1
|
De Vos L, van der Nest MA, Santana QC, van Wyk S, Leeuwendaal KS, Wingfield BD, Steenkamp ET. Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum. Pathogens 2024; 13:70. [PMID: 38251377 PMCID: PMC10819268 DOI: 10.3390/pathogens13010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome's distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.
Collapse
Affiliation(s)
- Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Magriet A. van der Nest
- Hans Merensky Chair in Avocado Research, Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute FABI, University of Pretoria, Pretoria 0002, South Africa;
| | - Quentin C. Santana
- Biotechnology Platform, Agricultural Research Council, 100 Old Soutpan Road, Onderstepoort, Pretoria 0010, South Africa;
| | - Stephanie van Wyk
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South-East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Cape Town 7925, South Africa;
| | - Kyle S. Leeuwendaal
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| |
Collapse
|
2
|
Steins L, Guerreiro MA, Duhamel M, Liu F, Wang QM, Boekhout T, Begerow D. Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus Pseudozyma (Ustilaginales). BMC Genomics 2023; 24:321. [PMID: 37312063 DOI: 10.1186/s12864-023-09387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND The Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genus Pseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilaginales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi. RESULTS In this study, we sequenced genomes of five Pseudozyma species together with six parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate potentially functional mating and meiosis genes that are conserved throughout the whole group. CONCLUSION Our data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.
Collapse
Affiliation(s)
- Lena Steins
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
| | - Marco Alexandre Guerreiro
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
- Environmental Genomics, Germany and Max Planck Institute for Evolutionary Biology, Botanical Institute, Christian-Albrechts University of Kiel, Plön, Germany
| | - Marine Duhamel
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Gif-Sur-Yvette, Paris, France
| | - Fei Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Teun Boekhout
- College of Science, King Saud University, Riyadh, Saudi Arabia
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany.
- Organismic Botany and Mycology, University of Hamburg, IPM, Hamburg, Germany.
| |
Collapse
|
3
|
Yang J, Liu L, Yang L, Liu R, Gao C, Hu W, Yan Q, Yang Z, Fan L. High-quality genome assembly of Verticillium dahliae VD991 allows for screening and validation of pathogenic genes. Front Microbiol 2023; 14:1177078. [PMID: 37362919 PMCID: PMC10289290 DOI: 10.3389/fmicb.2023.1177078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Verticillium dahliae (V. dahliae) is a notorious soil-borne pathogen causing Verticillium wilt in more than 400 dicotyledonous plants, including a wide range of economically important crops, such as cotton, tomato, lettuce, potato, and romaine lettuce, which can result in extensive economic losses. In the last decade, several studies have been conducted on the physiological and molecular mechanisms of plant resistance to V. dahliae. However, the lack of a complete genome sequence with a high-quality assembly and complete genomic annotations for V. dahliae has limited these studies. In this study, we produced a full genomic assembly for V. dahliae VD991 using Nanopore sequencing technology, consisting of 35.77 Mb across eight pseudochromosomes and with a GC content of 53.41%. Analysis of the genome completeness assessment (BUSCO alignment: 98.62%; Illumina reads alignment: 99.17%) indicated that our efforts resulted in a nearly complete and high-quality genomic assembly. We selected 25 species closely related to V. dahliae for evolutionary analysis, confirming the evolutionary relationship between V. dahliae and related species, and the identification of a possible whole genome duplication event in V. dahliae. The interaction between cotton and V. dahliae was investigated by transcriptome sequencing resulting in the identification of many genes and pathways associated with cotton disease resistance and V. dahliae pathogenesis. These results will provide new insights into the pathogenic mechanisms of V. dahliae and contribute to the cultivation of cotton varieties resistant to Verticillium wilt.
Collapse
Affiliation(s)
- Jiaxiang Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lan Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Renju Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Chenxu Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wei Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Qingdi Yan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liqiang Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| |
Collapse
|