The mitochondrial genome of Endoconidiophora resinifera is intron rich

Zubaer, Abdullah; Wai, Alvan; Hausner, Georg

doi:10.1038/s41598-018-35926-y

Cited by 40 publications

(68 citation statements)

References 81 publications

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“…Notably, the size of the mitochondrial genome of TWF154 (∼161 kb) is much larger than that of the human (∼17 kb), N. crassa (∼65 kb), or S. cerevisiae (∼79 kb) mitochondrial genomes. The expansion of the mitochondrial genome of TWF154 and other fungal mitochondrial genomes, namely in nematode-trapping fungus species (25)(26)(27)(28)(29)(30)(31)(32), can be attributed to the presence of a substantial number of genes encoding homing endonucleases (HEGs) of the LAGLI-DADG and GIY-YIG families in intronic and intergenic regions (Fig. 4C).…”

Section: Resultsmentioning

confidence: 99%

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi

Yang

Ulzurrun

Gonçalves

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Nematode-trapping fungi (NTF) are a group of specialized microbial predators that consume nematodes when food sources are limited. Predation is initiated when conserved nematode ascaroside pheromones are sensed, followed by the development of complex trapping devices. To gain insights into the coevolution of this interkingdom predator–prey relationship, we investigated natural populations of nematodes and NTF that we found to be ubiquitous in soils.Arthrobotrysspecies were sympatric with various nematode species and behaved as generalist predators. The ability to sense prey among wild isolates ofArthrobotrys oligosporavaried greatly, as determined by the number of traps after exposure toCaenorhabditis elegans. While some strains were highly sensitive toC. elegansand the nematode pheromone ascarosides, others responded only weakly. Furthermore, strains that were highly sensitive to the nematode prey also developed traps faster. The polymorphic nature of trap formation correlated with competency in prey killing, as well as with the phylogeny ofA. oligosporanatural strains, calculated after assembly and annotation of the genomes of 20 isolates. A chromosome-level genome assembly and annotation were established for one of the most sensitive wild isolates, and deletion of the only G-protein β-subunit–encoding gene ofA. oligosporanearly abolished trap formation. In summary, our study establishes a highly responsiveA. oligosporawild isolate as a model strain for the study of fungus–nematode interactions and demonstrates that trap formation is a fitness character in generalist predators of the nematode-trapping fungus family.

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Section: Resultsmentioning

confidence: 99%

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi

Yang

Ulzurrun

Gonçalves

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…Notably, the size of mitochondrial genome of TWF154 (∼161 kb) is much larger than that of the human (∼17 kb), N. crassa (∼65 kb) or S. cerevisiae (∼79 kb) mitochondrial genomes. The expansion of the mitochondrial genome of TWF154 and other fungal mitochondrial genomes, namely in NTF species (26–34) can be attributed to the presence of a substantial number of genes encoding homing endonucleases (HEG) of the LAGLI-DADG and GIY-YIG families in intronic and intergenic regions (Fig. 4C).…”

Section: Resultsmentioning

confidence: 99%

Natural diversity in the predatory behavior facilitates the establishment of a new robust model strain for nematode-trapping fungi

Yang

Ulzurrun

Gonçalves

et al. 2019

Preprint

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33Nematode-trapping fungi (NTF) are a group of specialized microbial predators that consume 34 nematodes when food sources are limited. Predation is initiated when conserved nematode 35 ascaroside pheromones are sensed, followed by the development of complex trapping devices. 36To gain insights into the co-evolution of this inter-kingdom predator-prey relationship, we 37 investigated natural populations of nematodes and NTF, that we found to be ubiquitous in soils. 38Arthrobotrys species were sympatric with various nematode species and behaved as generalist 39 predators. The ability to sense prey amongst wild isolates of A. oligospora varied greatly, as 40 determined by the number of traps after exposure to Caenorhabditis elegans. While some strains 41 were highly sensitive to C. elegans and the nematode pheromone ascarosides, others responded 42 only weakly. Furthermore, strains that were highly sensitive to the nematode prey also developed 43 traps faster. The polymorphic nature of trap formation correlated with competency in prey 44 killing, as well as with the phylogeny of A. oligospora natural strains, calculated after assembly 45 and annotation of the genomes of twenty isolates. A chromosome level genome assembly and 46 annotation was established for one of the most sensitive wild isolate, and deletion of the only G 47 protein b subunit-encoding gene of A. oligospora nearly abolished trap formation, implicating G 48 protein signaling in predation. In summary, our study establishes a highly responsive A. 49 oligospora wild isolate as a novel model strain for the study of fungal-nematode interactions and 50 demonstrates that trap formation is a fitness character in generalist predators of the NTF family. 51 52 Significance statement 53Nematode-trapping fungi (NTF) are carnivorous microbes that hold potential to be used 54 as biological control agents due to their ability to consume nematodes. In this work we show that 55 NTF are ubiquitous generalist predators found in sympatry with their prey in soil samples. Wild 56 isolates of NTF displayed a naturally diverse ability to execute their predatory lifestyle. We 57 generated a large whole genome sequencing dataset for many of the fungal isolates that will 58 serve as the basis of future projects isolates. In particular, we establish TWF154, a highly 59 responsive strain of Arthrobotrys oligospora, as a model strain to study the genetics of NTF. 60Lastly, we provide evidence that G-protein signaling is necessary for trap induction in NTF. 61 62 63 64The living component of soils are in permanent interaction and play central roles in 65 various aspects of biogeochemistry, including nutrient cycling and transport across distances (1). 66Specifically, nematodes are the most abundant animals in nature, amounting to a staggering 0.3 67 gigatonnes or 4.5 x 10 20 individuals, many of which are devastating parasites of plants, animals 68 and humans (2). Although available, nematicide chemicals pose severe environmental and health 69 risks and therefore, biological cont...

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“…For example, the Chinese caterpillar fungus Ophiocordyceps sinensis has a mitogenome of 157.5 kb due to the presence of 54 introns (Kang et al, 2017). The blue-stain fungus Endoconidiophora resinifera has a mitogenome of 220.2 kb, containing as many as 81 introns (Zubaer et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of the Chan‐hua fungus Isaria cicadae: a tale of intron evolution in Cordycipitaceae

Fan

Zhang

2019

Environmental Microbiology

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Summary Isaria cicadae is an entomogenous fungus of great medicinal value. Its nuclear genome has been reported, while its mitogenome remains unknown. Herein, we first described its mitogenome and then inferred intron evolution from both intraspecific and interspecific perspectives. The fungus represented the largest mitogenome (56.6 kb in strain CCAD02) known in Cordycipitaceae due to the presence of 25 introns interrupting nine genes. Comparison of three I. cicadae strains revealed intron presence/absence dynamics at six intron loci plus a few indels and single nucleotide polymorphisms. Phylogenetic analyses confirmed the placement of I. cicadae in Cordycipitaceae. Comparison of 10 Cordycipitaceae species revealed a high degree of synteny and conserved genetic content. They, however, varied in intron numbers (1–25 per species) with overall 34 intron loci identified, which resulted in more than twofold variations in mitogenome sizes (24.5–56.6 kb). An rnl intron encoding ribosomal protein S3 was present in all species, suggesting its early invasion in Cordycipitaceae, while further divergence occurred for this intron. The other introns identified in this study were present in some, but not all of the species and have undergone multiple gains and losses in Cordycipitaceae. This study greatly enhanced our understanding of intron evolution in Cordycipitaceae.

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The mitochondrial genome of Endoconidiophora resinifera is intron rich

Cited by 40 publications

References 81 publications

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi

Natural diversity in the predatory behavior facilitates the establishment of a new robust model strain for nematode-trapping fungi

The complete mitochondrial genome of the Chan‐hua fungus Isaria cicadae: a tale of intron evolution in Cordycipitaceae

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