Metataxonomics cocoa lab-scale
Metagenomic DNA extraction was performed according to the protocol described by our research group in the reference (Almeida et al. 2020). In summary, three random seeds were selected, and their pulp were scraped. Then, DNA extraction was performed according to the recommendations of the manufacturer of the Zymobiomics DNA MINI KIT (California, USA). The extracted DNA was quantified by Qubit fluorometer (ThermoFischer) and nanodrop (ThermoFischer) and sent to the BPI Biotecnologia EPP facility for 16S rRNA V3-V4 region (forward primer: 5'  TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG -3'; reverse primer: 5'-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC- 3') and ITS region amplification (primer 86F: 5'- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTGAATCATCGAATCTTTGAA-3'; 4R: 5'- GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCCTCCGCTTATTGATATGC-3') and sequencing on the MiniSeq platform (Illumina) to generate paired-end (PE) 2x250 bp reads following the facilitys protocols.
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