Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model

Ergot fungi (<i>Claviceps</i> spp.) are infamous for producing sclerotia containing a wide spectrum of ergot alkaloids (EA) toxic to humans and animals, making them nefarious villains in the agricultural and food industries, but also treasures for pharmaceuticals. In addition to three cl...

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Autores principales:	Miao Liu, Wendy Findlay, Jeremy Dettman, Stephen A. Wyka, Kirk Broders, Parivash Shoukouhi, Kasia Dadej, Miroslav Kolařík, Arpeace Basnyat, Jim G. Menzies
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	ergot alkaloids ergot fungi gene divergence gene diversity indole diterpenes phylogeny Medicine R
Acceso en línea:	https://doaj.org/article/12ae2b44251b418fb454d7b9e1877d19
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spelling	oai:doaj.org-article:12ae2b44251b418fb454d7b9e1877d192021-11-25T19:08:56ZMining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model10.3390/toxins131107992072-6651https://doaj.org/article/12ae2b44251b418fb454d7b9e1877d192021-11-01T00:00:00Zhttps://www.mdpi.com/2072-6651/13/11/799https://doaj.org/toc/2072-6651Ergot fungi (<i>Claviceps</i> spp.) are infamous for producing sclerotia containing a wide spectrum of ergot alkaloids (EA) toxic to humans and animals, making them nefarious villains in the agricultural and food industries, but also treasures for pharmaceuticals. In addition to three classes of EAs, several species also produce paspaline-derived indole diterpenes (IDT) that cause ataxia and staggers in livestock. Furthermore, two other types of alkaloids, i.e., loline (LOL) and peramine (PER), found in <i>Epichlo</i><i>ë</i> spp., close relatives of <i>Claviceps</i>, have shown beneficial effects on host plants without evidence of toxicity to mammals. The gene clusters associated with the production of these alkaloids are known. We examined genomes of 53 strains of 19 <i>Claviceps</i> spp. to screen for these genes, aiming to understand the evolutionary patterns of these genes across the genus through phylogenetic and DNA polymorphism analyses. Our results showed (1) varied numbers of <i>eas</i> genes in <i>C.</i> sect. <i>Claviceps</i> and sect. <i>Pusillae</i>, none in sect. <i>Citrinae</i>, six <i>idt/ltm</i> genes in sect. <i>Claviceps</i> (except four in <i>C. cyperi</i>), zero to one partial (<i>idtG</i>) in sect. <i>Pusillae</i>, and four in sect. <i>Citrinae</i>, (2) two to three copies of <i>dmaW</i>, <i>easE</i>, <i>easF</i>, <i>idt/ltmB</i>, <i>itd/ltmQ</i> in sect. <i>Claviceps</i>, (3) frequent gene gains and losses, and (4) an evolutionary hourglass pattern in the intra-specific <i>eas</i> gene diversity and divergence in <i>C. purpurea</i>.Miao LiuWendy FindlayJeremy DettmanStephen A. WykaKirk BrodersParivash ShoukouhiKasia DadejMiroslav KolaříkArpeace BasnyatJim G. MenziesMDPI AGarticleergot alkaloidsergot fungigene divergencegene diversityindole diterpenesphylogenyMedicineRENToxins, Vol 13, Iss 799, p 799 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	ergot alkaloids ergot fungi gene divergence gene diversity indole diterpenes phylogeny Medicine R
spellingShingle	ergot alkaloids ergot fungi gene divergence gene diversity indole diterpenes phylogeny Medicine R Miao Liu Wendy Findlay Jeremy Dettman Stephen A. Wyka Kirk Broders Parivash Shoukouhi Kasia Dadej Miroslav Kolařík Arpeace Basnyat Jim G. Menzies Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model
description	Ergot fungi (<i>Claviceps</i> spp.) are infamous for producing sclerotia containing a wide spectrum of ergot alkaloids (EA) toxic to humans and animals, making them nefarious villains in the agricultural and food industries, but also treasures for pharmaceuticals. In addition to three classes of EAs, several species also produce paspaline-derived indole diterpenes (IDT) that cause ataxia and staggers in livestock. Furthermore, two other types of alkaloids, i.e., loline (LOL) and peramine (PER), found in <i>Epichlo</i><i>ë</i> spp., close relatives of <i>Claviceps</i>, have shown beneficial effects on host plants without evidence of toxicity to mammals. The gene clusters associated with the production of these alkaloids are known. We examined genomes of 53 strains of 19 <i>Claviceps</i> spp. to screen for these genes, aiming to understand the evolutionary patterns of these genes across the genus through phylogenetic and DNA polymorphism analyses. Our results showed (1) varied numbers of <i>eas</i> genes in <i>C.</i> sect. <i>Claviceps</i> and sect. <i>Pusillae</i>, none in sect. <i>Citrinae</i>, six <i>idt/ltm</i> genes in sect. <i>Claviceps</i> (except four in <i>C. cyperi</i>), zero to one partial (<i>idtG</i>) in sect. <i>Pusillae</i>, and four in sect. <i>Citrinae</i>, (2) two to three copies of <i>dmaW</i>, <i>easE</i>, <i>easF</i>, <i>idt/ltmB</i>, <i>itd/ltmQ</i> in sect. <i>Claviceps</i>, (3) frequent gene gains and losses, and (4) an evolutionary hourglass pattern in the intra-specific <i>eas</i> gene diversity and divergence in <i>C. purpurea</i>.
format	article
author	Miao Liu Wendy Findlay Jeremy Dettman Stephen A. Wyka Kirk Broders Parivash Shoukouhi Kasia Dadej Miroslav Kolařík Arpeace Basnyat Jim G. Menzies
author_facet	Miao Liu Wendy Findlay Jeremy Dettman Stephen A. Wyka Kirk Broders Parivash Shoukouhi Kasia Dadej Miroslav Kolařík Arpeace Basnyat Jim G. Menzies
author_sort	Miao Liu
title	Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model
title_short	Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model
title_full	Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model
title_fullStr	Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model
title_full_unstemmed	Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model
title_sort	mining indole alkaloid synthesis gene clusters from genomes of 53 <i>claviceps</i> strains revealed redundant gene copies and an approximate evolutionary hourglass model
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/12ae2b44251b418fb454d7b9e1877d19
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Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 <i>Claviceps</i> Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model

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