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Syazwan SA, Mohd-Farid A, Yih Lee S, Mohamed R. Comparative analysis of mitochondrial genomes in Ceratocystis fimbriata complex across diverse hosts. Gene 2024; 921:148539. [PMID: 38710292 DOI: 10.1016/j.gene.2024.148539] [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: 01/08/2024] [Revised: 04/16/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due to Ceratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next-Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment. The mitochondrial genome-based phylogenetic analysis revealed a significant genetic relationship between the studied isolates and theC. fimbriatacomplex in the South American Subclade, indicating that theC. fimbriatacomplex discovered in Malaysia isC. manginecans. The comparative mitochondrial genome demonstrates the adaptability of the complex due to mobile genetic components and genomic rearrangements in the studiedfungal isolates. This research enhances our knowledge of the genetic diversity and evolutionary patterns within theC. fimbriatacomplex, aiding in a deeper understanding of fungal disease development and host adaption processes. The acquired insights are crucial for creating specific management strategies for CWCD, improving the overall understanding of fungal disease evolution and control.
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Affiliation(s)
- Samsuddin Ahmad Syazwan
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia; Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
| | - Ahmad Mohd-Farid
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia.
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, 71800 Nilai, Negeri Sembilan, Malaysia.
| | - Rozi Mohamed
- Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
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Malik M, Malik F, Fatma T, Qasim Hayat M, Jamal A, Gul A, Faraz Bhatti M. The complete mitochondrial genome of Penicillium expansum: Insights into the fungal evolution and phylogeny. Gene 2024; 910:148315. [PMID: 38417689 DOI: 10.1016/j.gene.2024.148315] [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: 12/26/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Penicillium expansum is an important phytopathogenic fungus that causes blue mold disease. In this study, the novel mitochondrial genome of P. expansum was sequenced, assembled, annotated, and compared with the previously published Penicillium mitogenomes. P. expansum mitogenome is composed of circular DNA molecules with a genome size of 25,496 bp. It encodes 16 protein-encoding genes (PCGs), two rRNA genes, and 25 tRNA genes. Comparative analysis with six other Penicillium species revealed that gene length, GC content, AT skew, and GC skew were variable among the core protein-coding genes. The Penicillium species' gene synteny analysis identified several gene rearrangements. Among the core 15 PCGs, atp8 had the lowest K2P genetic distance, which shows that this gene is highly conserved. The Ka/Ks value of most PCGs was less than 1, which shows that these genes have undergone purifying selection. Phylogenetic analysis based on 14 concatenated core mitochondrial genes revealed that P. expansum shares a close relationship with P. solitum. This study served as a first report on the complete mitochondrial genome of P. expansum and its comparative analysis that will contribute to population genetics and rapid evolutionary studies among Penicillium species.
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Affiliation(s)
- Mahnoor Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Fatima Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Muhammad Qasim Hayat
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
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3
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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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4
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Zhiyuan H, Lin C, Yihan W, Meng D, Yanzi L, Zhenggang X. Reexamination of Aspergillus cristatus phylogeny in dark tea: Characteristics of the mitochondrial genome. Open Life Sci 2024; 19:20220838. [PMID: 38585639 PMCID: PMC10997147 DOI: 10.1515/biol-2022-0838] [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: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/12/2024] [Indexed: 04/09/2024] Open
Abstract
To enhance our understanding of Aspergillus cristatus, an important functional microorganism, the characteristics of its mitochondrial genome were analyzed and compared with related species. The mitochondrial genome of A. cristatus was determined to be 77,649 bp in length, with 15 protein-coding regions. Notably, its length surpassed that of the other species, primarily attributable to the intron length. Gene order exhibited significant variations, with greater conservation observed in the genus Penicillium compared to Aspergillus. Phylogenetic tree analyses indicated that the genera Aspergillus and Penicillium are closely related but monophyletic. Furthermore, the phylogenetic tree constructed based on protein-coding genes effectively distinguished all strains with high branching confidence. This approach provides a robust reflection of the evolutionary relationship between A. cristatus and its related species, offering potential for the development of molecular markers suitable for Aspergillus and Penicillium.
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Affiliation(s)
- Hu Zhiyuan
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Chen Lin
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Wang Yihan
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Dong Meng
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Li Yanzi
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Xu Zhenggang
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
- College of Forestry, Northwest A & F University, Yangling712100, Shaanxi, China
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Thorn V, Xu J. Mitogenome Variations in a Global Population of Aspergillus fumigatus. J Fungi (Basel) 2023; 9:995. [PMID: 37888251 PMCID: PMC10608017 DOI: 10.3390/jof9100995] [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: 09/13/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
Aspergillus fumigatus is a ubiquitous, critical priority human fungal pathogen. Despite its clinical importance, there is limited knowledge regarding the variations of the genome within mitochondria, the powerhouse organelle within eukaryotic cells. In this study, we leveraged publicly available, raw, whole genome sequence data isolates from 1939 to investigate the variations in the mitochondrial genomes of A. fumigatus. These isolates were isolated from 22 countries on six continents, as well as from outer space and from within the International Space Station. In total, our analysis revealed 39 mitochondrial single nucleotide polymorphisms (mtSNPs) within this global sample, and, together, these 39 mtSNPs grouped the 1939 isolates into 79 mitochondrial multilocus genotypes (MLGs). Among the 79 MLGs, 39 were each distributed in at least two countries and 30 were each shared by at least two continents. The two most frequent MLGs were also broadly distributed: MLG11 represented 420 isolates from 11 countries and four continents and while MLG79 represented 418 isolates from 18 countries and five continents, consistent with long-distance dispersals of mitogenomes. Our population genetic analyses of the mtSNPs revealed limited differentiation among continental populations, but highly variable genetic differences among national populations, largely due to localized clonal expansions of different MLGs. Phylogenetic analysis and Discriminant Analysis of Principal Components of mtSNPs suggested the presence of at least three mitogenome clusters. Linkage disequilibrium, Index of Association, and phylogenetic incompatibility analyses collectively suggested evidence for mitogenome recombination in natural populations of A. fumigatus. In addition, sequence read depth analyses revealed an average ratio of ~20 mitogenomes per nuclear genome in this global population, but the ratios varied among strains within and between certain geographic populations. Together, our results suggest evidence for organelle dynamics, genetic differentiation, recombination, and both widespread and localized clonal expansion of the mitogenomes in the global A. fumigatus population.
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Affiliation(s)
| | - Jianping Xu
- Department of Biology, Institute of Infectious Diseases Research, McMaster University, Hamilton, ON L8S 4K1, Canada;
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Li ZC, Xie TC, Feng XL, Wang ZX, Lin C, Li GM, Li XZ, Qi J. The First Five Mitochondrial Genomes for the Family Nidulariaceae Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of Agaricales. Int J Mol Sci 2023; 24:12599. [PMID: 37628782 PMCID: PMC10454537 DOI: 10.3390/ijms241612599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The family Nidulariaceae, consisting of five genera including Cyathus, is a unique group of mushrooms commonly referred to as bird's nest fungi due to their striking resemblance to bird's nests. These mushrooms are considered medicinal mushrooms in Chinese medicine and have received attention in recent years for their anti-neurodegenerative properties. However, despite the interest in these mushrooms, very little is known about their mitochondrial genomes (mitogenomes). This study is the first comprehensive investigation of the mitogenomes of five Nidulariaceae species with circular genome structures ranging in size from 114,236 bp to 129,263 bp. Comparative analyses based on gene content, gene length, tRNA, and codon usage indicate convergence within the family Nidulariaceae and heterogeneity within the order Agaricales. Phylogenetic analysis based on a combined mitochondrial conserved protein dataset provides a well-supported phylogenetic tree for the Basidiomycetes, which clearly demonstrates the evolutionary relationships between Nidulariaceae and other members of Agaricales. Furthermore, phylogenetic inferences based on four different gene sets reveal the stability and proximity of evolutionary relationships within Agaricales. These results reveal the uniqueness of the family Nidulariaceae and its similarity to other members of Agaricales; provide valuable insights into the origin, evolution, and genetics of Nidulariaceae species; and enrich the fungal mitogenome resource. This study will help to expand the knowledge and understanding of the mitogenomes in mushrooms.
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Affiliation(s)
- Zhao-chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tian-chen Xie
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chao Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Guo-ming Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiu-Zhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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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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Pham HM, Le DT, Le LT, Chu PTM, Tran LH, Pham TT, Nguyen HM, Luu TT, Hoang H, Chu HH. A highly quality genome sequence of Penicillium oxalicum species isolated from the root of Ixora chinensis in Vietnam. G3 (BETHESDA, MD.) 2022; 13:6858938. [PMID: 36454044 PMCID: PMC9911084 DOI: 10.1093/g3journal/jkac300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022]
Abstract
Penicillium oxalicum has been reported as a multienzyme-producing fungus and is widely used in industry due to great potential for cellulase release. Until now, there are only 10 available genome assemblies of P. oxalicum species deposited in the GenBank database. In this study, the genome of the I1R1 strain isolated from the root of Ixora chinensis was completely sequenced by Pacbio Sequel sequencing technology, assembled into 8 chromosomes with the genome size of 30.8 Mb, as well as a mitogenome of 26 kb. The structural and functional analyses of the I1R1 genome revealed gene model annotations encoding an enzyme set involved in significant metabolic processes, along with cytochrome P450s and secondary metabolite biosynthesis. The comparative analysis of the P. oxalicum species based on orthology and gene family duplications indicated their large and closed pan-genome of 9,500 orthologous groups. This is valuable data for future phylogenetic and population genomics studies.
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Affiliation(s)
- Huong Mai Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Dung Thi Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Lam Tung Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Phuong Thi Minh Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Linh Huyen Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Tung Thanh Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Hung Mau Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Tien Thuy Luu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Ha Hoang
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Hoang Ha Chu
- Corresponding authors: Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi 10072, Vietnam.
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Hugaboom M, Hatmaker EA, LaBella AL, Rokas A. Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi. G3 (BETHESDA, MD.) 2022; 13:6777267. [PMID: 36305682 PMCID: PMC9836360 DOI: 10.1093/g3journal/jkac285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.
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Affiliation(s)
- Miya Hugaboom
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Elizabeth Anne Hatmaker
- Corresponding author: Department of Biological Sciences, Vanderbilt University, VU Station B 35-1364, Nashville, TN 37235, USA. (AH)
| | - Abigail L LaBella
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Antonis Rokas
- Corresponding author: Department of Biological Sciences, Vanderbilt University, VU Station B 35-1364, Nashville, TN 37235, USA. (AR)
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Telomere-to-telomere genome sequence of the model mould pathogen Aspergillus fumigatus. Nat Commun 2022; 13:5394. [PMID: 36104328 PMCID: PMC9472742 DOI: 10.1038/s41467-022-32924-7] [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: 03/29/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
The pathogenic fungus Aspergillus fumigatus is a major etiological agent of fungal invasive and chronic diseases affecting tens of millions of individuals worldwide. Draft genome sequences of two clinical isolates (Af293 and A1163) are commonly used as reference genomes for analyses of clinical and environmental strains. However, the reference sequences lack coverage of centromeres, an accurate sequence for ribosomal repeats, and a comprehensive annotation of chromosomal rearrangements such as translocations and inversions. Here, we used PacBio Single Molecule Real-Time (SMRT), Oxford Nanopore and Illumina HiSeq sequencing for de novo genome assembly and polishing of two laboratory reference strains of A. fumigatus, CEA10 (parental isolate of A1163) and its descendant A1160. We generated full length chromosome assemblies and a comprehensive telomere-to-telomere coverage for CEA10 and near complete assembly of A1160 including ribosomal repeats and the sequences of centromeres, which we discovered to be composed of long transposon elements. We envision these high-quality reference genomes will become fundamental resources to study A. fumigatus biology, pathogenicity and virulence, and to discover more effective treatments against diseases caused by this fungus. The fungus Aspergillus fumigatus causes invasive and chronic diseases worldwide. Here, Bowyer et al. use long-read and short-read sequencing to generate complete chromosome assemblies and telomere-to-telomere coverage for two isolates, thus providing high-quality reference genomes as fundamental resources to study this pathogen.
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Towards Understanding the Function of Aegerolysins. Toxins (Basel) 2022; 14:toxins14090629. [PMID: 36136567 PMCID: PMC9505663 DOI: 10.3390/toxins14090629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Aegerolysins are remarkable proteins. They are distributed over the tree of life, being relatively widespread in bacteria and fungi, but also present in some insects, plants, protozoa, and viruses. Despite their abundance in cells of certain developmental stages and their presence in secretomes, only a few aegerolysins have been studied in detail. Their function, in particular, is intriguing. Here, we summarize previously published findings on the distribution, molecular interactions, and function of these versatile aegerolysins. They have very diverse protein sequences but a common fold. The machine learning approach of the AlphaFold2 algorithm, which incorporates physical and biological knowledge of protein structures and multisequence alignments, provides us new insights into the aegerolysins and their pore-forming partners, complemented by additional genomic support. We hypothesize that aegerolysins are involved in the mechanisms of competitive exclusion in the niche.
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Intraspecific comparison of mitochondrial genomes reveals the evolution in medicinal fungus Ganoderma lingzhi. J Biosci Bioeng 2022; 134:374-383. [PMID: 36075811 DOI: 10.1016/j.jbiosc.2022.07.003] [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: 09/25/2021] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/21/2022]
Abstract
Several mitogenomes of the genus Ganoderma have been assembled, but intraspecific comparisons of mitogenomes in Ganoderma lingzhi have not been reported. In this study, 19 G. lingzhi mitogenomes were assembled and analyzed combined with three mitogenomes of G. lingzhi from GenBank in term of the characteristics, evolution, and phylogeny. The results showed that the mitogenomes of the G. lingzhi strains are closed circular ranging from 49.23 kb to 68.37 kb. The genetic distance, selective pressure, and base variation indicate that the 14 common protein coding genes were highly conserved. The differences in introns, open reading frames, and repetitive sequences in the mitogenome were the main factors leaded to the variations in mitogenome. The introns were horizontally transferred in mitogenomes, and the differences between introns in the same insertion, which were primarily caused by the repetitive sequence, showed that the introns may be under degeneration. Besides, the frequent insertion and deletion of introns showed an evolutionary rate faster than protein coding genes. Phylogenetic analysis showed that the G. lingzhi strains gathered with high support, and those with the same intron distribution law had closer clustering relationships.
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13
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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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14
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Ellena V, Steiger MG. The importance of complete and high-quality genome sequences in Aspergillus niger research. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:935993. [PMID: 37746178 PMCID: PMC10512394 DOI: 10.3389/ffunb.2022.935993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/27/2022] [Indexed: 09/26/2023]
Abstract
The possibility to sequence the entire genome of an organism revolutionized the fields of biology and biotechnology. The first genome sequence of the important filamentous fungus Aspergillus niger was obtained in 2007, 11 years after the release of the first eukaryotic genome sequence. From that moment, genomics of A. niger has seen major progresses, facilitated by the advances in the sequencing technologies and in the methodologies for gene function prediction. However, there are still challenges to face when trying to obtain complete genomes, equipped with all the repetitive sequences that they contain and without omitting the mitochondrial sequences. The aim of this perspective article is to discuss the current status of A. niger genomics and draw attention to the open challenges that the fungal community should address to move research of this important fungus forward.
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Affiliation(s)
- Valeria Ellena
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
| | - Matthias G. Steiger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
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15
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Abstract
AbstractThe order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.
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16
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Chen S, Fan L, Song J, Zhang H, Doucette C, Hughes T, Campbell L. Quantitative proteomic analysis of Neosartorya pseudofischeri ascospores subjected to heat treatment. J Proteomics 2022; 252:104446. [PMID: 34883268 DOI: 10.1016/j.jprot.2021.104446] [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: 04/23/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
Neosartorya pseudofischeri, a heat- resistant fungus, was isolated from contaminated blueberry juice in our laboratory. To obtain a better understanding of the cellular process of heat- resistant fungus, a quantitative proteomic investigation employing stable isotope labeling by peptide demethylation was conducted on changes in intracellular proteins of N. pseudofischeri ascospores subjected to heat treatment at 93 °C for 0, 1 or 8 min. In total, 811 proteins were identified and quantified. Using the normalized ratio of protein abundance, proteins that changed more than two- fold after heat treatment were identified as significantly increased or decreased proteins and grouped into four clusters based on their quantitative changes. Decreased proteins were found mainly involved in the central carbon metabolism, heat stress responses, reactive oxygen intermediates elimination and translation events. A group of proteins in relation to toxicant degradation and antibiotic neutralization linking to environmental adaptability and tolerance of heat- resistant, was also identified. These findings provide insights into protein changes of N. pseudofischeri ascospores and lay foundations for further investigations on heat- resistant molds using targeted quantitative approaches. SIGNIFICANCE OF THE RESEARCH: Heat- resistant fungi can survive pasteurization processes, and subsequently germinate and grow to cause spoilage of food products, leading to significant economic losses for the food industry and potential health risk for the consumers. To obtain a better understanding of the cellular process of heat- resistant fungi, a quantitative proteomic approach employing stable isotope labeling by peptide demethylation has been used to investigate the intracellular protein changes of N. pseudofischeri ascospores isolated from blueberry juice and subjected to heat treatment. 150 significantly changed proteins were grouped into four clusters based on their quantitative changes. The significant decrease in protein abundance in response to heat treatment revealed possible mechanism that N. pseudofischeri ascospores could survive the heat treatment. This is the first proteomic profile report for N. pseudofischeri. These findings provide insights into protein changes of N. pseudofischeri and lay foundations for further investigations on heat- resistant fungi using targeted quantitative approaches to evaluate the efficiency of thermal treatment for processed food products.
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Affiliation(s)
- Si Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China; Laboratory of aquatic product processing and quality safety, Marine Fisheries Research Institute of Zhejiang Province, Zhejiang, China
| | - Lihua Fan
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada.
| | - Jun Song
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Hong Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China.
| | - Craig Doucette
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Timothy Hughes
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Leslie Campbell
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
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17
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Fonseca PLC, De-Paula RB, Araújo DS, Tomé LMR, Mendes-Pereira T, Rodrigues WFC, Del-Bem LE, Aguiar ERGR, Góes-Neto A. Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements. Front Microbiol 2021; 12:787283. [PMID: 34925295 PMCID: PMC8672057 DOI: 10.3389/fmicb.2021.787283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023] Open
Abstract
Fungi comprise a great diversity of species with distinct ecological functions and lifestyles. Similar to other eukaryotes, fungi rely on interactions with prokaryotes and one of the most important symbiotic events was the acquisition of mitochondria. Mitochondria are organelles found in eukaryotic cells whose main function is to generate energy through aerobic respiration. Mitogenomes (mtDNAs) are double-stranded circular or linear DNA from mitochondria that may contain core genes and accessory elements that can be replicated, transcribed, and independently translated from the nuclear genome. Despite their importance, investigative studies on the diversity of fungal mitogenomes are scarce. Herein, we have evaluated 788 curated fungal mitogenomes available at NCBI database to assess discrepancies and similarities among them and to better understand the mechanisms involved in fungal mtDNAs variability. From a total of 12 fungal phyla, four do not have any representative with available mitogenomes, which highlights the underrepresentation of some groups in the current available data. We selected representative and non-redundant mitogenomes based on the threshold of 90% similarity, eliminating 81 mtDNAs. Comparative analyses revealed considerable size variability of mtDNAs with a difference of up to 260 kb in length. Furthermore, variation in mitogenome length and genomic composition are generally related to the number and length of accessory elements (introns, HEGs, and uORFs). We identified an overall average of 8.0 (0–39) introns, 8.0 (0–100) HEGs, and 8.2 (0–102) uORFs per genome, with high variation among phyla. Even though the length of the core protein-coding genes is considerably conserved, approximately 36.3% of the mitogenomes evaluated have at least one of the 14 core coding genes absent. Also, our results revealed that there is not even a single gene shared among all mitogenomes. Other unusual genes in mitogenomes were also detected in many mitogenomes, such as dpo and rpo, and displayed diverse evolutionary histories. Altogether, the results presented in this study suggest that fungal mitogenomes are diverse, contain accessory elements and are absent of a conserved gene that can be used for the taxonomic classification of the Kingdom Fungi.
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Affiliation(s)
- Paula L C Fonseca
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Ruth B De-Paula
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States
| | - Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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18
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Abstract
Nuclear genome sequences incompletely characterize the genomic content and thus the genetic diversity of fungal species. Here, we present the complete mitochondrial genome sequences of nine Aspergillus flavus strains, providing useful information for inter- and intraspecific analyses.
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19
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Aspergillus fumigatus versus Genus Aspergillus: Conservation, Adaptive Evolution and Specific Virulence Genes. Microorganisms 2021; 9:microorganisms9102014. [PMID: 34683335 PMCID: PMC8539515 DOI: 10.3390/microorganisms9102014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
Aspergillus is an important fungal genus containing economically important species, as well as pathogenic species of animals and plants. Using eighteen fungal species of the genus Aspergillus, we conducted a comprehensive investigation of conserved genes and their evolution. This also allows us to investigate the selection pressure driving the adaptive evolution in the pathogenic species A. fumigatus. Among single-copy orthologs (SCOs) for A. fumigatus and the closely related species A. fischeri, we identified 122 versus 50 positively selected genes (PSGs), respectively. Moreover, twenty conserved genes of unknown function were established to be positively selected and thus important for adaption. A. fumigatus PSGs interacting with human host proteins show over-representation of adaptive, symbiosis-related, immunomodulatory and virulence-related pathways, such as the TGF-β pathway, insulin receptor signaling, IL1 pathway and interfering with phagosomal GTPase signaling. Additionally, among the virulence factor coding genes, secretory and membrane protein-coding genes in multi-copy gene families, 212 genes underwent positive selection and also suggest increased adaptation, such as fungal immune evasion mechanisms (aspf2), siderophore biosynthesis (sidD), fumarylalanine production (sidE), stress tolerance (atfA) and thermotolerance (sodA). These genes presumably contribute to host adaptation strategies. Genes for the biosynthesis of gliotoxin are shared among all the close relatives of A. fumigatus as an ancient defense mechanism. Positive selection plays a crucial role in the adaptive evolution of A. fumigatus. The genome-wide profile of PSGs provides valuable targets for further research on the mechanisms of immune evasion, antimycotic targeting and understanding fundamental virulence processes.
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20
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Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1-2 locus of Aspergillus niger. BMC Genomics 2021; 22:679. [PMID: 34548025 PMCID: PMC8454179 DOI: 10.1186/s12864-021-07990-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Background Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Its genome was one of the first Aspergillus genomes to be sequenced in 2007, due to its economic importance and its role as model organism to study fungal fermentation. Nowadays, the genome sequences of more than 20 A. niger strains are available. These, however, do not include the neotype strain CBS 554.65. Results The genome of CBS 554.65 was sequenced with PacBio. A high-quality nuclear genome sequence consisting of 17 contigs with a N50 value of 4.07 Mbp was obtained. The assembly covered all the 8 centromeric regions of the chromosomes. In addition, a complete circular mitochondrial DNA assembly was obtained. Bioinformatic analyses revealed the presence of a MAT1-2-1 gene in this genome, contrary to the most commonly used A. niger strains, such as ATCC 1015 and CBS 513.88, which contain a MAT1-1-1 gene. A nucleotide alignment showed a different orientation of the MAT1–1 locus of ATCC 1015 compared to the MAT1–2 locus of CBS 554.65, relative to conserved genes flanking the MAT locus. Within 24 newly sequenced isolates of A. niger half of them had a MAT1–1 locus and the other half a MAT1–2 locus. The genomic organization of the MAT1–2 locus in CBS 554.65 is similar to other Aspergillus species. In contrast, the region comprising the MAT1–1 locus is flipped in all sequenced strains of A. niger. Conclusions This study, besides providing a high-quality genome sequence of an important A. niger strain, suggests the occurrence of genetic flipping or switching events at the MAT1–1 locus of A. niger. These results provide new insights in the mating system of A. niger and could contribute to the investigation and potential discovery of sexuality in this species long thought to be asexual. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07990-8.
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21
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Wyrębek J, Molcan T, Myszczyński K, van Diepeningen AD, Stakheev AA, Żelechowski M, Bilska K, Kulik T. Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto. Front Microbiol 2021; 12:714651. [PMID: 34531839 PMCID: PMC8439580 DOI: 10.3389/fmicb.2021.714651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.
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Affiliation(s)
- Joanna Wyrębek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Alexander A Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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22
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Hu Z, Liu S, Xu Z, Liu S, Li T, Yu S, Zhao W. Comparison of
Aspergillus chevalieri
and related species in dark tea at different aspects: Morphology, enzyme activity and mitochondrial genome. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhi‐Yuan Hu
- College of Food Science and Technology Hunan Agricultural University Changsha China
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Su‐Chun Liu
- College of Food Science and Technology Hunan Agricultural University Changsha China
| | - Zheng‐Gang Xu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western College of Forestry Northwest A & F University Yangling China
| | - Shi‐Quan Liu
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Tao‐Tao Li
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Song‐Lin Yu
- Hunan Provincial Key Lab of Dark Tea and Jin‐hua Hunan City University Yiyang China
| | - Wei‐Ping Zhao
- College of Business Hunan Agricultural University Changsha China
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23
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Skerker JM, Pianalto KM, Mondo SJ, Yang K, Arkin AP, Keller NP, Grigoriev IV, Louise Glass NL. Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357. G3 (BETHESDA, MD.) 2021; 11:6310016. [PMID: 34849826 PMCID: PMC8496237 DOI: 10.1093/g3journal/jkab213] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/10/2021] [Indexed: 01/22/2023]
Abstract
Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally isolated from peanut and has been used as a model organism for understanding the regulation and production of secondary metabolites, such as aflatoxin. A draft genome of NRRL 3357 was previously constructed, enabling the development of molecular tools and for understanding population biology of this particular species. Here, we describe an updated, near complete, telomere-to-telomere assembly and re-annotation of the eight chromosomes of A. flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. A total of 13,715 protein-coding genes were predicted. Using RNA-seq data, a significant improvement was achieved in predicted 5’ and 3’ untranslated regions, which were incorporated into the new gene models.
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Affiliation(s)
- Jeffrey M Skerker
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kaila M Pianalto
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stephen J Mondo
- The U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kunlong Yang
- Department of Medical Microbiology & Immunology and Bacteriology, University of Wisconsin, Madison, WI 53706, USA
| | - Adam P Arkin
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nancy P Keller
- Department of Medical Microbiology & Immunology and Bacteriology, University of Wisconsin, Madison, WI 53706, USA
| | - Igor V Grigoriev
- The U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - N Louise Louise Glass
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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24
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Megarioti AH, Kouvelis VN. The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG). Genome Biol Evol 2021; 12:1337-1354. [PMID: 32585032 PMCID: PMC7487136 DOI: 10.1093/gbe/evaa126] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
Fungal mitochondrial (mt) genomes exhibit great diversity in size which is partially attributed to their variable intergenic regions and most importantly to the inclusion of introns within their genes. These introns belong to group I or II, and both of them are self-splicing. The majority of them carry genes encoding homing endonucleases, either LAGLIDADG or GIY-YIG. In this study, it was found that these intronic homing endonucleases genes (HEGs) may originate from mt free-standing open reading frames which can be found nowadays in species belonging to Early Diverging Fungi as “living fossils.” A total of 487 introns carrying HEGs which were located in the publicly available mt genomes of representative species belonging to orders from all fungal phyla was analyzed. Their distribution in the mt genes, their insertion target sequence, and the phylogenetic analyses of the HEGs showed that these introns along with their HEGs form a composite structure in which both selfish elements coevolved. The invasion of the ancestral free-standing HEGs in the introns occurred through a perpetual mechanism, called in this study as “aenaon” hypothesis. It is based on recombination, transpositions, and horizontal gene transfer events throughout evolution. HEGs phylogenetically clustered primarily according to their intron hosts and secondarily to the mt genes carrying the introns and their HEGs. The evolutionary models created revealed an “intron-early” evolution which was enriched by “intron-late” events through many different independent recombinational events which resulted from both vertical and horizontal gene transfers.
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Affiliation(s)
- Amalia H Megarioti
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
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25
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Salgado-Salazar C, Skaltsas DN, Phipps T, Castlebury LA. Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea. G3-GENES GENOMES GENETICS 2021; 11:6163289. [PMID: 33693679 DOI: 10.1093/g3journal/jkab071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/25/2021] [Indexed: 11/14/2022]
Abstract
Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.
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Affiliation(s)
- Catalina Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
| | - Demetra N Skaltsas
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA.,Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37831, USA
| | - Tunesha Phipps
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
| | - Lisa A Castlebury
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
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A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers. Int J Genomics 2021; 2021:6652508. [PMID: 34212028 PMCID: PMC8208876 DOI: 10.1155/2021/6652508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/20/2022] Open
Abstract
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
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27
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Mayers CG, Harrington TC, Wai A, Hausner G. Recent and Ongoing Horizontal Transfer of Mitochondrial Introns Between Two Fungal Tree Pathogens. Front Microbiol 2021; 12:656609. [PMID: 34149643 PMCID: PMC8208691 DOI: 10.3389/fmicb.2021.656609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/23/2022] Open
Abstract
Two recently introduced fungal plant pathogens (Ceratocystis lukuohia and Ceratocystis huliohia) are responsible for Rapid ‘ōhi‘a Death (ROD) in Hawai‘i. Despite being sexually incompatible, the two pathogens often co-occur in diseased ‘ōhi‘a sapwood, where genetic interaction is possible. We sequenced and annotated 33 mitochondrial genomes of the two pathogens and related species, and investigated 35 total Ceratocystis mitogenomes. Ten mtDNA regions [one group I intron, seven group II introns, and two autonomous homing endonuclease (HE) genes] were heterogeneously present in C. lukuohia mitogenomes, which were otherwise identical. Molecular surveys with specific primers showed that the 10 regions had uneven geographic distribution amongst populations of C. lukuohia. Conversely, identical orthologs of each region were present in every studied isolate of C. huliohia regardless of geographical origin. Close relatives of C. lukuohia lacked or, rarely, had few and dissimilar orthologs of the 10 regions, whereas most relatives of C. huliohia had identical or nearly identical orthologs. Each region included or worked in tandem with HE genes or reverse transcriptase/maturases that could facilitate interspecific horizontal transfers from intron-minus to intron-plus alleles. These results suggest that the 10 regions originated in C. huliohia and are actively moving to populations of C. lukuohia, perhaps through transient cytoplasmic contact of hyphal tips (anastomosis) in the wound surface of ‘ōhi‘a trees. Such contact would allow for the transfer of mitochondria followed by mitochondrial fusion or cytoplasmic exchange of intron intermediaries, which suggests that further genomic interaction may also exist between the two pathogens.
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Affiliation(s)
- Chase G Mayers
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Thomas C Harrington
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Yildiz G, Ozkilinc H. Pan-Mitogenomics Approach Discovers Diversity and Dynamism in the Prominent Brown Rot Fungal Pathogens. Front Microbiol 2021; 12:647989. [PMID: 34054750 PMCID: PMC8149612 DOI: 10.3389/fmicb.2021.647989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/29/2021] [Indexed: 01/26/2023] Open
Abstract
Monilinia fructicola and Monilinia laxa species are the most destructive and economically devastating fungal plant pathogens causing brown rot disease on stone and pome fruits worldwide. Mitochondrial genomes (mitogenomes) play critical roles influencing the mechanisms and directions of the evolution of fungal pathogens. The pan-mitogenomics approach predicts core and accessory regions of the mitochondrial genomes and explains the gain or loss of variation within and between species. The present study is a fungal pan-mitogenome of M. fructicola (N = 8) and M. laxa (N = 8) species. The completely sequenced and annotated mitogenomes showed high variability in size within and between the species. The mitogenomes of M. laxa were larger, ranging from 178,351 to 179,780bp, than the mitogenomes of M. fructicola, ranging from 158,607 to 167,838bp. However, size variation within the species showed that M. fructicola isolates were more variable in the size range than M. laxa isolates. All the mitogenomes included conserved mitochondrial genes, as well as variable regions including different mobile introns encoding homing endonucleases or maturase, non-coding introns, and repetitive elements. The linear model analysis supported the hypothesis that the mitogenome size expansion is due to presence of variable (accessory) regions. Gene synteny was mostly conserved among all samples, with the exception for order of the rps3 in the mitogenome of one isolate. The mitogenomes presented AT richness; however, A/T and G/C skew varied among the mitochondrial genes. The purifying selection was detected in almost all the protein-coding genes (PCGs) between the species. However, cytochrome b was the only gene showing a positive selection signal among the total samples. Combined datasets of amino acid sequences of 14 core mitochondrial PCGs and rps3 obtained from this study together with published mitochondrial genome sequences from some other species from Heliotales were used to infer a maximum likelihood (ML) phylogenetic tree. ML tree indicated that both Monilinia species highly diverged from each other as well as some other fungal species from the same order. Mitogenomes harbor much information about the evolution of fungal plant pathogens, which could be useful to predict pathogenic life strategies.
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Affiliation(s)
- Gozde Yildiz
- School of Graduate Studies, MSc Program in Biomolecular Sciences, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Hilal Ozkilinc
- School of Graduate Studies, MSc Program in Biomolecular Sciences, Çanakkale Onsekiz Mart University, Çanakkale, Turkey.,Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
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29
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de Almeida JR, Riaño Pachón DM, Franceschini LM, dos Santos IB, Ferrarezi JA, de Andrade PAM, Monteiro-Vitorello CB, Labate CA, Quecine MC. Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes. PLoS One 2021; 16:e0248054. [PMID: 33705433 PMCID: PMC7951889 DOI: 10.1371/journal.pone.0248054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.
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Affiliation(s)
- Jaqueline Raquel de Almeida
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Livia Maria Franceschini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Isaneli Batista dos Santos
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Jessica Aparecida Ferrarezi
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Pedro Avelino Maia de Andrade
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Carlos Alberto Labate
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
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30
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The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies. Life (Basel) 2021; 11:life11030215. [PMID: 33803147 PMCID: PMC7999263 DOI: 10.3390/life11030215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/26/2022] Open
Abstract
Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease’s complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes.
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31
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Araújo DS, De-Paula RB, Tomé LMR, Quintanilha-Peixoto G, Salvador-Montoya CA, Del-Bem LE, Badotti F, Azevedo VAC, Brenig B, Aguiar ERGR, Drechsler-Santos ER, Fonseca PLC, Góes-Neto A. Comparative mitogenomics of Agaricomycetes: Diversity, abundance, impact and coding potential of putative open-reading frames. Mitochondrion 2021; 58:1-13. [PMID: 33582235 DOI: 10.1016/j.mito.2021.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
The mitochondrion is an organelle found in eukaryote organisms, and it is vital for different cellular pathways. The mitochondrion has its own DNA molecule and, because its genetic content is relatively conserved, despite the variation of size and structure, mitogenome sequences have been widely used as a promising molecular biomarker for taxonomy and evolution in fungi. In this study, the mitogenomes of two fungal species of Agaricomycetes class, Phellinotus piptadeniae and Trametes villosa, were assembled and annotated for the first time. We used these newly sequenced mitogenomes for comparative analyses with other 55 mitogenomes of Agaricomycetes available in public databases. Mitochondrial DNA (mtDNA) size and content are highly variable and non-coding and intronic regions, homing endonucleases (HEGs), and unidentified ORFs (uORFs) significantly contribute to the total size of the mitogenome. Furthermore, accessory genes (most of them as HEGs) are shared between distantly related species, most likely as a consequence of horizontal gene transfer events. Conversely, uORFs are only shared between taxonomically related species, most probably as a result of vertical evolutionary inheritance. Additionally, codon usage varies among mitogenomes and the GC content of mitochondrial features may be used to distinguish coding from non-coding sequences. Our results also indicated that transposition events of mitochondrial genes to the nuclear genome are not common. Despite the variation of size and content of the mitogenomes, mitochondrial genes seemed to be reliable molecular markers in our time-divergence analysis, even though the nucleotide substitution rates of mitochondrial and nuclear genomes of fungi are quite different. We also showed that many events of mitochondrial gene shuffling probably happened amongst the Agaricomycetes during evolution, which created differences in the gene order among species, even those of the same genus. Altogether, our study revealed new information regarding evolutionary dynamics in Agaricomycetes.
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Affiliation(s)
- Daniel S Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luiz M R Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Quintanilha-Peixoto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R G R Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | - Paula L C Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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32
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Chen C, Wang J, Li Q, Fu R, Jin X, Huang W, Lu D. Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny. Front Microbiol 2020; 11:573064. [PMID: 33193177 PMCID: PMC7644776 DOI: 10.3389/fmicb.2020.573064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Phallus indusiatus and Phallus echinovolvatus are edible bamboo mushrooms with pharmacological properties. We sequenced, assembled, annotated, and compared the mitogenomes of these species. Both mitogenomes were composed of circular DNA molecules, with sizes of 89,139 and 50,098 bp, respectively. Introns were the most important factor in mitogenome size variation within the genus Phallus. Phallus indusiatus, P. echinovolvatus, and Turbinellus floccosus in the subclass Phallomycetidae have conservative gene arrangements. Large-scale gene rearrangements were observed in species representing 42 different genera of Basidiomycetes. A variety of intron position classes were found in the 44 Basidiomycete species analyzed. A novel group II intron from the P. indusiatus mitogenome was compared with other fungus species containing the same intron, and we demonstrated that the insertion sites of the intron had a base preference. Phylogenetic analyses based on combined gene datasets yielded well-supported Bayesian posterior probability (BPP = 1) topologies. This indicated that mitochondrial genes are reliable molecular markers for analyzing the phylogenetic relationships of the Basidiomycetes. This is the first study of the mitogenome of the genus Phallus, and it increases our understanding of the population genetics and evolution of bamboo mushrooms and related species.
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Affiliation(s)
- Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
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33
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Park J, Lee MK, Yu JH, Kim JH, Han KH. Complete mitochondrial genome sequence of Afla-Guard ®, commercially available non-toxigenic Aspergillus flavus. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3590-3592. [PMID: 33367022 PMCID: PMC7594763 DOI: 10.1080/23802359.2020.1825129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Afla-Guard® is a commercial non-toxigenic Aspergillus flavus strain used to decrease aflatoxin contamination level in field. Its mitochondrial genome was sequenced, showing that its length is 29,208 bp with typical configuration of Aspergillus mitochondrial genome. 17 SNPs and 27 INDELs were identified by comparing with previous A. flavus mitochondrial genome. Phylogenetic trees present that A. flavus of Afla-Guard® was clustered with the previous A. flavus mitochondrial genome.
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Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd, Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Mi-Kyung Lee
- Department of Bacteriology, The University of Wisconsin-Madison, Madison, WI, USA.,Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Jae-Hyuk Yu
- Department of Bacteriology, The University of Wisconsin-Madison, Madison, WI, USA
| | - Jong-Hwa Kim
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
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34
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Park J, Lee MK, Yu JH, Zhu B, Kim JH, Han KH. Complete mitochondrial genome sequence of Aspergillus flavus SRRC1009: insight of intraspecific variations on A. flavus mitochondrial genomes. Mitochondrial DNA B Resour 2020; 5:3585-3587. [PMID: 33367020 PMCID: PMC7594760 DOI: 10.1080/23802359.2020.1771226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 04/26/2020] [Indexed: 11/21/2022] Open
Abstract
The mitogenome of Aspergillus flavus SRRC1009 was sequenced to investigate intraspecific variations on mitochondrial genomes of A. flavus. It shows 29,202 bp with a typical configuration of Aspergillus mitogenome. Sixteen SNPs and 22 INDELs and 17 SNPs and 27 INDELs were identified against AflaGuard® and JQ355000, respectively. Phylogenetic trees present in the three A. flavus mitochondrial genomes were clustered with A. oryzae mitochondrial genome in one clade.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Mi-Kyung Lee
- Department of Bacteriology, The University of Wisconsin-Madison, Madison, WI, USA
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Jae-Hyuk Yu
- Department of Bacteriology, The University of Wisconsin-Madison, Madison, WI, USA
| | - Bohan Zhu
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
| | - Jong-Hwa Kim
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
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35
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Park J, Kwon W, Hong SB, Han KH. First Record of the Complete Mitochondrial Genome of a Saprotrophic and Opportunistic Human Pathogenic Fungus, Scopulariopsis brevicaulis. MYCOBIOLOGY 2020; 48:528-531. [PMID: 33312021 PMCID: PMC7717690 DOI: 10.1080/12298093.2020.1823554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/01/2020] [Accepted: 09/09/2020] [Indexed: 06/12/2023]
Abstract
Scopulariopsis brevicaulis is a widely distributed soil fungus known as a common saprotroph of biodegradation. It is also an opportunistic human pathogen that can produce various secondary metabolites. Here, we report the first complete mitochondrial genome sequence of S. brevicaulis isolated from air in South Korea. Total length of the mitochondrial genome is 28,829 bp and encoded 42 genes (15 protein-coding genes, 2 rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 26.2%, and overall GC content is 27.6%. Phylogenetic trees present that S. brevicaulis is clustered with Lomentospora prolificans with presenting various mitochondrial genome length.
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Affiliation(s)
- Jongsun Park
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Woochan Kwon
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Seung-Beom Hong
- Korean Agricultural Culture Collection, National Institute of Agricultural Science, RDA, Wanju, Republic of Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
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36
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Yildiz G, Ozkilinc H. First characterization of the complete mitochondrial genome of fungal plant-pathogen Monilinia laxa which represents the mobile intron rich structure. Sci Rep 2020; 10:13644. [PMID: 32788650 PMCID: PMC7424523 DOI: 10.1038/s41598-020-70611-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022] Open
Abstract
Monilinia laxa is an important fungal plant pathogen causing brown rot on many stone and pome fruits worldwide. Mitochondrial genome (mitogenome) plays a critical role in evolutionary biology of the organisms. This study aimed to characterize the complete mitogenome of M. laxa by using next-generation sequencing and approaches of de novo assembly and annotation. The total length of the mitogenome of M. laxa was 178,357 bp, and its structure was circular. GC content of the mitogenome was 30.1%. Annotation of the mitogenome presented 2 ribosomal RNA (rRNA) genes, 32 transfer RNA genes (tRNA), 1 gene encoding mitochondrial ribosomal protein S3, 14 protein-coding genes and 15 open reading frame encoding hypothetical proteins. Moreover, the group I mobile introns encoding homing endonucleases including LAGLIDADG and GIY-YIG families were found both within coding regions (genic) and intergenic regions of the mitogenome, indicating an enlarged size and a dynamic structure of the mitogenome. Furthermore, a comparative mitogenomic analysis was performed between M. laxa and the three closely related fungal phytopathogen species (Botryotinia fuckeliana, Sclerotinia sclerotiorum and, S. borealis). Due to the number and distribution of introns, the large extent of structural rearrangements and diverse mitogenome sizes were detected among the species investigated. Monilinia laxa presented the highest number of homing endonucleases among the fungal species considered in the analyses. This study is the first to report a detailed annotation of the mitogenome of an isolate of M. laxa, providing a solid basis for further investigations of mitogenome variations for the other Monilinia pathogens causing brown rot disease.
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Affiliation(s)
- Gozde Yildiz
- Graduate School of Natural and Applied Sciences, MSc Program in Biomolecular Sciences, Canakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Hilal Ozkilinc
- Graduate School of Natural and Applied Sciences, MSc Program in Biomolecular Sciences, Canakkale Onsekiz Mart University, Çanakkale, Turkey.
- Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Canakkale Onsekiz Mart University, Çanakkale, Turkey.
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37
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Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics. G3-GENES GENOMES GENETICS 2020; 10:2275-2296. [PMID: 32354705 PMCID: PMC7341126 DOI: 10.1534/g3.120.401290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host. An apparent increase in activity and wandering behaviors precedes a final summiting and biting behavior onto vegetation, which positions the manipulated ant in a site beneficial for fungal growth and transmission. We investigated the genetic underpinnings of host manipulation by: (i) producing a high-quality hybrid assembly and annotation of the Ophiocordyceps camponoti-floridani genome, (ii) conducting laboratory infections coupled with RNAseq of O. camponoti-floridani and its host, Camponotus floridanus, and (iii) comparing these data to RNAseq data of Ophiocordyceps kimflemingiae and Camponotus castaneus as a powerful method to identify gene expression patterns that suggest shared behavioral manipulation mechanisms across Ophiocordyceps-ant species interactions. We propose differentially expressed genes tied to ant neurobiology, odor response, circadian rhythms, and foraging behavior may result by activity of putative fungal effectors such as enterotoxins, aflatrem, and mechanisms disrupting feeding behaviors in the ant.
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38
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Hu Z, Liu S, Xu Z, Liu S. Sequencing and phylogenetic analysis of mitochondrial genome of Aspergillus cristatus. Mitochondrial DNA B Resour 2020; 5:2615-2616. [PMID: 33457881 PMCID: PMC7782343 DOI: 10.1080/23802359.2020.1782279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Aspergillus cristatus are the dominantly present microorganisms in dark tea. The whole mitochondrial genome sequence of A. cristatus was sequenced and reported in this study. The mitochondrial genome in A. cristatushas a full length of 77,649 bp, which is reported to be the longest among the mitochondrial genomes of Aspergillus species. The basesincluding A (34.14%), T (37.64%), C (15.61%) and G (12.61%) are found in their genome. A total of 42 genes (15 protein-coding genes, lrRNA/srRNA and 25 tRNAs) are encoded by the mitochondrial genome of this fungus. Phylogenetic analysis showed a closest relationship betweenA. pseudoglaucusand the taxonomic status of A. cristatus.
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Affiliation(s)
- Zhiyuan Hu
- College of Food Science and Technology, Hunan Agricultural University, Changsha, China.,School of Materials and Chemical Engineering, Hunan City University, Yiyang, China
| | - Suchun Liu
- College of Food Science and Technology, Hunan Agricultural University, Changsha, China
| | - Zhenggang Xu
- School of Materials and Chemical Engineering, Hunan City University, Yiyang, China
| | - Shiquan Liu
- School of Materials and Chemical Engineering, Hunan City University, Yiyang, China
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39
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Medina R, Franco MEE, Bartel LC, Martinez Alcántara V, Saparrat MCN, Balatti PA. Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management. Front Microbiol 2020; 11:978. [PMID: 32547508 PMCID: PMC7272585 DOI: 10.3389/fmicb.2020.00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.
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Affiliation(s)
- Rocio Medina
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Laura Cecilia Bartel
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Virginia Martinez Alcántara
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina.,Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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40
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Kulik T, Brankovics B, van Diepeningen AD, Bilska K, Żelechowski M, Myszczyński K, Molcan T, Stakheev A, Stenglein S, Beyer M, Pasquali M, Sawicki J, Wyrȩbek J, Baturo-Cieśniewska A. Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes. Front Microbiol 2020; 11:1002. [PMID: 32528440 PMCID: PMC7263005 DOI: 10.3389/fmicb.2020.01002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them promising candidates for diagnostic purposes. Fungi of the genus Fusarium display a high variation in MGE content, from MGE-poor (Fusarium oxysporum and Fusarium fujikuroi species complex) to MGE-rich mitogenomes found in the important cereal pathogens F. culmorum and F. graminearum sensu stricto. In this study, we investigated the MGE variation in these latter two species by mitogenome analysis of geographically diverse strains. In addition, a smaller set of F. cerealis and F. pseudograminearum strains was included for comparison. Forty-seven introns harboring from 0 to 3 endonucleases (HEGs) were identified in the standard set of mitochondrial protein-coding genes. Most of them belonged to the group I intron family and harbored either LAGLIDADG or GIY-YIG HEGs. Among a total of 53 HEGs, 27 were shared by all fungal strains. Most of the optional HEGs were irregularly distributed among fungal strains/species indicating ancestral mosaicism in MGEs. However, among optional MGEs, one exhibited species-specific conservation in F. culmorum. While in F. graminearum s.s. MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L may facilitate the identification of this species. Thus, our results demonstrate distinctive traits of mitogenomes for diagnostic purposes of Fusaria.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Balazs Brankovics
- Biointeractions & Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina.,Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
| | - Marco Beyer
- Department of Environmental Research and Innovation, Agro-Environmental Systems, Luxembourg Institute of Science and Technology, Belval, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Joanna Wyrȩbek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Baturo-Cieśniewska
- Laboratory of Phytopathology and Molecular Mycology, Department of Biology and Plant Protection, UTP University of Science and Technology, Bydgoszcz, Poland
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41
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Odoni DI, Vazquez-Vilar M, van Gaal MP, Schonewille T, Martins Dos Santos VAP, Tamayo-Ramos JA, Suarez-Diez M, Schaap PJ. Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions. FEMS Microbiol Lett 2020; 366:5437674. [PMID: 31062025 PMCID: PMC6502548 DOI: 10.1093/femsle/fnz071] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023] Open
Abstract
Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion. We hypothesise that depending on the experimental setup, extracellular citrate accumulation can have fundamentally different underlying transcriptomic landscapes. We show that varying the amount and type of supplement of an arginine auxotrophic A. niger strain results in transcriptional down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations when increased citrate production is triggered by iron limitation. By combining gene expression data obtained from these two very distinct experimental setups with hidden Markov models and transporter homology approaches, we were able to compile a shortlist of the most likely citrate transporter candidates. Two candidates (An17g01710 and An09g06720m.01) were heterologously expressed in the yeast Saccharomyces cerevisiae, and one of the resultant mutants showed the ability to secrete citrate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we demonstrate how a comparative transcriptomics approach complemented with further bioinformatics analyses can be used to pinpoint a fungal citrate exporter.
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Affiliation(s)
- Dorett I Odoni
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Merlijn P van Gaal
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom Schonewille
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Juan Antonio Tamayo-Ramos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,International Research Center in Critical Raw Materials-ICCRAM, Advanced Materials, Nuclear Technology and Applied Bio/Nanotechnology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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42
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Fonseca PLC, Badotti F, De-Paula RB, Araújo DS, Bortolini DE, Del-Bem LE, Azevedo VA, Brenig B, Aguiar ERGR, Góes-Neto A. Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes. Front Microbiol 2020; 11:765. [PMID: 32411111 PMCID: PMC7202290 DOI: 10.3389/fmicb.2020.00765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/30/2020] [Indexed: 12/24/2022] Open
Abstract
The order Hypocreales (Ascomycota) is composed of ubiquitous and ecologically diverse fungi such as saprobes, biotrophs, and pathogens. Despite their phylogenetic relationship, these species exhibit high variability in biomolecules production, lifestyle, and fitness. The mitochondria play an important role in the fungal biology, providing energy to the cells and regulating diverse processes, such as immune response. In spite of its importance, the mechanisms that shape fungal mitogenomes are still poorly understood. Herein, we investigated the variability and evolution of mitogenomes and its relationship with the divergence time using the order Hypocreales as a study model. We sequenced and annotated for the first time Trichoderma harzianum mitochondrial genome (mtDNA), which was compared to other 34 mtDNAs species that were publicly available. Comparative analysis revealed a substantial structural and size variation on non-coding mtDNA regions, despite the conservation of copy number, length, and structure of protein-coding elements. Interestingly, we observed a highly significant correlation between mitogenome length, and the number and size of non-coding sequences in mitochondrial genome. Among the non-coding elements, group I and II introns and homing endonucleases genes (HEGs) were the main contributors to discrepancies in mitogenomes structure and length. Several intronic sequences displayed sequence similarity among species, and some of them are conserved even at gene position, and were present in the majority of mitogenomes, indicating its origin in a common ancestor. On the other hand, we also identified species-specific introns that advocate for the origin by different mechanisms. Investigation of mitochondrial gene transfer to the nuclear genome revealed that nuclear copies of the nad5 are the most frequent while atp8, atp9, and cox3 could not be identified in any of the nuclear genomes analyzed. Moreover, we also estimated the divergence time of each species and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.
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Affiliation(s)
- Paula L. C. Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B. De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Daniel S. Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Dener E. Bortolini
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiz-Eduardo Del-Bem
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A. Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R. G. R. Aguiar
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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43
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Kulik T, Bilska K, Żelechowski M. Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA. Int J Mol Sci 2020; 21:E2645. [PMID: 32290169 PMCID: PMC7177237 DOI: 10.3390/ijms21072645] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
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.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
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44
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Park J, Xi H, Park J, Lee W. The complete mitochondrial genome of fungal endosymbiont, Ophiocordycipitaceae sp., isolated from Ricania speculum (Hemiptera: Ricaniidae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1754141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Jongsun Park
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Hong Xi
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jonghyun Park
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Wonhoon Lee
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Republic of Korea
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45
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Liu W, Cai Y, Zhang Q, Chen L, Shu F, Ma X, Bian Y. The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences. Int J Biol Macromol 2019; 143:373-381. [PMID: 31830457 DOI: 10.1016/j.ijbiomac.2019.12.056] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 12/11/2022]
Abstract
The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.
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Affiliation(s)
- Wei Liu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingli Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Qianqian Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Shu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolong Ma
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
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46
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Ametrano CG, Grewe F, Crous PW, Goodwin SB, Liang C, Selbmann L, Lumbsch HT, Leavitt SD, Muggia L. Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 2019; 10:19. [PMID: 32647623 PMCID: PMC7325674 DOI: 10.1186/s43008-019-0018-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.
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Affiliation(s)
- Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
| | - Felix Grewe
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85176, 3508 AD Utrecht, The Netherlands
| | - Stephen B Goodwin
- USDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Chen Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell' Università, 01100 Viterbo, Italy.,Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | - H Thorsten Lumbsch
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Steven D Leavitt
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602 USA
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
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47
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Wang G, Lin J, Shi Y, Chang X, Wang Y, Guo L, Wang W, Dou M, Deng Y, Ming R, Zhang J. Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya. BMC Genomics 2019; 20:765. [PMID: 31640544 PMCID: PMC6805638 DOI: 10.1186/s12864-019-6133-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells. RESULTS In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene. CONCLUSIONS Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.
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Affiliation(s)
- Gang Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jingxian Lin
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yang Shi
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoguang Chang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuanyuan Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lin Guo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Wenhui Wang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Meijie Dou
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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48
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Park J, Kwon W, Kim JB, Park MJ, Kim TS. Complete mitochondrial genome sequence of lettuce pathogenic fungus, Fusarium oxysporum f. sp. lactucae 09-002. Mitochondrial DNA B Resour 2019; 4:3434-3436. [PMID: 33366027 PMCID: PMC7706453 DOI: 10.1080/23802359.2019.1667902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022] Open
Abstract
Fusarium oxysporum is a famous plant pathogenic filamentous fungus. Here, we report the complete mitochondrial genome sequence of F. oxysporum f. sp. lactucae isolated from the lettuce field in Suwon area, Korea. Total length of the mitochondrial genome is 45,020 bp and it encodes 42 genes (15 protein-coding genes, two rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 32.7%, and overall GC content is 32.4%. Phylogenetic tree presented that F. oxysporum f. sp. lactucae 09-002 was clustered with Fusarium commune not like another F. oxysporum mitochondrial genomes, requiring further analyses.
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Affiliation(s)
- Jongsun Park
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Woochan Kwon
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Jung-Bun Kim
- Department of Agriculture and Life Sciences, Korea National Open University, Seoul, Korea
| | - Mi-Jeong Park
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Korea
| | - Tae-Sung Kim
- Department of Agriculture and Life Sciences, Korea National Open University, Seoul, Korea
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49
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Park J, Kwon W, Huang X, Mageswari A, Heo IB, Han KH, Hong SB. Complete mitochondrial genome sequence of a xerophilic fungus, Aspergillus pseudoglaucus. Mitochondrial DNA B Resour 2019; 4:2422-2423. [PMID: 33365569 PMCID: PMC7687513 DOI: 10.1080/23802359.2019.1586468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 02/10/2019] [Indexed: 01/06/2023] Open
Abstract
Aspergillus pseudoglaucus is a xerophilic filamentous fungus which can produce various secondary metabolites. Here, we reported the complete mitochondrial genome sequence of A. pseudoglaucus isolated from Meju, a soybean brick in Korea. Its mitochondrial genome was successfully assembled from raw reads sequenced using MiSeq by Velvet and SOAPGapCloser. Total length of the mitochondrial genome is 53,882 bp, which is third longest among known Aspergillus mitochondrial genomes and encoded 58 genes (30 protein-coding genes including hypothetical ORFs, two rRNAs, and 26 tRNAs). Nucleotide sequence of coding regions takes over 66.6% and overall GC content is 27.8%. Phylogenetic trees present that A. pseudoglaucus is located outside of section Nidulantes. Additional researches will be required for clarifying phylogenetic position of section Aspergillus.
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Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Woochan Kwon
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Xiaoxiao Huang
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
| | - Anbazhagan Mageswari
- Department of Microbiology, D.G. Vaishnav College, Chennai, India
- Agricultural Microbial Division, National Institute of Agricultural Scinece, Wanjugun, Republic of Korea
| | - In-Beom Heo
- Department of Microbiology, D.G. Vaishnav College, Chennai, India
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbial Division, National Institute of Agricultural Scinece, Wanjugun, Republic of Korea
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50
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Kolesnikova AI, Putintseva YA, Simonov EP, Biriukov VV, Oreshkova NV, Pavlov IN, Sharov VV, Kuzmin DA, Anderson JB, Krutovsky KV. Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species. BMC Genomics 2019; 20:351. [PMID: 31068137 PMCID: PMC6506933 DOI: 10.1186/s12864-019-5732-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/24/2019] [Indexed: 12/03/2022] Open
Abstract
Background Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time. Results Here we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes. Conclusions Our study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5732-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna I Kolesnikova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia
| | - Yuliya A Putintseva
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
| | - Evgeniy P Simonov
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Institute of Animal Systematics and Ecology, Siberian Branch of Russian Academy of Sciences, 630091, Novosibirsk, Russia
| | - Vladislav V Biriukov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia
| | - Natalya V Oreshkova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Igor N Pavlov
- Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Vadim V Sharov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - Dmitry A Kuzmin
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - James B Anderson
- Department of Biology, University of Toronto, Mississauga, ON, l5L 1C6, Canada
| | - Konstantin V Krutovsky
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany. .,Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. .,Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA.
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