Table 1 Definitions of commonly used terminology.
From: High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS
Term | Definition |
|---|---|
16S-ITS Region | An instance of the 16S ribosomal RNA and its adjacent ITS region |
16S-ITS Product | The PCR product consisting of an instance of the 16S and ITS region defined by the RoC-ITS 27F and RoC-ITS 189R primers |
V4 Region | The 4th variable region of the 16S gene as defined by the Earth Microbiome F515/R806 primers |
RoC-ITS Consensus Sequence | Consensus sequence derived from multiple independent RoC-ITS sequences |
RoC-ITS Sequence | Consensus sequence derived from the amplification and iterated sequencing of a specific 16S-ITS region |
RoC-ITS Read | A long Nanopore read derived from a circularized 16S-ITS product consisting of 0 or more sub-reads |
Sub-Read | An individual 16S-ITS product found in a RoC-ITS read |
Splint DNA | Derived from the lambda virus genome, a sequence used to circularize the 16S-ITS products |
ITS | Internally transcribed spacer region; part of the ribosomal RNA operon |
ASV | Amplicon sequencing variants; unique sequences identified by DADA2 here derived from the V4 region |
Set of Sub-Reads | Multiple sub-reads derived from a single RoC-ITS read |
MSA | Multiple sequence alignment |
rrn | Ribosomal RNA operon including the 16S and 23S genes flanking the ITS region |
