scholarly journals Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

PLoS Biology ◽  
2017 ◽  
Vol 15 (11) ◽  
pp. e2003583 ◽  
Author(s):  
Abigail L. Lind ◽  
Jennifer H. Wisecaver ◽  
Catarina Lameiras ◽  
Philipp Wiemann ◽  
Jonathan M. Palmer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Clusters ◽  
Fungal Species ◽  
Metabolic Gene

scholarly journals Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

2017 ◽  
Author(s):  
Abigail L. Lind ◽  
Jennifer H. Wisecaver ◽  
Catarina Lameiras ◽  
Philipp Wiemann ◽  
Jonathan M. Palmer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Cluster ◽  
Metabolic Pathways ◽  
Point Mutations ◽  
Gene Clusters ◽  
Fungal Species ◽  
Species Variation ◽  
Gene Gain ◽  
Genome Wide ◽  
Gain And Loss

SummaryFilamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed five general types of variation in SM gene clusters: non-functional gene polymorphisms, gene gain and loss polymorphisms, whole cluster gain and loss polymorphisms, allelic polymorphisms where different alleles corresponded to distinct, non-homologous clusters, and location polymorphisms in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid, as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms whose detection requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and non-homologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, genomic deletion and insertion events, as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.

scholarly journals Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

2021 ◽  
Vol 9 (8) ◽  
pp. 1612
Author(s):  
Werner Ruppitsch ◽  
Andjela Nisic ◽  
Patrick Hyden ◽  
Adriana Cabal ◽  
Jasmin Sucher ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Safety Evaluation ◽  
Gene Clusters ◽  
Northern Region ◽  
Genomic Diversity ◽  
High Genetic Diversity ◽  
Pathogenic Factors ◽  
Flavor Development ◽  
Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

scholarly journals Isolation, Molecular Identification, and Mycotoxin Production of Aspergillus Species Isolated from the Rhizosphere of Sugarcane in the South of Iran

Toxins ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 122 ◽  
Author(s):  
Maryam Tavakol Noorabadi ◽  
Valiollah Babaeizad ◽  
Rasoul Zare ◽  
Bita Asgari ◽  
Miriam Haidukowski ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Aspergillus Terreus ◽  
Plant Pathogens ◽  
Fungal Species ◽  
Aspergillus Species ◽  
Aspergillus Tubingensis ◽  
Ecological Role ◽  
The South ◽  
Mycotoxin Production ◽  
Aspergillus Section

Knowledge of the genetic diversity detected among fungal species belonging to the genus Aspergillus is of key importance for explaining their important ecological role in the environment and agriculture. The current study aimed to identify Aspergillus species occurring in the rhizosphere of sugarcane in the South of Iran, and to investigate their mycotoxin profiles. One-hundred and twenty-five Aspergillus strains were isolated from the soil of eight major sugarcane-producing sites, and were molecularly identified using sequences of partial -tubulin (benA) and partial calmodulin (CaM) genes. Our molecular and phylogenetic results showed that around 70% of strains belonged to the Aspergillus section Nigri, and around 25% of species belonged to the Aspergillus section Terrei. Species belonging to both sections are able to produce different mycotoxins. The production of mycotoxins was measured for each species, according to their known mycotoxin profile: patulin (PAT) and sterigmatocystin (STG) for Aspergillus terreus; ochratoxin A (OTA) and fumonisins for Aspergillus welwitschiae; and OTA alone for Aspergillus tubingensis. The data showed that the production of OTA was detected in only 4 out of 10 strains of A. welwitschiae, while none of the A. tubingensis strains analyzed produced the mycotoxin. Fumonisins were produced by 8 out of 10 strains of A. welwitschiae. Finally, none of the 23 strains of A. terreus produced STG, while 13 of them produced PAT. The occurrence of such mycotoxigenic plant pathogens among the fungal community occurring in soil of sugarcane fields may represent a significant source of inoculum for the possible colonization of sugarcane plants, since the early stages of plant growth, due to the mycotoxin production capability, could have worrisome implications in terms of both the safety and loss of products at harvest.

scholarly journals A Rare Thioquinolobactin Siderophore Present in a Bioactive Pseudomonas sp. DTU12.1

2019 ◽  
Vol 11 (12) ◽  
pp. 3529-3533
Author(s):  
Pavelas Sazinas ◽  
Morten Lindqvist Hansen ◽  
May Iren Aune ◽  
Marie Højmark Fischer ◽  
Lars Jelsbak
Keyword(s):  
Gene Cluster ◽  
Secondary Metabolite ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Plant Pathogens ◽  
Gene Clusters ◽  
Fungal Species ◽  
Antagonistic Activity ◽  
Evolutionary Origins

Abstract Many of the soil-dwelling Pseudomonas species are known to produce secondary metabolite compounds, which can have antagonistic activity against other microorganisms, including important plant pathogens. It is thus of importance to isolate new strains of Pseudomonas and discover novel or rare gene clusters encoding bioactive products. In an effort to accomplish this, we have isolated a bioactive Pseudomonas strain DTU12.1 from leaf-covered soil in Denmark. Following genome sequencing with Illumina and Oxford Nanopore technologies, we generated a complete genome sequence with the length of 5,943,629 base pairs. The DTU12.1 strain contained a complete gene cluster for a rare thioquinolobactin siderophore, which was previously described as possessing bioactivity against oomycetes and several fungal species. We placed the DTU12.1 strain within Pseudomonas gessardii subgroup of fluorescent pseudomonads, where it formed a distinct clade with other Pseudomonas strains, most of which also contained a complete thioquinolobactin gene cluster. Only two other Pseudomonas strains were found to contain the gene cluster, though they were present in a different phylogenetic clade and were missing a transcriptional regulator of the whole cluster. We show that having the complete genome sequence and establishing phylogenetic relationships with other strains can enable us to start evaluating the distribution and evolutionary origins of secondary metabolite clusters.

scholarly journals Genetic Diversity among Clostridium botulinum Strains Harboringbont/A2andbont/A3Genes

2012 ◽  
Vol 78 (24) ◽  
pp. 8712-8718 ◽  
Author(s):  
Carolina Lúquez ◽  
Brian H. Raphael ◽  
Lavin A. Joseph ◽  
Sarah R. Meno ◽  
Rafael A. Fernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clostridium Botulinum ◽  
Type A ◽  
Gene Clusters ◽  
Nucleotide Sequencing ◽  
Toxin Gene ◽  
Content Type ◽  
Geographic Origins ◽  
Diversity Studies ◽  
Insight Into

ABSTRACTClostridium botulinumtype A strains are known to be genetically diverse and widespread throughout the world. Genetic diversity studies have focused mainly on strains harboring one type A botulinum toxin gene,bont/A1, although all reportedbont/Agene variants have been associated with botulism cases. Our study provides insight into the genetic diversity ofC. botulinumtype A strains, which containbont/A2(n= 42) andbont/A3(n= 4) genes, isolated from diverse samples and geographic origins. Genetic diversity was assessed by usingbontnucleotide sequencing, content analysis of thebontgene clusters, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Sequences ofbontgenes obtained in this study showed 99.9 to 100% identity with otherbont/A2orbont/A3gene sequences available in public databases. The neurotoxin gene clusters of the subtype A2 and A3 strains analyzed in this study were similar in gene content.C. botulinumstrains harboringbont/A2andbont/A3genes were divided into six and two MLST profiles, respectively. Four groups of strains shared a similarity of at least 95% by PFGE; the largest group included 21 out of 46 strains. The strains analyzed in this study showed relatively limited genetic diversity using either MLST or PFGE.

scholarly journals Metabolic gene clusters encoding the enzymes of two branches of the 3-oxoadipate pathway in the pathogenic yeast Candida albicans

2015 ◽  
Vol 15 (3) ◽  
Author(s):  
Gabriela Gérecová ◽  
Martina Neboháčová ◽  
Igor Zeman ◽  
Leszek P. Pryszcz ◽  
Ľubomír Tomáška ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Gene Clusters ◽  
Pathogenic Yeast ◽  
Metabolic Gene

scholarly journals RNA sequencing of an nsdC mutant reveals global regulation of secondary metabolic gene clusters in Aspergillus flavus

2016 ◽  
Vol 182 ◽  
pp. 150-161 ◽  
Author(s):  
Matthew K. Gilbert ◽  
Brian M. Mack ◽  
Qijian Wei ◽  
John M. Bland ◽  
Deepak Bhatnagar ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Aspergillus Flavus ◽  
Gene Clusters ◽  
Global Regulation ◽  
Metabolic Gene

scholarly journals Delineation of metabolic gene clusters in plant genomes by chromatin signatures

2016 ◽  
Vol 44 (5) ◽  
pp. 2255-2265 ◽  
Author(s):  
Nan Yu ◽  
Hans-Wilhelm Nützmann ◽  
James T. MacDonald ◽  
Ben Moore ◽  
Ben Field ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Plant Genomes ◽  
Metabolic Gene
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