Genomic Characteristics and Comparative Genomics Analysis of Parafenestella ontariensis sp. nov.

Ilyukhin, Evgeny; Markovskaja, Svetlana; Elgorban, Abdallah M.; Al-Rejaie, Salim S.; Maharachchikumbura, Sajeewa S. N.

doi:10.3390/jof8070732

Cited by 6 publications

(2 citation statements)

References 56 publications

(69 reference statements)

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“…S. weigelae has a large number of terpene synthesis genes relative to reports regarding those in other medicinal mushrooms ( Table 3 ). NRPSs are considered key factors in host-pathogen interactions of medicinal mushrooms, yet their specific functions have not been identified ( Oide and Turgeon, 2020 ; Ilyukhin et al., 2022 ). Further, no function of NRPSs in Basidiomycetes has been reported to date ( Duan et al., 2022 ).…”

Section: Discussionmentioning

confidence: 99%

First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution

Jin,

Ma,

Wang

et al. 2024

Front. Cell. Infect. Microbiol.

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Sanghuangporus, also known as “Sanghuang” in China, is a well-known genus of traditional Chinese medicinal macrofungi. To make more effective use of Sanghuangporus resources, we completed the first genome assembly and annotation of a monokaryon strain of S. weigelae in the present study. A 33.96-Mb genome sequence was assembled as 13 contigs, leading to prediction of 9377 protein-coding genes. Phylogenetic and average nucleotide identity analyses indicated that the S. weigelae genome is closely related to those of other Sanghuangporus species in evolutionary tree, which clustered in one clade. Collinearity analysis revealed a high level of collinearity of S. weigelae with S. baumii, S. vaninii, and S. sanghuang. Biosynthesis pathways potentially involved in medicinal properties, including terpenoid and polysaccharide synthesis, were identified in S. weigelae, while polysaccharides were identified as the main medicinal metabolites in S. weigelae, with flavonoids more important in Sanghuangporus than other medicinal mushroom groups. Genes encoding 332 carbohydrate-active enzymes were identified in the S. weigelae genome, including major glycoside hydrolases and glycosyltransferases predicted, revealing the robust lignocellulose degradation capacity of S. weigelae. Further, 130 genes, clustered in seven classes were annotated to encode cytochromes P450 in the S. weigelae genome. Overall, our results reveal the remarkably medicinal capacity of S. weigelae and provide new insights that will inform the study of evolution and medicinal application of S. weigelae. The data are a reference resource for the formulation of scientific and rational ecological protection policies for Sanghuangporus species.

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Section: Discussionmentioning

confidence: 99%

First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution

Jin,

Ma,

Wang

et al. 2024

Front. Cell. Infect. Microbiol.

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“…It is worth noting that compared with other reported fungi, O. raphanipes is also predominate in the number of terpene synthesis genes [ 18 , 51 ]. NRPSs in fungi are considered to be corresponding to the virulence determinants during host-pathogen interactions, yet the exact role they play remains elusive in many cases [ 54 , 55 ]. To date, the function of NPRSs in Basidiomycetes has not been reported [ 19 ].…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu)

Zhu

Gao²,

Zhang

et al. 2023

JoF

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Oudemansiella raphanipes, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on O. raphanipes is rare. To obtain a comprehensive overview of genetic characteristics and enhance the value of O. raphanipes, two mating-compatible monokaryons isolated from the dikaryon were applied for de novo genome sequencing and assembly using Nanopore and /or Illumina sequencing platforms. One of the monokaryons, O. raphanipes CGG-A-s1, was annotated with 21,308 protein-coding genes, of which 56 were predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I PKS, NRPS, and siderophore. Phylogenetic and comparative analysis of multiple fungi genomes revealed a close evolutionary relationship between O. raphanipes and Mucidula mucid based on single-copy orthologous protein genes. Significant collinearity was detected between O. raphanipes and Flammulina velutipes on the synteny of inter-species genomes. 664 CAZyme genes in CGG-A-s1 were identified with GHs and AAs families significantly elevated when compared with the other 25 sequenced fungi, indicating a strong wood degradation ability. Furthermore, the mating type locus analysis revealed that CGG-A-s1 and CGG-A-s2 were conserved in the gene organization of the mating A locus but various in that of the mating B locus. The genome resource of O. raphanipes will provide new insights into its development of genetic studies and commercial production of high-quality varieties.

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A revision of the family Cucurbitariaceae with additional new taxa from forest trees in Iran

Eisvand,

Mehrabi-Koushki,

Crous

2024

Mycol Progress

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The family Cucurbitariaceae is rich in species diversity, and has a wide host range and geographic distribution. In this study, we identi ed 12 Cucurbitariaceae isolates which were obtained from disease symptoms in two forest trees in Khuzestan province, Iran. In addition, this family is reassessed using phylogenetic analyses based on DNA sequences from ve nuclear regions (ITS, LSU, tub2, tef1a and rpb2). The phylogenetic analyses showed that the present isolates represent one new genus, Nothocucurbitaria, and two new species, Nothocucurbitaria izehica and Parafenestella quercicola which are described and illustrated. Furthermore, the genus Allocucurbitaria is emended to accommodate species of Seltsamia, that grouped with the type species of Allocucurbitaria. Parafenestella pittospori and A. prunicola are recombined into the genera Neocucurbitaria and Nothocucurbitaria, respectively. Comparative analysis of single-locus trees revealed that the tub2 and tef1a can distinguish most genera and species in Cucurbitariaceae, while the ITS and LSU phylogenies show low resolution at both generic and species level. The best single locus marker, rpb2, was able to distinguish all generic and most species lineages in Cucurbitariaceae.

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Genomic Characteristics and Comparative Genomics Analysis of Parafenestella ontariensis sp. nov.

Cited by 6 publications

References 56 publications

First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution

First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution

Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu)

A revision of the family Cucurbitariaceae with additional new taxa from forest trees in Iran

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