Computational protocol: Seed and Root Endophytic Fungi in a Range Expanding and a Related Plant Species

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Protocol publication

[…] Obtained chromatograms from all cultures were manually curated in Chromas Lite v 2.1. Curated sequences were aligned using MAFFT () and visualized in Seaview v4.6.1 ().The resulting 46 consensus sequences were subjected to BLASTn searched against the NCBI nucleotide database. For all consensus sequences, two best matches of known fungal species (three in case different species showed identical matches to best Blast matches of cultivated taxa, or unknown sequences), were aligned using MAFFT and visualized in Seaview. This resulted in an alignment containing 130 sequences.Maximum likelihood (ML) and Bayesian analyses were performed to assess the phylogenetic relatedness of all cultivated fungi. Maximum likelihood analyses were run in RAxML v8. () using the GTR+gamma model with eight rate categories. Rapid hill-climbing tree search algorithm with 1000 bootstrap replicates were used to build and assess the most stable shape of phylogenetic relationships. The phylogenetic tree was visualized in FigTree () and labeling of the final branches optimized in Gimp. […]

Pipeline specifications

Software tools MAFFT, SeaView, BLASTN, RAxML, FigTree
Application Phylogenetics