Polymorphism in Mitochondrial Group I Introns among Cryptococcus neoformans and Cryptococcus gattii Genotypes and Its Association with Drug Susceptibility

Lee

et al. 2020

Sci Rep

Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 93%

The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

Lee

et al. 2020

Sci Rep

“…The cox1 gene of C. fumosa contained the largest number of introns among the 22 Agaricales species, while four novel Pcls were detected in the cox1 gene of C. fumosa . Intron considered as an important genetic element in the mitogenome of fungi (Burke 1988 ; Gomes et al 2018 ), and its dynamic changes can significantly affect the organization and size of the mitogenome of fungi (Hamari et al 2002 ; Himmelstrand et al 2014 ). The origin and evolution of the novel Pcls needed to be further analyzed to understand the evolution of the C. fumosa mitogenome.…”

Section: Discussionmentioning

confidence: 99%

The 256 kb mitochondrial genome of Clavaria fumosa is the largest among phylum Basidiomycota and is rich in introns and intronic ORFs

et al. 2020

IMA Fungus

In the present study, the complete mitogenome of Clavaria fumosa, was sequenced, assembled, and compared. The complete mitogenome of C. fumosa is 256,807 bp in length and is the largest mitogenomes among all Basidiomycota mitogenomes reported. Comparative mitogenomic analysis indicated that the C. fumosa mitogenome contained the most introns and intronic ORFs among all fungal mitogenomes. Large intergenic regions, intronic regions, accumulation of repeat sequences and plasmid-derived genes together promoted the size expansion of the C. fumosa mitogenome. In addition, the rps3 gene was found subjected to positive selection between some Agaricales species. We found frequent intron gain/loss events in Agaricales mitogenomes, and four novel intron classes were detected in the C. fumosa mitogenome. Large-scale gene rearrangements were found occurred in Agaricales species and the C. fumosa mitogenome had a unique gene arrangement which differed from other Agaricales species. Phylogenetic analysis for 76 Basidiomycetes based on combined mitochondrial gene sets indicated that mitochondrial genes could be used as effective molecular markers for reconstructing evolution of Basidiomycota. The study served as the first report on the mitogenomes of the family Clavariaceae, which will promote the understanding of the genetics, evolution and taxonomy of C. fumosa and related species.

“…A species-specific pattern of intron distribution has been also observed in F. oxysporum [188] and Fusarium fujikuroi species complex (FFSC) [212]. Recently, Gomes et al (2018) [213] suggested that group I introns are promising targets for developing novel tools for fungicide susceptibility. Some fungicides inhibit self-splicing of group I introns, which is indispensable for pathogen survival under parasitic conditions [213].…”

Section: Perspectives Of Targeting Mtdna For Barcoding Of Plant Pathomentioning

confidence: 96%

“…Recently, Gomes et al (2018) [213] suggested that group I introns are promising targets for developing novel tools for fungicide susceptibility. Some fungicides inhibit self-splicing of group I introns, which is indispensable for pathogen survival under parasitic conditions [213]. Intron distribution has been suggested as an important contributor to the virulence and drug tolerance of human fungal pathogens Cryptococcus neoformans and Cryptococcus gattii.…”

Section: Perspectives Of Targeting Mtdna For Barcoding Of Plant Pathomentioning

confidence: 99%

Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA

Kulik

Bilska

Żelechowski

2020

IJMS

Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.