Bioinformatics and phylogenetic analysis
Paired reads from Illumina MiSeq sequencing were processed with the
open-source QIIME2 software (version 2019.1)
(Bolyen et al., 2018)
and the DADA2 pipeline
(Callahan et al.,
2016) to denoise the dataset from artefacts and to generate amplicon
sequence variants (ASVs). We assigned taxonomy within QIIME2 by building
a classifier using the RESCRIPt
(Robeson et al.,
2020) and the NCBI database using BLASTnt (Table S1). For phylogenetic
analyses we included Fusarium spp., isolated from sea
and Amazonian river turtles’ eggs, crops, environment and humans, and in addition, we included Fusarium spp., from the Fusarium Tricinctum Species Complex
(FTSC) and Fusarium Fujikuroi Species Complex (FFSC), to show the
different complexes’ clusters. We aligned and generated a Bayesian
phylogenetic tree with 26 sequences and an outgroup sequence by using
the MrBayes 3.2.6
(Ronquist et al.,
2012) module within Geneious v.11.0.5 (Kearse et al., 2012). Detailed
information on bioinformatics and the phylogenetic analysis is provided
in the supplementary material.