Computational protocol: A new species of Trichoderma hypoxylon harbours abundant secondary metabolites

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Protocol publication

[…] The ITS and TEF1-α data sets used sequences of isolates CGMCC 3.17906, CGMCC 3.17907 and reference sequences were downloaded from GenBank (). The ITS, TEF1-α and RPB2 data sets were aligned by MAFFT ver.7.03 using the Q-INS-I strategy, individually. The ambiguous areas of alignment were located and removed using Gblocks 0.91b. Previous phylogenetic analysis of ITS, RPB2 and TEF1-α sequence data from 260 Trichoderma species was conducted seperately with N. berolinensis and N. eustromatica as outgroup. Then, single and combined genes analyses of ITS, TEF1-α and RPB2 sequence data of 60 phylogenetic closed Trichoderma species in Brevicompactum, Deliquescens, Hypoceanum, Longibrachiatum, Polysporum, Psychrophila and green spore sections were carried out. N. berolinensis and N. eustromatica were arranged as outgroup taxa.Maximum parsimony (MP) analysis was conducted by PAUP 4.0b10 using a heuristic search with tree-bisection-reconnection branch swapping. All characters were treated as unordered and unweighted, gaps were treated as missing data, sequences were auto-increased and Maxtrees was 5,000. Topological confidence of resulted trees was tested by bootstrap proportion with 1,000 replicates, each with 100 replicates of random addition. Bootstrap proportion (BP) higher than 50% from maximum parsimony analysis from PAUP are given.Maximum-likelihood (ML) analysis was performed in RAxML implemented in raxml GUI v.1.3. GTRGAMMAI was specified as the model. The analysis was run with a rapid bootstrap analysis using a random start with rapid bootstrap analysis with 1,000 replicates. Bootstrap proportion (BP) higher than 50% from maximum likelihood analysis from RAxML are given.Bayesian Inference (BI) analysis was performed with MrBayes 3.1.2 using Markov chain Monte Carlo (MCMC) algorithm. Appropriate nucleotide substitution models was determined by MrModeltest 2.3 and the best fit model “GTR + I + G” was selected by Akaike Information Criterion for the investigated data set. Six chains (one cold and three heated) of 135,000 Markov chain Monte Carlo generations were run, sampling every 100 generation resulting in 1,350 total trees (in two simultaneous analyses). The initial 337 trees (25%) were discarded as burn-in phase of the analyses, and the remaining trees in each analysis were used to calculate posterior probabilities (PP) in the majority rule consensus tree, posterior probabilities greater than 0.95 are given.All trees were viewed in TreeView 1.6.6 and revised in Adobe Illustrator CS5. […]

Pipeline specifications

Software tools MAFFT, Gblocks, PAUP*, RAxML, MrBayes, MrModelTest, TreeViewX, Adobe Illustrator
Applications Miscellaneous, Phylogenetics
Organisms Aspergillus fumigatus
Chemicals Trichothecenes