Computational protocol: Enniatin and Beauvericin Biosynthesis in Fusarium Species: Production Profiles and Structural Determinant Prediction

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Protocol publication

[…] The esyn1 sequences of the 13 Fusarium isolates were extracted from the published and unpublished genomes by BLASTN search by querying with the available sequences of F. equiseti (ex scirpi) (NCBI Accession Number Z18755.3) and F. proliferatum (NCBI Accession Number JF826561.1). The protein sequences were predicted using the Sequence Translation tools of the EMBOSS Programs (EMBL-EBI), manually curated with exon/intron boundary predictions from SpliceView (http://bioinfo4.itb.cnr.it/) and confirmed by RT-PCR of different partial sequences (Multifasta S1 and S2).The esyn1 mRNA from the F. verticillioides strain FGSC 7600 did not contain the 568-bp intron predicted by Ma et al. [] (Ensembl Fungi Accession Number FVEG_09993). This intron was predicted incorrectly because the sequence was partially mapped on two different contigs with a region missing. This intron also was missing in all of the other sequences included in this study. The F. proliferatum transcripts lacked the 134-bp intron reported by Zhang et al. []. The esyn1 mRNA from KSU 3089G had a 13-bp duplicated insertion that results in a premature stop and the synthesis of a truncated protein (Multifasta S2).The protein tree inferred from the Clustal Omega multi-alignment of the 13 amino acid sequences () separates the F. fujikuroi and F. proliferatum groups and the other species. […]

Pipeline specifications

Software tools BLASTN, EMBOSS, SpliceView, Clustal Omega
Databases esyN
Application WGS analysis
Chemicals Amino Acids