Computational protocol: Phialosimplex salinarum, a new species of Eurotiomycetes from a hypersaline habitat

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Protocol publication

[…] The TSR1 and ITS sequences were compared with data in GenBank, using the BLAST function of NCBI (). The eight TSR1 sequences found to represent Phialosimplex salinarum, their closest relatives found, and representative species of Sagenomella, Aspergillus, and Penicillium were aligned using Muscle implemented in Geneious v. 6 (Biomatters, Auckland, New Zealand).Only unambiguously alignable positions were included in the phylogenetic analyses of TSR1 sequences, which correspond to base pairs 1–516 and 554–610 of sequence JN121732 (Phialosimplex chlamydosporus). A subsequent alignment of ITS sequences comprised only sequences of taxa with closer relationship to Phialosimplex as revealed by preliminary analysis (data not shown). It included the base pair positions 1761–1767, 1772–1803, 1806–1826, 1848–1859, 1865–1895, 1900–1914, 1916–1935, 1940–2149, 2159–2230, 2232–2252 of sequence GQ169326 (P. chlamydosporus). A maximum likelihood tree was calculated using PhyML v. 2.2.0 (Guindon & Gascuel 2003). Node support was evaluated based on 500 bootstrap replicates and a GTR (general-time-reversible) substitution model, as suggested by modeltest v. 3.7. In accordance with , the phylogenetic tree including only the genera Phialosimplex and Sagenomella was rooted with Eremascus albus (U18359.1). Penicillium olsonii (JN121771) was used as the outgroup in the initial Trichocomaceae tree. […]

Pipeline specifications

Software tools Geneious, PhyML, ModelTest-NG
Application Phylogenetics
Organisms Canis lupus familiaris
Diseases Mycoses