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Godbole RC, Kadam SB, Pable AA, Singh S, Barvkar VT. Phylogenomics of transcriptionally active AP2/ERF and bHLH transcription factors and study of their promoter regions in Nothapodytes nimmoniana (J.Graham) Mabb. Genome 2023; 66:235-250. [PMID: 37163758 DOI: 10.1139/gen-2023-0009] [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] [Indexed: 05/12/2023]
Abstract
Nothapodytes nimmoniana is a medicinally important plant producing anticancer monoterpene indole alkaloid (MIA), camptothecin (CPT). The CPT is synthesised through the strictosidine intermediate following the MIA pathway; however, transcriptional regulation of CPT pathway is still elusive in N. nimmoniana. Biosynthesis of MIA is regulated by various transcription factors (TFs) belonging to AP2/ERF, bHLH, MYB, and WRKY families. The present study identified transcriptionally active full-length 105 AP2/ERF and 68 bHLH family TFs from the N. nimmoniana. AP2/ERF TFs were divided into three subfamilies along with a soloist, while bHLH TFs were divided into 10 subfamilies according to their phylogenetic similarities. Three group IXa ERFs, Nn-ERF22, Nn-ERF29, and Nn-ERF41, one subfamily IVa TF Nn-bHLH7, and three subfamilies IIIe Nn-bHLH33, Nn-bHLH51, and Nn-bHLH52 clustered with the TFs regulating alkaloid biosynthesis in Catharanthus roseus, tomato, tobacco, and Artemisia annua. Expression of these TFs in N. nimmoniana was higher in roots, which is a primary CPT accumulating tissue. Moreover, genome skimming approach was used to reconstruct the promoter regions of candidate ERF genes to identify the cis-regulatory elements. The presence of G-boxes and other jasmonic acid-responsive elements in the promoter suggests the regulation of ERFs by bHLHs. The present study effectively generated and used genomics resource for characterisation of regulatory TFs from non-model medicinal plant.
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Affiliation(s)
- Rucha C Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Swapnil B Kadam
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Sudhir Singh
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
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2
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Gamboa M, Kitamura N, Miura K, Noda S, Kaminuma O. Evolutionary mechanisms underlying the diversification of nuclear factor of activated T cells across vertebrates. Sci Rep 2023; 13:6468. [PMID: 37156933 PMCID: PMC10167247 DOI: 10.1038/s41598-023-33751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The mechanisms of immunity linked to biological evolution are crucial for understanding animal morphogenesis, organogenesis, and biodiversity. The nuclear factor of activated T cells (NFAT) family consists of five members (NFATc1-c4, 5) with different functions in the immune system. However, the evolutionary dynamics of NFATs in vertebrates has not been explored. Herein, we investigated the origin and mechanisms underlying the diversification of NFATs by comparing the gene, transcript and protein sequences, and chromosome information. We defined an ancestral origin of NFATs during the bilaterian development, dated approximately 650 million years ago, where NFAT5 and NFATc1-c4 were derived independently. The conserved parallel evolution of NFATs in multiple species was probably attributed to their innate nature. Conversely, frequent gene duplications and chromosomal rearrangements in the recently evolved taxa have suggested their roles in the adaptive immune evolution. A significant correlation was observed between the chromosome rearrangements with gene duplications and the structural fixation changes in vertebrate NFATs, suggesting their role in NFAT diversification. Remarkably, a conserved gene structure around NFAT genes with vertebrate evolutionary-related breaking points indicated the inheritance of NFATs with their neighboring genes as a unit. The close relationship between NFAT diversification and vertebrate immune evolution was suggested.
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Affiliation(s)
- Maribet Gamboa
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan.
- Department of Ecology, Faculty of Sciences, Universidad Católica de la Santísima Concepción, 4090541, Concepción, Chile.
| | - Noriko Kitamura
- Neurovirology Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Kento Miura
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Satoko Noda
- Graduate School of Science and Engineering, Ibaraki University, Ibaraki, 310-8512, Japan
| | - Osamu Kaminuma
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan.
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3
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Weyandt N, Aghdam SA, Brown AMV. Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes. Front Microbiol 2022; 13:867392. [PMID: 35547116 PMCID: PMC9084900 DOI: 10.3389/fmicb.2022.867392] [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: 02/01/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.
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Affiliation(s)
- Nicholas Weyandt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Shiva A Aghdam
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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Crane CF, Nemacheck JA, Subramanyam S, Williams CE, Goodwin SB. SLAG: A Program for Seeded Local Assembly of Genes in Complex Genomes. Mol Ecol Resour 2022; 22:1999-2017. [PMID: 34995394 PMCID: PMC9303413 DOI: 10.1111/1755-0998.13580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/11/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022]
Abstract
Although finished genomes have become more common, there is still a need for assemblies of individual genes or chromosomal regions when only unassembled reads are available. slag (Seeded Local Assembly of Genes) fulfils this need by performing iterative local assembly based on cycles of matching‐read retrieval with blast and assembly with cap3, phrap, spades, canu or unicycler. The target sequence can be nucleotide or protein. Read fragmentation allows slag to use phrap or cap3 to assemble long reads at lower coverage (e.g., 5×) than is possible with canu or unicycler. In simple, nonrepetitive genomes, a slag assembly can cover a whole chromosome, but in complex genomes the growth of target‐matching contigs is limited as additional reads are consumed by consensus contigs consisting of repetitive elements. Apart from genomic complexity, contig length and correctness depend on read length and accuracy. With pyrosequencing or Illumina reads, slag‐assembled contigs are accurate enough to allow design of PCR primers, while contigs assembled from Oxford Nanopore or pre‐HiFi Pacific Biosciences long reads are generally only accurate enough to design baiting sequences for further targeted sequencing. In an application with real reads, slag successfully extended sequences for four wheat genes, which were verified by cloning and Sanger sequencing of overlapping amplicons. slag is a robust alternative to atram2 for local assemblies, especially for read sets with less than 20× coverage. slag is freely available at https://github.com/cfcrane/SLAG.
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Affiliation(s)
- Charles F Crane
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Botany & Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA
| | - Jill A Nemacheck
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Subhashree Subramanyam
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Christie E Williams
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA
| | - Stephen B Goodwin
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Botany & Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA
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Schultz CJ, Wu Y, Baumann U. A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina. MYCORRHIZA 2022; 32:45-66. [PMID: 35031894 PMCID: PMC8786786 DOI: 10.1007/s00572-021-01066-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Diversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.
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Affiliation(s)
- Carolyn J Schultz
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
| | - Yue Wu
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ute Baumann
- School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
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6
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Ametrano CG, Lumbsch HT, Di Stefano I, Sangvichien E, Muggia L, Grewe F. Should we hail the Red King? Evolutionary consequences of a mutualistic lifestyle in genomes of lichenized ascomycetes. Ecol Evol 2022; 12:e8471. [PMID: 35136549 PMCID: PMC8809443 DOI: 10.1002/ece3.8471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
The Red Queen dynamic is often brought into play for antagonistic relationships. However, the coevolutionary effects of mutualistic interactions, which predict slower evolution for interacting organisms (Red King), have been investigated to a lesser extent. Lichens are a stable, mutualistic relationship of fungi and cyanobacteria and/or algae, which originated several times independently during the evolution of fungi. Therefore, they represent a suitable system to investigate the coevolutionary effect of mutualism on the fungal genome. We measured substitution rates and selective pressure of about 2000 protein-coding genes (plus the rDNA region) in two different classes of Ascomycota, each consisting of closely related lineages of lichenized and non-lichenized fungi. Our results show that independent lichenized clades are characterized by significantly slower rates for both synonymous and non-synonymous substitutions. We hypothesize that this evolutionary pattern is connected to the lichen life cycle (longer generation time of lichenized fungi) rather than a result of different selection strengths, which is described as the main driver for the Red Kind dynamic. This first empirical evidence of slower evolution in lichens provides an important insight on how biotic cooperative interactions are able to shape the evolution of symbiotic organisms.
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Affiliation(s)
- Claudio G. Ametrano
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - H. Thorsten Lumbsch
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - Isabel Di Stefano
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - Ek Sangvichien
- Department of BiologyFaculty of ScienceRamkhamhaeng UniversityBangkokThailand
| | | | - Felix Grewe
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
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7
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Terraneo TI, Mariappan KG, Forsman Z, Arrigoni R. Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS). Methods Mol Biol 2022; 2498:1-18. [PMID: 35727537 DOI: 10.1007/978-1-0716-2313-8_1] [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] [Indexed: 06/15/2023]
Abstract
Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zac Forsman
- Hawaii Institute of Marine Biology, Kaneohe, HI, USA
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy.
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8
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Deng S, Ma X, Chen Y, Feng H, Zhou D, Wang X, Zhang Y, Zhao M, Zhang J, Daly P, Wei L. LAMP Assay for Distinguishing Fusarium oxysporum and Fusarium commune in Lotus ( Nelumbo nucifera) Rhizomes. PLANT DISEASE 2022; 106:231-246. [PMID: 34494867 DOI: 10.1094/pdis-06-21-1223-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yields of edible rhizome from cultivation of the perennial hydrophyte lotus (Nelumbo nucifera) can be severely reduced by rhizome rot disease caused by Fusarium species. There is a lack of rapid field-applicable methods for detection of these pathogens on lotus plants displaying symptoms of rhizome rot. Fusarium commune (91%) and Fusarium oxysporum (9%) were identified at different frequencies from lotus samples showing symptoms of rhizome rot. Because these two species can cause different severity of disease and their morphology is similar, molecular diagnostic-based methods to detect these two species were developed. Based on the comparison of the mitochondrial genome of the two species, three specific DNA loci targets were found. The designed primer sets for conventional PCR, quantitative PCR, and loop-mediated isothermal amplification (LAMP) precisely distinguished the above two species when isolated from lotus and other plants. The LAMP detection limits were 10 pg/μl and 1 pg/μl of total DNA for F. commune and F. oxysporum, respectively. We also carried out field-mimicked experiments on lotus seedlings and rhizomes (including inoculated samples and field-diseased samples), and the results indicated that the LAMP primer sets and the supporting portable methods are suitable for rapid diagnosis of the lotus disease in the field. The LAMP-based detection method will aid in the rapid identification of whether F. oxysporum or F. commune is infecting lotus plants with symptoms of rhizome rot and can facilitate efficient pesticide use and prevent disease spread through vegetative propagation of Fusarium-infected lotus rhizomes.
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Affiliation(s)
- Sheng Deng
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Xin Ma
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yifan Chen
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu Province, P.R. China
| | - Hui Feng
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Dongmei Zhou
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Xiaoyu Wang
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Yong Zhang
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, U.S.A
| | - Min Zhao
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Jinfeng Zhang
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Paul Daly
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Lihui Wei
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R. China
- School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu Province, P.R. China
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Li L, Zhu T, Song Y, Feng L, Kear PJ, Riseh RS, Sitohy M, Datla R, Ren M. Salicylic acid fights against Fusarium wilt by inhibiting target of rapamycin signaling pathway in Fusarium oxysporum. J Adv Res 2021; 39:1-13. [PMID: 35777900 PMCID: PMC9263656 DOI: 10.1016/j.jare.2021.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/11/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023] Open
Abstract
Isolating and sequencing the genome of F. oxysporum from potato tubers with dry rot symptoms. SA efficiently arrests hyphal growth, sporular production and pathogenicity of F. oxysporum. SA inhibits the activity of FoTORC1 via activating FoSNF1 in F. oxysporum. Transgenic potato plants with interference of FoTOR1 and FoSAH1 genes prevent the occurrence of Fusarium wilt. Providing insights SA into controlling various fungal diseases by targeting the SNF1-TORC1 pathway of pathogens.
Introduction Objectives Methods Results Conclusion
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Affiliation(s)
- Linxuan Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Tingting Zhu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yun Song
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China
| | - Li Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Philip James Kear
- International Potato Center (CIP) China Center Asia Pacific, Beijing 100000, China
| | - Rooallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Mahmoud Sitohy
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Raju Datla
- Global Institute for Food Security in Saskatoon, University of Saskatchewan, Saskatoon S7N0W9, Canada
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu 610000, China; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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10
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G Ribeiro P, Torres Jiménez MF, Andermann T, Antonelli A, Bacon CD, Matos-Maraví P. A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics. Mol Ecol 2021; 30:6021-6035. [PMID: 34674330 PMCID: PMC9298010 DOI: 10.1111/mec.16240] [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: 11/30/2020] [Revised: 09/24/2021] [Accepted: 10/16/2021] [Indexed: 11/28/2022]
Abstract
The increasing availability of short‐read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr, a pipeline that processes short‐read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low‐coverage WGS (<30×) and target sequence capture into a flexible framework, while optimizing de novo contig assembly and loci extraction. Specifically, we test different assembly strategies by contrasting their ability to recover loci from targeted butterfly protein‐coding genes, using four data sets: a WGS data set across different average coverages (10×, 5× and 2×) and a data set for which these loci were enriched prior to sequencing via target sequence capture. Using the resulting de novo contigs, we account for potential errors within contigs and infer phylogenetic trees to evaluate the ability of each assembly strategy to recover species relationships. We demonstrate that choosing multiple sizes of kmer simultaneously for assembly results in the highest yield of extracted loci from de novo assembled contigs, while data sets derived from sequencing read depths as low as 5× recovers the expected species relationships in phylogenetic trees. By making the tested assembly approaches available in the secapr pipeline, we hope to inspire future studies to incorporate complementary data and make an informed choice on the optimal assembly strategy.
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Affiliation(s)
- Pedro G Ribeiro
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - María Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.,Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.,Royal Botanical Gardens Kew, Richmond, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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11
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Brandt SC, Brognaro H, Ali A, Ellinger B, Maibach K, Rühl M, Wrenger C, Schlüter H, Schäfer W, Betzel C, Janssen S, Gand M. Insights into the genome and secretome of Fusarium metavorans DSM105788 by cultivation on agro-residual biomass and synthetic nutrient sources. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:74. [PMID: 33743779 PMCID: PMC7981871 DOI: 10.1186/s13068-021-01927-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The transition to a biobased economy involving the depolymerization and fermentation of renewable agro-industrial sources is a challenge that can only be met by achieving the efficient hydrolysis of biomass to monosaccharides. In nature, lignocellulosic biomass is mainly decomposed by fungi. We recently identified six efficient cellulose degraders by screening fungi from Vietnam. RESULTS We characterized a high-performance cellulase-producing strain, with an activity of 0.06 U/mg, which was identified as a member of the Fusarium solani species complex linkage 6 (Fusarium metavorans), isolated from mangrove wood (FW16.1, deposited as DSM105788). The genome, representing nine potential chromosomes, was sequenced using PacBio and Illumina technology. In-depth secretome analysis using six different synthetic and artificial cellulose substrates and two agro-industrial waste products identified 500 proteins, including 135 enzymes assigned to five different carbohydrate-active enzyme (CAZyme) classes. The F. metavorans enzyme cocktail was tested for saccharification activity on pre-treated sugarcane bagasse, as well as untreated sugarcane bagasse and maize leaves, where it was complemented with the commercial enzyme mixture Accellerase 1500. In the untreated sugarcane bagasse and maize leaves, initial cell wall degradation was observed in the presence of at least 196 µg/mL of the in-house cocktail. Increasing the dose to 336 µg/mL facilitated the saccharification of untreated sugarcane biomass, but had no further effect on the pre-treated biomass. CONCLUSION Our results show that F. metavorans DSM105788 is a promising alternative pre-treatment for the degradation of agro-industrial lignocellulosic materials. The enzyme cocktail promotes the debranching of biopolymers surrounding the cellulose fibers and releases reduced sugars without process disadvantages or loss of carbohydrates.
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Affiliation(s)
- Sophie C Brandt
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Hévila Brognaro
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, CEP, 05508-000, Brazil
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Arslan Ali
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi, 75270, Pakistan
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, Campus Research. Martinistr. 52, N27, 20246, Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Department ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Katharina Maibach
- Department Biology and Chemistry, Algorithmic Bioinformatics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392, Gießen, Germany
| | - Martin Rühl
- Department Biology and Chemistry, Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Gießen, Germany
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, CEP, 05508-000, Brazil
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, Campus Research. Martinistr. 52, N27, 20246, Hamburg, Germany
| | - Wilhelm Schäfer
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Stefan Janssen
- Department Biology and Chemistry, Algorithmic Bioinformatics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392, Gießen, Germany
| | - Martin Gand
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
- Department Biology and Chemistry, Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Gießen, Germany.
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12
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Li N, Bai JQ, Gao S, Yang L, Li J, Du SB, Wang XP. The complete molecular sequence of chloroplast genome of Lablab purpureus (L.) Sweet. Mitochondrial DNA B Resour 2021; 6:758-759. [PMID: 33763570 PMCID: PMC7954507 DOI: 10.1080/23802359.2021.1878958] [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: 10/26/2022] Open
Abstract
The complete molecular sequence of chloroplast genome of Lablab purpureus (L.) Sweet was firstly assembled and characterized using Illumina sequencing technology. It is 151916 bp in length, with a GC content of 35.4%, and has a typical quadrant structure, including a large single-copy region (LSC), a pair of inverted repeat regions (IRs) and a small single-copy region (SSC), the sequence length is 81132, 53244, 17540 bp, respectively. There are 131 genes in the L. purpureus chloroplast genome, including 84 encoding protein genes, 8 rRNA genes, and 38 tRNA genes. Phylogenetic analysis showed that L. purpureus clustered into a large evolutionary clade with three Vigna species.
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Affiliation(s)
- Na Li
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Ji-Qing Bai
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China.,Shaanxi Quality Monitoring and Technology Service Center for Chinese Materia Medica Raw Materials, Xianyang, PR China
| | - Su Gao
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Lei Yang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Jing Li
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Shao-Bing Du
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Xiao-Ping Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
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13
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Neumann P, Oliveira L, Čížková J, Jang TS, Klemme S, Novák P, Stelmach K, Koblížková A, Doležel J, Macas J. Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genus Cuscuta. THE NEW PHYTOLOGIST 2021; 229:2365-2377. [PMID: 33090498 DOI: 10.1111/nph.17003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/01/2020] [Indexed: 05/06/2023]
Abstract
The parasitic genus Cuscuta (Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes. We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition. A remarkable 102-fold variation in genome sizes (342-34 734 Mbp/1C) was detected for monocentric Cuscuta species, while genomes of holocentric species were of moderate sizes (533-1545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of LTR-retrotransposons and satellite DNA. The transition to holocentric chromosomes in the subgenus Cuscuta was associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, basic chromosome number of holocentric species (x = 7) was smaller than in monocentrics (x = 15 or 16). We demonstrated that the transition to holocentricity in Cuscuta was accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.
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Affiliation(s)
- Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Ludmila Oliveira
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-779 00, Czech Republic
| | - Tae-Soo Jang
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sonja Klemme
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Katarzyna Stelmach
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
- Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, 29 Listopada 54, Krakow, 31-425, Poland
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-779 00, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
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14
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Ávila Robledillo L, Neumann P, Koblížková A, Novák P, Vrbová I, Macas J. Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae. Mol Biol Evol 2020; 37:2341-2356. [PMID: 32259249 PMCID: PMC7403623 DOI: 10.1093/molbev/msaa090] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Satellite repeats are major sequence constituents of centromeres in many plant and animal species. Within a species, a single family of satellite sequences typically occupies centromeres of all chromosomes and is absent from other parts of the genome. Due to their common origin, sequence similarities exist among the centromere-specific satellites in related species. Here, we report a remarkably different pattern of centromere evolution in the plant tribe Fabeae, which includes genera Pisum, Lathyrus, Vicia, and Lens. By immunoprecipitation of centromeric chromatin with CENH3 antibodies, we identified and characterized a large and diverse set of 64 families of centromeric satellites in 14 species. These families differed in their nucleotide sequence, monomer length (33-2,979 bp), and abundance in individual species. Most families were species-specific, and most species possessed multiple (2-12) satellites in their centromeres. Some of the repeats that were shared by several species exhibited promiscuous patterns of centromere association, being located within CENH3 chromatin in some species, but apart from the centromeres in others. Moreover, FISH experiments revealed that the same family could assume centromeric and noncentromeric positions even within a single species. Taken together, these findings suggest that Fabeae centromeres are not shaped by the coevolution of a single centromeric satellite with its interacting CENH3 proteins, as proposed by the centromere drive model. This conclusion is also supported by the absence of pervasive adaptive evolution of CENH3 sequences retrieved from Fabeae species.
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Affiliation(s)
- Laura Ávila Robledillo
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Iva Vrbová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
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15
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Brankovics B, van Diepeningen AD, de Hoog GS, van der Lee TAJ, Waalwijk C. Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics. Front Microbiol 2020; 11:1092. [PMID: 32582074 PMCID: PMC7285627 DOI: 10.3389/fmicb.2020.01092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/30/2020] [Indexed: 11/18/2022] Open
Abstract
The Fusarium fujikuroi species complex (FFSC) and F. oxysporum species complex (FOSC) are two related groups of plant pathogens causing a wide diversity of diseases in agricultural crops world wide. The aims of this study are (1) to clarify the phylogeny of the FFSC, (2) to identify potential deviation from tree-like evolution, (3) to explore the value of using mitogenomes for these kinds of analyses, and (4) to better understand mitogenome evolution. In total, we have sequenced 24 species from the FFSC and a representative set of recently analyzed FOSC strains was chosen, while F. redolens was used as outgroup for the two species complexes. A species tree was constructed based on the concatenated alignment of seven nuclear genes and the mitogenome, which was contrasted to individual gene trees to identify potential conflicts. These comparisons indicated conflicts especially within the previously described African clade of the FFSC. Furthermore, the analysis of the mitogenomes revealed the presence of a variant of the large variable (LV) region in FFSC which was previously only reported for FOSC. The distribution of this variant and the results of sequence comparisons indicate horizontal genetic transfer between members of the two species complexes, most probably through introgression. In addition, a duplication of atp9 was found inside an intron of cob, which suggests that even highly conserved mitochondrial genes can have paralogs. Paralogization in turn may lead to inaccurate single gene phylogenies. In conclusion, mitochondrial genomes provide a robust basis for phylogeny. Comparative phylogenetic analysis indicated that gene flow among and between members of FFSC and FOSC has played an important role in the evolutionary history of these two groups. Since mitogenomes show greater levels of conservation and synteny than nuclear regions, they are more likely to be compatible for recombination than nuclear regions. Therefore, mitogenomes can be used as indicators to detect interspecies gene flow.
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Affiliation(s)
- Balázs Brankovics
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Anne D van Diepeningen
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - G Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, KNAW, Utrecht, Netherlands.,Center of Expertise in Mycology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Theo A J van der Lee
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Cees Waalwijk
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
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16
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Yang M, Zhang H, van der Lee TAJ, Waalwijk C, van Diepeningen AD, Feng J, Brankovics B, Chen W. Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum. Front Microbiol 2020; 11:839. [PMID: 32431686 PMCID: PMC7214670 DOI: 10.3389/fmicb.2020.00839] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/07/2020] [Indexed: 11/26/2022] Open
Abstract
Fusarium asiaticum is one of the pivotal members of the Fusarium graminearum species complex (FGSC) causing Fusarium head blight (FHB) on wheat, barley and rice in large parts of Asia. Besides resulting in yield losses, FHB also causes the accumulation of mycotoxins such as nivalenol (NIV) and deoxynivalenol (DON). The aim of this study was to conduct population studies on F. asiaticum from Southern China through mitochondrial genome analyses. All strains were isolated from wheat or rice from several geographic areas in seven provinces in Southern China. Based on geographic location and host, 210 isolates were selected for next generation sequencing, and their mitogenomes were assembled by GRAbB and annotated to explore the mitochondrial genome variability of F. asiaticum. The F. asiaticum mitogenome proves extremely conserved and variation is mainly caused by absence/presence of introns harboring homing endonuclease genes. These variations could be utilized to develop molecular markers for track and trace of migrations within and between populations. This study illustrates how mitochondrial introns can be used as markers for population genetic analysis. SNP analysis demonstrate the occurrence of mitochondrial recombination in F. asiaticum as was previously found for F. oxysporum and implied for F. graminearum. Furthermore, varying degrees of genetic diversity and recombination showed a high association with different geographic regions as well as with cropping systems. The mitogenome of F. graminearum showed a much higher SNP diversity while the interspecies intron variation showed no evidence of gene flow between the two closely related and sexual compatible species.
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Affiliation(s)
- Meixin Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China.,Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | | | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Balázs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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17
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Abstract
Endoplasmic reticulum-associated degradation (ERAD) is an essential process that removes misfolded proteins from the ER, preventing cellular dysfunction and disease. While most of the key components of ERAD are known, their specific localization remains a mystery. This study uses in situ cryo-electron tomography to directly visualize the ERAD machinery within the native cellular environment. Proteasomes and Cdc48, the complexes that extract and degrade ER proteins, cluster together in non–membrane-bound cytosolic microcompartments that contact ribosome-free patches on the ER membrane. This discrete molecular organization may facilitate efficient ERAD. Structural analysis reveals that proteasomes directly engage ER-localized substrates, providing evidence for a noncanonical “direct ERAD” pathway. In addition, live-cell fluorescence microscopy suggests that these ER-associated proteasome clusters form by liquid–liquid phase separation. To promote the biochemical reactions of life, cells can compartmentalize molecular interaction partners together within separated non–membrane-bound regions. It is unknown whether this strategy is used to facilitate protein degradation at specific locations within the cell. Leveraging in situ cryo-electron tomography to image the native molecular landscape of the unicellular alga Chlamydomonas reinhardtii, we discovered that the cytosolic protein degradation machinery is concentrated within ∼200-nm foci that contact specialized patches of endoplasmic reticulum (ER) membrane away from the ER–Golgi interface. These non–membrane-bound microcompartments exclude ribosomes and consist of a core of densely clustered 26S proteasomes surrounded by a loose cloud of Cdc48. Active proteasomes in the microcompartments directly engage with putative substrate at the ER membrane, a function canonically assigned to Cdc48. Live-cell fluorescence microscopy revealed that the proteasome clusters are dynamic, with frequent assembly and fusion events. We propose that the microcompartments perform ER-associated degradation, colocalizing the degradation machinery at specific ER hot spots to enable efficient protein quality control.
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18
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Dalsass M, Bodini M, Lambert C, Mortier MC, Romanelli M, Medini D, Muzzi A, Brozzi A. STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data. BMC Bioinformatics 2019; 20:347. [PMID: 31757201 PMCID: PMC6873635 DOI: 10.1186/s12859-019-2887-1] [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: 04/12/2019] [Accepted: 05/08/2019] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set.
Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query.
Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets.
Results
Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%).
Conclusions
STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.
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19
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van de Vossenberg BTLH, Warbroek T, Ingerson-Mahar J, Waalwijk C, van der Gouw LP, Eichinger B, Loomans AJM. Tracking outbreak populations of the pepper weevil Anthonomus eugenii (Coleoptera; Curculionidae) using complete mitochondrial genomes. PLoS One 2019; 14:e0221182. [PMID: 31412079 PMCID: PMC6693850 DOI: 10.1371/journal.pone.0221182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/31/2019] [Indexed: 11/19/2022] Open
Abstract
The pepper weevil, Anthonomus eugenii, is a major pest on Capsicum species. Apart from natural spread, there is a risk of spread via international pepper trade. In the Netherlands, a pepper weevil outbreak occurred in 2012 and affected six greenhouses producing different sweet pepper varieties. The following year, a pepper weevil outbreak occurred in Italy. To trace the origin of the Dutch outbreak and to establish if the Dutch and Italian outbreaks were linked, we determined the mitogenomes of A. eugenii specimens collected at outbreak locations, and compared these with specimens from the native area, and other areas where the pest was introduced either by natural dispersal or via trade. The circular 17,257 bp A. eugenii mitogenome comprises thirteen mitochondrial genes typically found in insect species. Intra-species variation of these mitochondrial genes revealed four main mitochondrial lineages encompassing 41 haplotypes. The highest diversity was observed for specimens from its presumed native area (i.e. Mexico). The Dutch outbreak specimens represented three highly similar haplotypes, suggesting a single introduction of the pest. The major Dutch haplotype was also found in two specimens from New Jersey. As the Netherlands does not have pepper trade with New Jersey, it is likely that the specimens sampled in New Jersey and those sampled in the Netherlands originate from a shared source that was not included in this study. In addition, our analysis shows that the Italian and Dutch outbreaks were not linked. The mitochondrial genome is a useful tool to trace outbreak populations and the methodology presented in this paper could prove valuable for other invasive pest species, such as the African fruit moth Thaumatotibia leucotreta and emerald ash borer Agrilus planipennis.
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Affiliation(s)
- Bart T. L. H. van de Vossenberg
- National Reference Centre of plant health, Dutch National Plant Protection Organization, Wageningen, Gelderland, the Netherlands
- * E-mail:
| | - Tim Warbroek
- National Reference Centre of plant health, Dutch National Plant Protection Organization, Wageningen, Gelderland, the Netherlands
| | - Joseph Ingerson-Mahar
- Department of Entomology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Cees Waalwijk
- Biointeractions and Plant health, Wageningen University & Research, Wageningen, Gelderland, the Netherlands
| | - Lucas P. van der Gouw
- National Reference Centre of plant health, Dutch National Plant Protection Organization, Wageningen, Gelderland, the Netherlands
| | - Bernadette Eichinger
- Department of Entomology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Antoon J. M. Loomans
- National Reference Centre of plant health, Dutch National Plant Protection Organization, Wageningen, Gelderland, the Netherlands
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20
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Waters NR, Abram F, Brennan F, Holmes A, Pritchard L. riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions. Nucleic Acids Res 2019; 46:e68. [PMID: 29608703 PMCID: PMC6009695 DOI: 10.1093/nar/gky212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/12/2018] [Indexed: 11/12/2022] Open
Abstract
The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome’s rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome.
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Affiliation(s)
- Nicholas R Waters
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland.,Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Florence Abram
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland
| | - Fiona Brennan
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland.,Soil and Environmental Microbiology, Environmental Research Centre, Teagasc, Johnstown Castle, Wexford, Y35 TC97, Ireland
| | - Ashleigh Holmes
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Leighton Pritchard
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
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21
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Hahn C. Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence. Methods Mol Biol 2019; 1963:195-213. [PMID: 30875055 DOI: 10.1007/978-1-4939-9176-1_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent methodological advances have transformed the field of ancient DNA (aDNA). Basic bioinformatics skills are becoming essential requirements to process and analyze the sheer amounts of data generated by current aDNA studies and in biomedical research in general. This chapter is intended as a practical guide to the assembly of ancient mitochondrial genomes, directly from genomic DNA-derived next-generation sequencing (NGS) data, specifically in the absence of closely related reference genomes. In a hands-on tutorial suitable for readers with little to no prior bioinformatics experience, we reconstruct the mitochondrial genome of a woolly mammoth deposited ~45,000 years ago. We introduce key software tools and outline general strategies for mitogenome assembly, including the critical quality assessment of assembly results without a reference genome.
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Affiliation(s)
- Christoph Hahn
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
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22
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Brankovics B, Kulik T, Sawicki J, Bilska K, Zhang H, de Hoog GS, van der Lee TA, Waalwijk C, van Diepeningen AD. First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes. PeerJ 2018; 6:e5963. [PMID: 30588394 PMCID: PMC6304159 DOI: 10.7717/peerj.5963] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/16/2018] [Indexed: 01/13/2023] Open
Abstract
There is a gradual shift from representing a species' genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The "intronless" mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the "host" gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.
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Affiliation(s)
- Balázs Brankovics
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, P.R. China
| | - G Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Theo Aj van der Lee
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Anne D van Diepeningen
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
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23
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van de Vossenberg BTLH, Brankovics B, Nguyen HDT, van Gent-Pelzer MPE, Smith D, Dadej K, Przetakiewicz J, Kreuze JF, Boerma M, van Leeuwen GCM, André Lévesque C, van der Lee TAJ. The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen. BMC Evol Biol 2018; 18:136. [PMID: 30200892 PMCID: PMC6131824 DOI: 10.1186/s12862-018-1246-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g. Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease. S. endobioticum has an obligate biotrophic lifestyle and isolates can be further characterized as pathotypes based on their virulence on a differential set of potato cultivars. Quarantine measures have been implemented globally to control the disease and prevent its spread. We used a comparative approach using chytrid mitogenomes to determine taxonomical relationships and to gain insights into the evolution and recent history of introductions of this plant pathogen. RESULTS We assembled and annotated the complete mitochondrial genome of 30 S. endobioticum isolates and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum is linear with terminal inverted repeats which was validated by tailing and PCR amplifying the telomeric ends. Surprisingly, no conservation in organisation and orientation of mitochondrial genes was observed among the Chytridiomycota except for S. endobioticum and its sister species Synchytrium microbalum. However, the mitochondrial genome of S. microbalum is circular and comprises only a third of the 72.9 Kbp found for S. endobioticum suggesting recent linearization and expansion. Four mitochondrial lineages were identified in the S. endobioticum mitochondrial genomes. Several pathotypes occur in different lineages, suggesting that these have emerged independently. In addition, variations for polymorphic sites in the mitochondrial genome of individual isolates were observed demonstrating that S. endobioticum isolates represent a community of different genotypes. Such communities were shown to be complex and stable over time, but we also demonstrate that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype associated with increased virulence. CONCLUSIONS Mitochondrial genomic variation shows that S. endobioticum has been introduced into Europe multiple times, that several pathotypes emerged multiple times, and that isolates represent communities of different genotypes. Our study represents the most comprehensive dataset of chytrid mitogenomes, which provides new insights into the extraordinary dynamics and evolution of mitochondrial genomes involving linearization, expansion and reshuffling.
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Affiliation(s)
- Bart T. L. H. van de Vossenberg
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 Utrecht, CT Netherlands
| | - Hai D. T. Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P. E. van Gent-Pelzer
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
| | - Donna Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - Kasia Dadej
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Jarosław Przetakiewicz
- Plant Breeding and Acclimatization Institute, National Research Institute, 05-870 Blonie, Radzikow, Warsaw, Poland
| | - Jan F. Kreuze
- International Potato Centre, Avenida La Molina, 1895 Lima, Peru
| | - Margriet Boerma
- Hilbrands Laboratorium BV, Kampsweg 27, 9418 PD Wijster, Wijster, The Netherlands
| | - Gerard C. M. van Leeuwen
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - C. André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A. J. van der Lee
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
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24
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Campbell MA, Sado T, Shinzato C, Koyanagi R, Okamoto M, Miya M. Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships. Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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25
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Kucuk E, Chu J, Vandervalk BP, Hammond SA, Warren RL, Birol I. Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics 2018; 33:1782-1788. [PMID: 28186221 PMCID: PMC5572715 DOI: 10.1093/bioinformatics/btx078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for gene-centric assemblies, whose resulting sequence can be readily utilized for more focused biological research. Here we describe Kollector, an alignment-free targeted assembly pipeline that uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector robustly reconstructs introns and novel sequences within these loci, and scales well to large genomes—properties that makes it especially useful for researchers working on non-model eukaryotic organisms. Results We demonstrate the performance of Kollector for assembling complete or near-complete Caenorhabditis elegans and Homo sapiens gene loci from their respective, input transcripts. In a time- and memory-efficient manner, the Kollector pipeline successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C.elegans and H.sapiens transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads. We also show that Kollector outperforms both established and recently released targeted assembly tools. Finally, we demonstrate three use cases for Kollector, including comparative and cancer genomics applications. Availability and Implementation Kollector is implemented as a bash script, and is available at https://github.com/bcgsc/kollector Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erdi Kucuk
- University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Justin Chu
- University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Benjamin P Vandervalk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Inanc Birol
- University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.,Simon Fraser University, Burnaby, BC, Canada
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26
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Abstract
Rhinocladiella mackenziei accounts for the majority of fungal brain infections in the Middle East, and is restricted to the arid climate zone between Saudi Arabia and Pakistan. Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper, we describe the whole-genome resequencing of two R. mackenziei strains from patients in Saudi Arabia and Qatar. We assessed intraspecies variation and genetic signatures to uncover the genomic basis of the pathogenesis, and potential niche adaptations. We found that the duplicated genes (paralogs) are more susceptible to accumulating significant mutations. Comparative genomics with other filamentous ascomycetes revealed a diverse arsenal of genes likely engaged in pathogenicity, such as the degradation of aromatic compounds and iron acquisition. In addition, intracellular accumulation of trehalose and choline suggests possible adaptations to the conditions of an arid climate region. Specifically, protein family contractions were found, including short-chain dehydrogenase/reductase SDR, the cytochrome P450 (CYP) (E-class), and the G-protein β WD-40 repeat. Gene composition and metabolic potential indicate extremotolerance and hydrocarbon assimilation, suggesting a possible environmental habitat of oil-polluted desert soil.
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27
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Zhan P, Dukik K, Li D, Sun J, Stielow JB, Gerrits van den Ende B, Brankovics B, Menken SBJ, Mei H, Bao W, Lv G, Liu W, de Hoog GS. Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum. Stud Mycol 2018; 89:153-175. [PMID: 29910521 PMCID: PMC6002342 DOI: 10.1016/j.simyco.2018.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.
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Affiliation(s)
- P Zhan
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.,Dermatology Hospital of Jiangxi Provinces, Jiangxi Dermatology Institute, Nanchang, China.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - K Dukik
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - D Li
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.,Georgetown University Medical Center, Department of Microbiology and Immunology, Washington, DC, USA
| | - J Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - J B Stielow
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Thermo Fisher Scientific, Landsmeer, The Netherlands.,Center of Expertise in Mycology of Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - B Brankovics
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - S B J Menken
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - H Mei
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - W Bao
- Nanjing General Hospital of Nanjing Command, Nanjing, China
| | - G Lv
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - W Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - G S de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,Thermo Fisher Scientific, Landsmeer, The Netherlands.,Center of Expertise in Mycology of Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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28
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Campbell MA, Tapper BA, Simpson WR, Johnson RD, Mace W, Ram A, Lukito Y, Dupont PY, Johnson LJ, Scott DB, Ganley ARD, Cox MP. Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy. Mycologia 2018; 109:715-729. [PMID: 29370579 DOI: 10.1080/00275514.2017.1406174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Endophytes of the genus Epichloë (Clavicipitaceae, Ascomycota) frequently occur within cool-season grasses and form interactions with their hosts that range from mutualistic to antagonistic. Many Epichloë species have arisen via interspecific hybridization, resulting in species with two or three subgenomes that retain all or nearly all of their original parental genomes, a process termed allopolyploidization. Here, we characterize Epichloë hybrida, sp. nov., a mutualistic species that has increasingly become a model system for investigating allopolyploidy in fungi. The Epichloë species so far identified as the closest known relatives of the two progenitors of E. hybrida are E. festucae var. lolii and E. typhina. We confirm that the nuclear genome of E. hybrida contains two homeologs of most protein-coding genes from E. festucae and E. typhina, with genome-wide gene expression analysis indicating a slight bias in overall gene expression from the E. typhina subgenome. Mitochondrial DNA is detectable only from E. festucae, whereas ribosomal DNA is detectable only from E. typhina. Inheriting ribosomal DNA from just one parent might be expected to preferentially favor interactions with ribosomal proteins from the same parent, but we find that ribosomal protein genes from both parental subgenomes are nearly all expressed equally in E. hybrida. Finally, we provide a comprehensive set of resources for this model system that are intended to facilitate further study of fungal hybridization by other researchers.
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Affiliation(s)
- Matthew A Campbell
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Brian A Tapper
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Wayne R Simpson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Richard D Johnson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Wade Mace
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Arvina Ram
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Yonathan Lukito
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Pierre-Yves Dupont
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Linda J Johnson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - D Barry Scott
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Austen R D Ganley
- c School of Biological Sciences, University of Auckland , Private Bag 92019, Auckland 1142 , New Zealand
| | - Murray P Cox
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
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29
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Shi-Kunne X, Faino L, van den Berg GCM, Thomma BPHJ, Seidl MF. Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ Microbiol 2018; 20:1362-1373. [PMID: 29282842 DOI: 10.1111/1462-2920.14037] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 01/09/2023]
Abstract
The fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plant pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor. Frequent occurrence of chromosomal rearrangement and gene family loss was identified. In addition to ∼11 000 genes that are shared at least between two species, only 200-600 species-specific genes occur. Intriguingly, these species-specific genes show different features than the shared genes.
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Affiliation(s)
- Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
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30
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Zeng L, Liu C, Lin R, Kang X, Xie B, Xiong X. Complete mitogenome of the high ethanol production fungus Fusarium oxysporum Mh2-2. Mitochondrial DNA B Resour 2017; 2:814-815. [PMID: 33473993 PMCID: PMC7799908 DOI: 10.1080/23802359.2017.1398601] [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] [Indexed: 11/18/2022] Open
Abstract
Fusarium spp. are significantly important plant pathogens, and some of them are ethanol-producing strains. During infection and/or ethanol production, Fusarium requires a plenty of energy that is mainly provided by mitochondria. Here we report the first mitogenome from a selected Fusarium oxysporum strain mh2-2 that produces ethanol from glucose and xylose. The size of this mitogenome, 46 kb, is different from the size of any reported Fusarium mitogenome. Our results provide insight into the functions and evolution of mitochondrial genes and genomes.
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Affiliation(s)
- Lu Zeng
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, Hunan, China
| | - Chichuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xincong Kang
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, Hunan, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingyao Xiong
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, Hunan, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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31
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Brankovics B, van Dam P, Rep M, de Hoog GS, J. van der Lee TA, Waalwijk C, van Diepeningen AD. Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex. BMC Genomics 2017; 18:735. [PMID: 28923029 PMCID: PMC5604515 DOI: 10.1186/s12864-017-4116-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 09/05/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. RESULTS A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. CONCLUSIONS The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.
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Affiliation(s)
- Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584CT The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - Peter van Dam
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - Martijn Rep
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584CT The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - Theo A. J. van der Lee
- Wageningen University and Research Centre, Droevendaalsesteeg 4, Wageningen, 6708 PB The Netherlands
| | - Cees Waalwijk
- Wageningen University and Research Centre, Droevendaalsesteeg 4, Wageningen, 6708 PB The Netherlands
| | - Anne D. van Diepeningen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584CT The Netherlands
- Wageningen University and Research Centre, Droevendaalsesteeg 4, Wageningen, 6708 PB The Netherlands
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van Dam P, Fokkens L, Ayukawa Y, van der Gragt M, Ter Horst A, Brankovics B, Houterman PM, Arie T, Rep M. A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species. Sci Rep 2017; 7:9042. [PMID: 28831051 PMCID: PMC5567276 DOI: 10.1038/s41598-017-07995-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
The genome of Fusarium oxysporum (Fo) consists of a set of eleven 'core' chromosomes, shared by most strains and responsible for housekeeping, and one or several accessory chromosomes. We sequenced a strain of Fo f.sp. radicis-cucumerinum (Forc) using PacBio SMRT sequencing. All but one of the core chromosomes were assembled into single contigs, and a chromosome that shows all the hallmarks of a pathogenicity chromosome comprised two contigs. A central part of this chromosome contains all identified candidate effector genes, including homologs of SIX6, SIX9, SIX11 and SIX 13. We show that SIX6 contributes to virulence of Forc. Through horizontal chromosome transfer (HCT) to a non-pathogenic strain, we also show that the accessory chromosome containing the SIX gene homologs is indeed a pathogenicity chromosome for cucurbit infection. Conversely, complete loss of virulence was observed in Forc016 strains that lost this chromosome. We conclude that also a non-wilt-inducing Fo pathogen relies on effector proteins for successful infection and that the Forc pathogenicity chromosome contains all the information necessary for causing root rot of cucurbits. Three out of nine HCT strains investigated have undergone large-scale chromosome alterations, reflecting the remarkable plasticity of Fo genomes.
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Affiliation(s)
- Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Yu Ayukawa
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Michelle van der Gragt
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Anneliek Ter Horst
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Petra M Houterman
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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Huang L, Gao W, Giosa D, Criseo G, Zhang J, He T, Huang X, Sun J, Sun Y, Huang J, Zhang Y, Brankovics B, Scordino F, D'Alessandro E, van Diepeningen A, de Hoog S, Huang H, Romeo O. Whole-Genome Sequencing and In Silico Analysis of Two Strains of Sporothrix globosa. Genome Biol Evol 2016; 8:3292-3296. [PMID: 27635048 PMCID: PMC5203775 DOI: 10.1093/gbe/evw230] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sporothrix globosa is a thermo-dimorphic fungus belonging to a pathogenic clade that also includes Sporothrix schenckii, which causes human and animal sporotrichosis. Here, we present the first genome assemblies of two S. globosa strains providing data for future comparative genomic studies in pathogenic Sporothrix species.
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Affiliation(s)
- Lilin Huang
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenchao Gao
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Domenico Giosa
- IRCCS Centro Neurolesi "Bonino-Pulejo", SS113, Messina, Italy
| | - Giuseppe Criseo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Jing Zhang
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.,Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangdong Province, China
| | - Tailong He
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaowen Huang
- Department of Dermatology, General Hospital of Guangzhou Military Command of PLA, Guangzhou, China
| | - Jiufeng Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yao Sun
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiamin Huang
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yunqing Zhang
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Fabio Scordino
- IRCCS Centro Neurolesi "Bonino-Pulejo", SS113, Messina, Italy
| | - Enrico D'Alessandro
- Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy
| | | | - Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Huaiqiu Huang
- Department of Dermatology and Venereology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Orazio Romeo
- IRCCS Centro Neurolesi "Bonino-Pulejo", SS113, Messina, Italy .,Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
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34
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Draft Genome Sequence of the Dimorphic Fungus Sporothrix pallida, a Nonpathogenic Species Belonging to Sporothrix, a Genus Containing Agents of Human and Feline Sporotrichosis. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00184-16. [PMID: 27034494 PMCID: PMC4816622 DOI: 10.1128/genomea.00184-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sporothrix pallida is considered to be a mostly avirulent environmental fungus, phylogenetically closely related to the well-known pathogen Sporothrix schenckii. Here, we present the first assembly of its genome, which provides a valuable resource for future comparative genomic studies between nonpathogenic and pathogenic Sporothrix spp.
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