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Song X, Geng Y, Xu C, Li J, Guo Y, Shi Y, Ma Q, Li Q, Zhang M. The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny. IMA Fungus 2024; 15:15. [PMID: 38863028 PMCID: PMC11167856 DOI: 10.1186/s43008-024-00149-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
In the present study, three mitogenomes from the Bipolaris genus (Bipolaris maydis, B. zeicola, and B. oryzae) were assembled and compared with the other two reported Bipolaris mitogenomes (B. oryzae and B. sorokiniana). The five mitogenomes were all circular DNA molecules, with lengths ranging from 106,403 bp to 135,790 bp. The mitogenomes of the five Bipolaris species mainly comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 13 PCGs in the five mitogenomes. Across the 13 core PCGs tested, nad6 had the least genetic distance among the 16 Pleosporales species we investigated, indicating that this gene was highly conserved. In addition, the Ka/Ks values for all 12 core PCGs (excluding rps3) were < 1, suggesting that these genes were subject to purifying selection. Comparative mitogenomic analyses indicate that introns were the main factor contributing to the size variation of Bipolaris mitogenomes. The introns of the cox1 gene experienced frequent gain/loss events in Pleosporales species. The gene arrangement and collinearity in the mitogenomes of the five Bipolaris species were almost highly conserved within the genus. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the five Bipolaris species formed well-supported topologies. This study is the first report on the mitogenomes of B. maydis and B. zeicola, as well as the first comparison of mitogenomes among Bipolaris species. The findings of this study will further advance investigations into the population genetics, evolution, and genomics of Bipolaris species.
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Affiliation(s)
- Xinzheng Song
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuehua Geng
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chao Xu
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiaxin Li
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yashuang Guo
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yan Shi
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qingzhou Ma
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
| | - Meng Zhang
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
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Liu T, Pyle AM. Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi. J Mol Biol 2024; 436:168513. [PMID: 38447889 DOI: 10.1016/j.jmb.2024.168513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Systemic fungal infections are a growing public health threat, and yet viable antifungal drug targets are limited as fungi share a similar proteome with humans. However, features of RNA metabolism and the noncoding transcriptomes in fungi are distinctive. For example, fungi harbor highly structured RNA elements that humans lack, such as self-splicing introns within key housekeeping genes in the mitochondria. However, the location and function of these mitochondrial riboregulatory elements has largely eluded characterization. Here we used an RNA-structure-based bioinformatics pipeline to identify the group I introns interrupting key mitochondrial genes in medically relevant fungi, revealing their fixation within a handful of genetic hotspots and their ubiquitous presence across divergent phylogenies of fungi, including all highest priority pathogens such as Candida albicans, Candida auris, Aspergillus fumigatus and Cryptococcus neoformans. We then biochemically characterized two representative introns from C. albicans and C. auris, demonstrating their exceptionally efficient splicing catalysis relative to previously-characterized group I introns. Indeed, the C. albicans mitochondrial intron displays extremely rapid catalytic turnover, even at ambient temperatures and physiological magnesium ion concentrations. Our results unmask a significant new set of players in the RNA metabolism of pathogenic fungi, suggesting a promising new type of antifungal drug target.
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Affiliation(s)
- Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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Xu H, Zhu Z, Tian Z, Wei C, Fan Q, Wang Y, Shen S, Deng G, Ding M. The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae. Genes (Basel) 2024; 15:111. [PMID: 38255000 PMCID: PMC10815617 DOI: 10.3390/genes15010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.
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Affiliation(s)
- Hui Xu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ziyi Zhu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zeyuan Tian
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Cuiyuan Wei
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qi Fan
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanbing Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Shikang Shen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Gang Deng
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
| | - Mingliang Ding
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Food Crops Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650200, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100083, China
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Österman-Udd J, Lundell TK. Complete mitochondrial genome sequence of the Agaricomycetes brown rot fungus Fomitopsis pinicola isolate FBCC1181. Microbiol Resour Announc 2023; 12:e0050323. [PMID: 37909782 PMCID: PMC10720572 DOI: 10.1128/mra.00503-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
The mitochondrial genome of the brown rot fungus Fomitopsis pinicola isolate FBCC 1181 is a 66.5 kbp circular chromosome. It contains 64 predicted genes, including a set typical for Basidiomycota Agaricomycetes mitogenomes. Introns of cox and cob genes contain several homing endonucleases of both LAGLIDADG and GIY-YIG types.
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Affiliation(s)
- Janina Österman-Udd
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Taina Kristina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
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Kulik T, van Diepeningen AD, Hausner G. Editorial: The significance of mitogenomics in mycology, volume II. Front Microbiol 2023; 14:1344877. [PMID: 38192293 PMCID: PMC10773717 DOI: 10.3389/fmicb.2023.1344877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anne D. van Diepeningen
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Anwar G, Mamut R, Wang J. Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species. J Fungi (Basel) 2023; 9:969. [PMID: 37888225 PMCID: PMC10607270 DOI: 10.3390/jof9100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 10/28/2023] Open
Abstract
In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (PCGs), 2 rRNAs, 26-27 tRNAs and an unidentified open reading frame (ORF). The PCG length, AT skew and GC skew varied among the 15 PCGs in the five mitogenomes. Among the 15 PCGs, cox2 had the least K2P genetic distance, indicating that the gene was highly conserved. The synteny analysis revealed that the coding regions were highly conserved in the Peltigera mitochondrial genomes, but gene rearrangement occurred in the intergenic regions. The phylogenetic analysis based on the 14 PCGs showed that the 11 Peltigera species formed well-supported topologies, indicating that the protein-coding genes in the mitochondrial genome may be used as a reliable molecular tool in the study of the phylogenetic relationship of Peltigera.
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Affiliation(s)
| | - Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830017, China; (G.A.); (J.W.)
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Mukhopadhyay J, Wai A, Hausner G. The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns. Front Microbiol 2023; 14:1240407. [PMID: 37637121 PMCID: PMC10448965 DOI: 10.3389/fmicb.2023.1240407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Many members of the Ophiostomatales are of economic importance as they are bark-beetle associates and causative agents for blue stain on timber and in some instances contribute towards tree mortality. The taxonomy of these fungi has been challenging due to the convergent evolution of many traits associated with insect dispersal and a limited number of morphological characters that happen to be highly pleomorphic. This study examines the mitochondrial genomes for three members of Leptographium sensu lato [Leptographium aureum (also known as Grosmannia aurea), Grosmannia fruticeta (also known as Leptographium fruticetum), and Leptographium sp. WIN(M)1376)]. Methods Illumina sequencing combined with gene and intron annotations and phylogenetic analysis were performed. Results Sequence analysis showed that gene content and gene synteny are conserved but mitochondrial genome sizes were variable: G. fruticeta at 63,821 bp, Leptographium sp. WIN(M)1376 at 81,823 bp and L. aureum at 104,547 bp. The variation in size is due to the number of introns and intron-associated open reading frames. Phylogenetic analysis of currently available mitochondrial genomes for members of the Ophiostomatales supports currently accepted generic arrangements within this order and specifically supports the separation of members with Leptographium-like conidiophores into two genera, with L. aureum grouping with Leptographium and G. fruticeta aligning with Grosmannia. Discussion Mitochondrial genomes are promising sequences for resolving evolutionary relationships within the Ophiostomatales.
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Affiliation(s)
| | | | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å. Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Front Microbiol 2023; 14:1159811. [PMID: 37275157 PMCID: PMC10234125 DOI: 10.3389/fmicb.2023.1159811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. Methods In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and Discussion Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
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Parra M, Libkind D, Hittinger CT, Álvarez L, Bellora N. Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation. Yeast 2023. [PMID: 37114349 DOI: 10.1002/yea.3853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/27/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Aureobasidium pullulans is a yeast-like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re-evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high-depth transcriptomic data. Our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.
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Affiliation(s)
- Micaela Parra
- Laboratorio de Genómica Computacional, Instituto de Tecnologías Nucleares para la Salud (INTECNUS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lucía Álvarez
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Nicolás Bellora
- Laboratorio de Genómica Computacional, Instituto de Tecnologías Nucleares para la Salud (INTECNUS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
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Li Q, Xiao W, Wu P, Zhang T, Xiang P, Wu Q, Zou L, Gui M. The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales. IMA Fungus 2023; 14:7. [PMID: 37004131 PMCID: PMC10064765 DOI: 10.1186/s43008-023-00112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85-38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
| | - Mingying Gui
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
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Ji X, Tian Y, Liu W, Lin C, He F, Yang J, Miao W, Li Z. Mitochondrial characteristics of the powdery mildew genus Erysiphe revealed an extraordinary evolution in protein-coding genes. Int J Biol Macromol 2023; 230:123153. [PMID: 36610569 DOI: 10.1016/j.ijbiomac.2023.123153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/17/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023]
Abstract
The genus Erysiphe was an obligate parasite causing powdery mildew disease on a wide range of higher plants. However, the knowledge of their mitogenome architecture for lifestyle adaptability was scarce. Here, we assembled the first complete mitogenome (190,559 bp in size) for rubber tree powdery mildew pathogen Erysiphe quercicola. Comparable analysis of the Erysiphe mitogenomes exhibited conserved gene content, genome organization and codon usage bias, but extensive dynamic intron gain/loss events were presented between Erysiphe species. The phylogeny of the Ascomycota species constructed in the phylogenetic analysis showed genetic divergences of the Erysiphe species. Compared with other distant saprophytic and plant pathogenic fungi, Erysiphe had a flat distribution of evolutionary pressures on fungal standard protein-coding genes (PCGs). The Erysiphe PCGs had the highest mean selection pressure. In particular, Erysiphe's cox1, nad1, cob and rps3 genes had the most elevated selection pressures among corresponding PCGs across fungal genera. Altogether, the investigations provided a novel insight into the potential evolutionary pattern of the genus Erysiphe to adapt obligate biotrophic lifestyle and promoted the understanding of the high plasticity and population evolution of fungal mitogenomes.
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Affiliation(s)
- Xiaobei Ji
- School of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan 570228, China
| | - Ye Tian
- School of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan 570228, China
| | - Wenbo Liu
- School of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan 570228, China
| | - Chunhua Lin
- School of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan 570228, China
| | - Fei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Yang
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Weiguo Miao
- School of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan 570228, China
| | - Zhigang Li
- School of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan 570228, China.
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Kim D, Gilchrist CLM, Chun J, Steinegger M. UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Res 2022; 51:D777-D784. [PMID: 36271795 PMCID: PMC9825530 DOI: 10.1093/nar/gkac894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/13/2022] [Accepted: 10/04/2022] [Indexed: 01/30/2023] Open
Abstract
In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in single-copy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic clade. Here we introduce the Universal Fungal Core Genes (UFCG) database and pipeline for genome-wide phylogenetic analysis of fungi. The UFCG database consists of 61 curated fungal marker genes, including a novel set of 41 computationally derived core genes and 20 canonical genes derived from literature, as well as marker gene sequences extracted from publicly available fungal genomes. Furthermore, we provide an easy-to-use, fully automated and open-source pipeline for marker gene extraction, training and phylogenetic tree reconstruction. The UFCG pipeline can identify marker genes from genomic, proteomic and transcriptomic data, while producing phylogenies consistent with those previously reported, and is publicly available together with the UFCG database at https://ufcg.steineggerlab.com.
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Affiliation(s)
- Dongwook Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Cameron L M Gilchrist
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongsik Chun
- Correspondence may also be addressed to Jongsik Chun. Tel: +82 2 880 8153;
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13
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Li Q, Li L, Zhang T, Xiang P, Wu Q, Tu W, Bao Z, Zou L, Chen C. The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota. IMA Fungus 2022; 13:16. [PMID: 36100951 PMCID: PMC9469536 DOI: 10.1186/s43008-022-00100-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
In the present study, we assembled and analyzed the mitogenomes of two Ramaria species. The assembled mitogenomes of Ramaria cfr. rubripermanens and R. rubella were circularized, with sizes of 126,497 bp and 143,271 bp, respectively. Comparative mitogenome analysis showed that intron region contributed the most (contribution rate, 43.74%) to the size variations of Ramaria mitogenomes. The genetic contents, gene length, tRNAs, and codon usages of the two Ramaria mitogenomes varied greatly. In addition, the evolutionary rates of different core protein coding genes (PCGs) in Phallomycetidae mitogenomes varied. We detected large-scale gene rearrangements between Phallomycetidae mitogenomes, including gene displacement and tRNA doubling. A total of 4499 bp and 7746 bp aligned fragments were detected between the mitochondrial and nuclear genomes of R. cfr. rubripermanens and R. rubella, respectively, indicating possible gene transferring events. We further found frequent intron loss/gain and potential intron transfer events in Phallomycetidae mitogenomes during the evolution, and the mitogenomes of R. rubella contained a novel intron P44. Phylogenetic analyses using both Bayesian inference (BI) and Maximum Likelihood (ML) methods based on a combined mitochondrial gene dataset obtained an identical and well-supported phylogenetic tree for Basidiomycota, wherein R. cfr. rubripermanens and Turbinellus floccosus are sister species. This study served as the first report on mitogenomes from the genus Ramaria, which provides a basis for understanding the evolution, genetics, and taxonomy of this important fungal group.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China.
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, People's Republic of China.
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14
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Ogaji YO, Lee RC, Sawbridge TI, Cocks BG, Daetwyler HD, Kaur S. De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea. J Fungi (Basel) 2022; 8:jof8080884. [PMID: 36012871 PMCID: PMC9410150 DOI: 10.3390/jof8080884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions.
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Affiliation(s)
- Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Robert C. Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Tim I. Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Benjamin G. Cocks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- Correspondence:
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15
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Visinoni F, Delneri D. Mitonuclear interplay in yeast: from speciation to phenotypic adaptation. Curr Opin Genet Dev 2022; 76:101957. [PMID: 35870233 DOI: 10.1016/j.gde.2022.101957] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
Abstract
Saccharomyces yeasts have evolved into an important model system to study mitonuclear incompatibilities, thanks to recent advances in the field of sequencing, yeast hybridisation and multigenerational breeding. Yeast hybrids contain two homologous proteomes but retain only one type of mitochondria allowing studies on the effect of mitochondria on phenotype and gene expression. Here, we discuss the recent developments in the growing field of yeast mitogenomics spanning from the impact that this organelle has in shaping yeast fitness and genome evolution to the dissection of molecular determinants of mitonuclear incompatibilities. Applying the state-of-the-art genetic tools to a broader range of natural yeast species from different environments will help progress the field and untap the mitochondrial potential in strain development.
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Affiliation(s)
- Federico Visinoni
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
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16
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Degradi L, Tava V, Prigitano A, Esposto MC, Tortorano AM, Saracchi M, Kunova A, Cortesi P, Pasquali M. Exploring Mitogenomes Diversity of Fusarium musae from Banana Fruits and Human Patients. Microorganisms 2022; 10:microorganisms10061115. [PMID: 35744633 PMCID: PMC9227538 DOI: 10.3390/microorganisms10061115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium musae has recently been described as a cross-kingdom pathogen causing post-harvest disease in bananas and systemic and superficial infection in humans. The taxonomic identity of fungal cross-kingdom pathogens is essential for confirming the identification of the species on distant infected hosts. Understanding the level of variability within the species is essential to decipher the population homogeneity infecting human and plant hosts. In order to verify that F. musae strains isolated from fruits and patients are part of a common population and to estimate their overall diversity, we assembled, annotated and explored the diversity of the mitogenomes of 18 F. musae strains obtained from banana fruits and human patients. The mitogenomes showed a high level of similarity among strains with different hosts’ origins, with sizes ranging from 56,493 to 59,256 bp. All contained 27 tRNA genes and 14 protein-coding genes, rps3 protein, and small and large ribosomal subunits (rns and rnl). Variations in the number of endonucleases were detected. A comparison of mitochondrial endonucleases distribution with a diverse set of Fusarium mitogenomes allowed us to specifically discriminate F. musae from its sister species F. verticillioides and the other Fusarium species. Despite the diversity in F. musae mitochondria, strains from bananas and strains from human patients group together, indirectly confirming F. musae as a cross-kingdom pathogen.
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Affiliation(s)
- Luca Degradi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Valeria Tava
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Maria Carmela Esposto
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Anna Maria Tortorano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
- Correspondence:
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Mukhopadhyay J, Wai A, Hutchison LJ, Hausner G. The mitogenome of Urnula craterium. Can J Microbiol 2022; 68:561-568. [PMID: 35623096 DOI: 10.1139/cjm-2022-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Urnula craterium (Schwein.) Fr. (1851) has been reported from North America, Europe, and Asia, and can be a pathogen on various hardwood species. In this study we investigated the mitochondrial genome of U. craterium. The biology and taxonomy of this fungus is poorly studied and there are no mitogenomes currently available for any member of the Sarcosomataceae (Order Pezizales). The complete mitogenome of U. craterium comprises 43 967 bps and encodes 14 protein-coding genes, a complete set of tRNAs and rRNA genes. A novel feature of the mitogenome is the presence of a single subunit DNA polymerase coding region that is typically associated with linear invertron-type plasmids. The mitogenome may offer insights into the evolution of mitogenomes among members of the Pezizales with regards to gene content and order, mobile elements, and genome sizes.
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Affiliation(s)
| | - Alvan Wai
- University of Manitoba, 8664, Winnipeg, Canada;
| | - Leonard J Hutchison
- Lakehead University Faculty of Natural Resources Management, 157776, Thunder Bay, Ontario, Canada;
| | - Georg Hausner
- University of Manitoba, 8664, Buller Building 213, Winnipeg, Manitoba, Canada;
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18
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Hao W. From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes? Front Microbiol 2022; 13:806575. [PMID: 35126340 PMCID: PMC8811140 DOI: 10.3389/fmicb.2022.806575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/03/2022] [Indexed: 11/26/2022] Open
Abstract
Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies.
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