mcrA gene amplicon classification and distribution across lake sediment samples

Amplicon libraries were prepared as described in Han <i>et al</i>. 2020 (https://doi.org/10.1111/1462-2920.15115) and involved the same <i>mcr</i>A primer combination as for qPCR. Sequencing was done on an Illumina MiSeq (Illumina Inc.). Raw sequence reads were quality-checked by <i>FastQC</i>, read ends trimmed using <i>seqtk</i>, paired end reads merged into amplicons by <i>FLASH</i>, primer sites trimmed by <i>usearch</i>, and quality filtering was done by <i>prinseq</i>. Zero-radius Operational Taxonomic Units (ZOTUs) were generated using UNOISE3 and clustered using a 97% similarity threshold to generate OTUs. OTUs were taxonomically identified based on neighbor-joining phylogenetic trees in ARB. This mcrA database used for classification contained &gt;2,400 high-quality <i>mcrA </i>sequences from a wide range of published amplicon and whole-genome sequencing studies with manually optimized sequence alignments (https://doi.org/10.3389/fmicb.2023.1192029).