Computational protocol: Distribution, Characterization, and Diversity of the Endophytic Fungal Communities on Korean Seacoasts Showing Contrasting Geographic Conditions

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Protocol publication

[…] To confirm the identity of the isolates, a phylogenetic tree was constructed. Endophytic fungal nrITS sequences showed greater than 99% similarity with the sequences of other fungal species in the GenBank databases of the National Center for Biotechnology Information (NCBI). Phylogenetic relationships were analyzed by MEGA ver. 6.0 using alignments prepared with ClustalW []. Phylogenetic trees were inferred using the maximum-likelihood algorithm and Kimura 2-parameter distances. The stability of relationships was evaluated by bootstrap analysis with 1,000 replications []. All endophytic fungal isolate sequences (207) were deposited in NCBI GenBank (accession Nos. KU555946 to KU556152) (). The diversity [] of the isolates was determined by assessing species richness based on the Margalef (Dmg) [] and Menhinick (Dmn) indices [], and species diversity was measured by Shannon (H) [] and Simpson (D) indices []. […]

Pipeline specifications

Software tools MEGA, Clustal W
Application Phylogenetics
Organisms cellular organisms