A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes.

ABSTRACT: The method of spiking synthetic internal standard genes (ISGs) to samples for amplicon sequencing, generating sequences and converting absolute gene numbers from read counts has been used only for phylogenetic markers and has not been applied to functional markers. In this study, we developed ISGs, including gene sequences of the 16S rRNA, pmoA, encoding a subunit of particulate methane monooxygenase and amoA, encoding a subunit of ammonia monooxygenase. We added ISGs to the samples, amplified the target genes and performed amplicon sequencing. For the mock community, the copy numbers converted from read counts using ISGs were equivalent to those obtained by the quantitative real-time polymerase chain reaction (4.0 × 10⁴ versus 4.1 × 10⁴ and 3.0 × 10³ versu

SUBMITTER: Koike K 

PROVIDER: S-EPMC10667660 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature