To preliminarily identify the species which the isolates obtained in this study, a standard nucleotide BLAST search was conducted using the tef1, tub2, cmdA and his3 sequences. The sequences of tef1, tub2, cmdA and his3 gene regions generated in this study were compared with sequences of type specimen strains of published Calonectria species for phylogenetic analyses. Sequences of all the published species in the relative species complexes were used for sequence comparisons and phylogenetic analyses. The datasets of Liu and co-authors [28] were used as templates for analyses.

Sequences of each of the tef1, tub2, cmdA and his3 gene regions as well as the combination of these four gene regions were aligned using the online version of MAFFT v. 7 ( with the alignment strategy FFT-NS-i (Slow; interactive refinement method). After initial alignments, sequence alignments were manually edited using MEGA v. 6.0.5 software [34].

Maximum parsimony (MP) and maximum likelihood (ML) were used frequently for phylogenetic analyses of Calonectria species [28,29,36]. To test whether the analysis results between the two methods are consistent, both MP and ML were used for phylogenetic analyses for sequence datasets of each of the four genes and the combination of four gene regions. The MP and ML analyses were conducted using the methods described by Liu and Chen [33]. Phylogenetic trees were viewed using MEGA v. 6.0.5 [34]. Sequence data of two isolates of Curvicladiella cignea (CBS 109167 and CBS 109168) were used as outgroups [28].

Note: The content above has been extracted from a research article, so it may not display correctly.

Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.

We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.