Abstract
The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene sequences was accomplished using PCR. Thirteen PKS, 5 NRPS, and 4 PKS-NRPS hybrids were identified and characterized with functions including swainsonine and melanin biosynthesis. Phylogenetic relationships among closest amino acid matches with Alternaria spp. were identified for seven highly conserved PKS and NRPS, including melanin synthesis. Three PKS and NRPS were most closely related to other fungi within the Pleosporaceae family, while five PKS and PKS-NRPS were closely related to fungi in the Pleosporales order. However, seven PKS and PKS-NRPS showed no identity with fungi in the Pleosporales or the class Dothideomycetes, suggesting a different evolutionary origin for those genes.
Document Type
Article
Publication Date
7-6-2021
Digital Object Identifier (DOI)
https://doi.org/10.3390/jof7070538
Related Content
Sequence data has been deposited into Genbank. See Table 1 for specific accession numbers.
The following are available online at https://www.mdpi.com/article/10.3390/jof7070538/s1, Figure S1: Domain order of PKS-NRPS 58882 and polyketide synthase of Metarhizium acridum XP_07815889, Figure S2: Domain order of PKS-NRPS 5601 and hypothetical protein of Setosphaeria turcica XP_008025924, Figure S3: Domain order of PKS-NRPS 21438 and hypothetical protein of Pyrenophora teres XP_003303559, Figure S4: Domain order of PKS-NRPS 62407 and hypothetical protein of Tolypocladium ophioglossoides KND87119, Figure S5: Domain order of PKS 2122 and ALT5 of Alternaria solani BAD83684, Figure S6: Domain order of PKS 1562 and PKS5 of Bipolaris maydis AAR90268, Figure S7: Domain order PKS 59499 and hypothetical protein of Aspergillus nomius KNG90368, Figure S8: Domain order of PKS 96133 and PKSF of Alternaria alternata AFN68297, Figure S9: Domain order of PKS 9132 and PKSD of Aspergillus niger XP_001394543, Figure S10: Domain order PKS 39849 and PPSA of Pyrenophora tritici-repentis XP_001937136, Figure S11: Domain order of PKS 17612 and PPSB of Pyrenothora tritici-repentis XP_001934720, Figure S12: Domain order of PKS 8407 and Alternaria solani PKSF BAE80697, Figure S13: Domain order of PKS 40283 and PKSA of Alternaria alternata AFN68292, Figure S14: Domain order of PKS 3398 and polyketide synthase of Metarhizium brunneum KID62944, Figure S15: Domain order of NRPS 33635 and NPS6 of Alternaria alternata AFN69082, Figure S16: Domain order of PKS 5682 and Alternaria brassicae nrps1 AAP78735, Figure S17: Domain order of NRPS 7859 and NPS9 of Cochliobolus heterostrophus AAX09991, Figure S18: Domain order of NRPS 8194 and HC-toxin synthetase of Pyrenophora tritici-repentis, Figure S19: Domain order of NRPS 40703 and NPS2 of Alternaria brassicicola, Figure S20: Domain order of PKS 12778 and hypothetical protein from Fusarium oxysporum f. sp. conglutinans EXL67078, Figure S21: Domain order of PKS 42460 and hypothetical polyketide synthase of Colletotrichum gloeosporioides XP_007270670, Figure S22: Domain order of PKS 29103 and hypothetical protein of Aspergillus parasiticus KJK63007, Figure S23: Maximum parsimony tree (MUSCLE alignment and 1000 replicates). Lasiodiplodia theobromae was used as the outgroup. Fungi in tree are pblast results of 17612 sequence; Figure S24: Maximum parsimony tree (MUSCLE alignment and 1000 replicates). Pyrenophora teres was used as the outgroup. Fungi in tree are pblast results of 5682 sequence.: Figure S25: Maximum parsimony tree (MUSCLE alignment and 1000 replicates). Aspergillus luchuensis was used as the outgroup. Fungi in tree are pblast results of 9132 sequence. Table S1: GenBank accession numbers and amino acid percent identity of blast results of 2122 sequence, Table S2: Genbank accession numbers and amino acid percent identity of blast results of 17612 sequence, Table S3: Genbank accession numbers and amino acid percent identity of blast results of 8407 sequence, Table S4: Genbank accession numbers and amino acid percent identity of blast results of 3398 sequence, Table S5: GenBank accession numbers and amino acid percent identity of blast results of 40283 sequence, Table S6: Genbank accession numbers and amino acid percent identity of blast results of 33635 sequence, Table S7: Genbank accession numbers and amino acid percent identity of blast results of 5682 sequence, Table S8: Genbank accession numbers and amino acid percent identity of blast results of 9132 sequence.
The above materials are also available for download as the additional file listed at the end of this record.
Repository Citation
Creamer, Rebecca; Hille, Deana Baucom; Neyaz, Marwa; Nusayr, Tesneem; Schardl, Christopher L.; and Cook, Daniel, "Genetic Relationships in the Toxin-Producing Fungal Endophyte, Alternaria oxytropis Using Polyketide Synthase and Non-Ribosomal Peptide Synthase Genes" (2021). Plant Pathology Faculty Publications. 101.
https://uknowledge.uky.edu/plantpath_facpub/101
Supplementary materials
Notes/Citation Information
Published in Journal of Fungi, v. 7, issue 7, 538.
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).