu at Kozugawa (SST) on 29-June-2017, 34°23′53″N 135°59′34″E. Sampling was performed in the run environment (slow riffle) of ARD and SST (SST-run), and in the rapid environment of SST (SST-rapid). The samples ARD1~ARD6 listed in Table 1 were obtained from ARD. The samples SST1~3, SST7~9, and SST13~15 were obtained from SST-rapid. The samples SST4~6, SST10~12, and SST16~18 were obtained from SST-run. 2. Amplicon sequencing High-throughput parallel sequencing was performed by Miseq (Illumina, San Diego, CA, USA) capable of generating 2 × 300 base paired-end reads. Primer sequences of PCR amplification, accession numbers of DNA sequence data are summarized in Table 1. 3. Operational taxonomic units (OTUs) Amplicon sequence reads of histone H3 (DRR131047~DRR131054) were classified into a total of 563 OTUs (file name: Takamigawa-H3.fasta) based on the criteria described previously by Wakimura et al. (doi: 10.1016/j.dib.2022.108599). Amplicon sequence reads of 18S rRNA (DRR131055~DRR131062) were classified into a total of 3001 OTUs (file name: Takamigawa-18S.fasta) by QIIME. The OTUs of cox1 are available in Mendeley Data (doi: 10.17632/pfhf4kt37s.1). OTUs are named and numbered arbitrarily. 4. GMYC analyses Phylogenetic trees of the OTUs were reconstructed using Markov chain Monte Carlo (MCMC) methods by MrBayes 3.2.7a with the GTR+I+G molecular clock model. Species boundaries were estimated using SPLITS package in R. The analyses delimited 369 species for cox1 data (figures 1a and 1b of Wakimura et al., doi: 10.1016/j.dib.2022.108599) and 141 species for histone H3 data (file name: H3_tree.pdf), respectively. In the cladograms of cox1 and histone H3, each vertical bar indicates a cluster of OTUs or singleton assigned to a single GMYC species. Numbers in parentheses after the OTU name indicate the number of reads of the OTU. Numbers with dotted lines refer to the GYMC species IDs. 5. Frequency of sequence reads Numbers of sequence reads within the GMYC-delimited species (cox1 and histone H3) or of each operational taxonomic unit (18S rRNA) are summarized in the Table 2 (cox1), Table 3 (histone H3) and Table 4 (18S rRNA), respectively.