Amplicon sequencing of PsbA gene, Short to medium-term impact of natural environmental changes on phytoplankton assemblage.
Sediment samples were collected off the Tohoku coast, Japan within a hundred and several tens kilometres (e.g. 70-140 km) from the epicentre of the 2011 magnitude 9.1, Tohoku earthquake. The PsbA gene, which codes for the D1 polypeptide of the photosystem II reaction centre complex, was amplified with primers using PCR. The PCR product mixtures were analysed for pair-end DNA sequencing of 300 bp Ã? 2 using MiSeq desktop sequencer (Illumina). The sequenced data were analysed in the Qiime bioinformatics pipeline (ver.1.7). Alpha diversity and beta diversity were calculated in QIIME workflow. As a result, we clarify how environmental fluctuations in temperature are related to phytoplankton assemblages over the past ~1,300 years, by sequencing the amplicon of the chloroplast gene from ancient DNA (aDNA) of sediments.