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Hao Z, Zhang Z, Jiang J, Pan L, Zhang J, Cui X, Li Y, Li J, Luo L. Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination. BMC PLANT BIOLOGY 2024; 24:645. [PMID: 38972991 PMCID: PMC11229266 DOI: 10.1186/s12870-024-05319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/21/2024] [Indexed: 07/09/2024]
Abstract
Melia azedarach is a species of enormous value of pharmaceutical industries. Although the chloroplast genome of M. azedarach has been explored, the information of mitochondrial genome (Mt genome) remains surprisingly limited. In this study, we used a hybrid assembly strategy of BGI short-reads and Nanopore long-reads to assemble the Mt genome of M. azedarach. The Mt genome of M. azedarach is characterized by two circular chromosomes with 350,142 bp and 290,387 bp in length, respectively, which encodes 35 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A pair of direct repeats (R1 and R2) were associated with genome recombination, resulting in two conformations based on the Sanger sequencing and Oxford Nanopore sequencing. Comparative analysis identified 19 homologous fragments between Mt and chloroplast genome, with the longest fragment of 12,142 bp. The phylogenetic analysis based on PCGs were consist with the latest classification of the Angiosperm Phylogeny Group. Notably, a total of 356 potential RNA editing sites were predicted based on 35 PCGs, and the editing events lead to the formation of the stop codon in the rps10 gene and the start codons in the nad4L and atp9 genes, which were verified by PCR amplification and Sanger sequencing. Taken together, the exploration of M. azedarach gap-free Mt genome provides a new insight into the evolution research and complex mitogenome architecture.
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Affiliation(s)
- Zhigang Hao
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, 572025, China
| | - Zhiping Zhang
- Department of Pesticide Science, College of Plant Protection, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Juan Jiang
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
| | - Lei Pan
- CAIQ Center for Biosafety in Sanya, Sanya, Hainan, 572000, China
| | - Jinan Zhang
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Xiufen Cui
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Yingbin Li
- Department of Pesticide Science, College of Plant Protection, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jianqiang Li
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China.
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China.
| | - Laixin Luo
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China.
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, MOA Key Lab of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China.
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Moonjely S, Ebert M, Paton-Glassbrook D, Noel ZA, Roze L, Shay R, Watkins T, Trail F. Update on the state of research to manage Fusarium head blight. Fungal Genet Biol 2023; 169:103829. [PMID: 37666446 DOI: 10.1016/j.fgb.2023.103829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
Fusarium head blight (FHB) is one of the most devastating diseases of cereal crops, causing severe reduction in yield and quality of grain worldwide. In the United States, the major causal agent of FHB is the mycotoxigenic fungus, Fusarium graminearum. The contamination of grain with mycotoxins, including deoxynivalenol and zearalenone, is a particularly serious concern due to its impact on the health of humans and livestock. For the past few decades, multidisciplinary studies have been conducted on management strategies designed to reduce the losses caused by FHB. However, effective management is still challenging due to the emergence of fungicide-tolerant strains of F. graminearum and the lack of highly resistant wheat and barley cultivars. This review presents multidisciplinary approaches that incorporate advances in genomics, genetic-engineering, new fungicide chemistries, applied biocontrol, and consideration of the disease cycle for management of FHB.
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Affiliation(s)
- Soumya Moonjely
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Malaika Ebert
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Drew Paton-Glassbrook
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA
| | - Zachary A Noel
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Ludmila Roze
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Rebecca Shay
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Tara Watkins
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA.
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Chavan AR, Khardenavis AA. Annotating Multiple Prebiotic Synthesizing Capabilities Through Whole Genome Sequencing of Fusarium Strain HFK-74. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04788-0. [PMID: 37994978 DOI: 10.1007/s12010-023-04788-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 11/24/2023]
Abstract
In the present study, seven fungal isolates from effluent treatment plants were screened for the production of prebiotic fructooligosaccharide synthesizing enzymes with the highest activity of fructofuranosidase (17.52 U/mL) and fructosyl transferase (18.92 U/mL) in strain HKF-74. Mining of genome sequence of strain revealed the annotation of genes providing multiple carbohydrate metabolizing capacities, such as amylases (AMY1), beta-galactosidase (BGAL), beta-xylosidase (Xyl), β-fructofuranosidase (ScrB), fructosyltransferase (FTF), and maltose hydrolases (malH). The annotated genes were further supported by β-galactosidase (15.90 U/mL), xylanase (17.91 U/mL), and α-amylase (14.05 U/mL) activities for synthesis of galactooligosaccharides, xylooligosaccarides, and maltooligosaccharides, respectively. In addition to genes encoding prebiotic synthesizing enzymes, four biosynthetic gene clusters (BGCs) including Type I polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), NRPS-like, and terpene were also predicted in strain HKF-74. This was significant considering their potential role in pharmaceutical and therapeutic applications as well as in virulence. Accurate taxonomic assignment of strain HKF-74 by in silico genomic comparison indicated its closest identity to type strains Fusarium verticillioides NRRL 20984, and 7600. The average nucleotide identity (ANI) of strain HKF-74 with these strains was 92.5% which was close to the species threshold cut-off value (95-96%) while the DNA-DNA hybridization (DDH) value was 83-84% which was greater than both, species delineating (79-80%), and also sub-species delineating (70%) boundaries. Our findings provide a foundation for further research into the use of Fusarium strains and their prebiotic synthesizing enzymes for the development of novel prebiotic supplements.
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Affiliation(s)
- Atul Rajkumar Chavan
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Li J, He K, Zhang Q, Wu X, Li Z, Pan X, Wang Y, Li C, Zhang M. Draft Genome and Biological Characteristics of Fusarium solani and Fusarium oxysporum Causing Black Rot in Gastrodia elata. Int J Mol Sci 2023; 24:ijms24054545. [PMID: 36901977 PMCID: PMC10003674 DOI: 10.3390/ijms24054545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Gastrodia elata is a valuable traditional Chinese medicinal plant. However, G. elata crops are affected by major diseases, such as brown rot. Previous studies have shown that brown rot is caused by Fusarium oxysporum and F. solani. To further understand the disease, we studied the biological and genome characteristics of these pathogenic fungi. Here, we found that the optimum growth temperature and pH of F. oxysporum (strain QK8) and F. solani (strain SX13) were 28 °C and pH 7, and 30 °C and pH 9, respectively. An indoor virulence test showed that oxime tebuconazole, tebuconazole, and tetramycin had significant bacteriostatic effects on the two Fusarium species. The genomes of QK8 and SX13 were assembled, and it was found that there was a certain gap in the size of the two fungi. The size of strain QK8 was 51,204,719 bp and that of strain SX13 was 55,171,989 bp. Afterwards, through phylogenetic analysis, it was found that strain QK8 was closely related to F. oxysporum, while strain SX13 was closely related to F. solani. Compared with the published whole-genome data for these two Fusarium strains, the genome information obtained here is more complete; the assembly and splicing reach the chromosome level. The biological characteristics and genomic information we provide here lay the foundation for further research on G. elata brown rot.
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Affiliation(s)
- Jinshao Li
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Ke He
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Qian Zhang
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xiaoyi Wu
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Zhong Li
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xuejun Pan
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Yong Wang
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Cheng Li
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence: (C.L.); (M.Z.)
| | - Manman Zhang
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (C.L.); (M.Z.)
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Kuang W, Zhang L, Ye L, Ma J, Shi X, Lin Y, Sun X, Cui R. Genome and Transcriptome Sequencing Analysis of Fusarium commune Provides Insights into the Pathogenic Mechanisms of the Lotus Rhizome Rot. Microbiol Spectr 2022; 10:e0017522. [PMID: 35867414 PMCID: PMC9431280 DOI: 10.1128/spectrum.00175-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/04/2022] [Indexed: 11/20/2022] Open
Abstract
Fusarium wilt, a vascular wilt caused by F. commune, has been a serious problem for the lotus. Although some F. commune isolate genomes have been sequenced, little is known about the genomic information of the strain that causes Fusarium wilt of aquatic plants. In this study, the genome of F. commune FCN23 isolated from lotuses in China was sequenced using Illumina and PacBio sequencing platforms. The FCN23 genome consisted of 53 scaffolds with a combined size of 46,211,149 bp. According to the reference genome, F. oxysporum f. sp. lycopersici 4287 isolated from tomato, it was finally assembled into 14 putative chromosomes, including 10 core and 4 lineage-specific chromosomes. The genome contains about 3.45% repeats and encodes 14,698 putative protein-coding genes. Among these, 1,038 and 296 proteins were potentially secreted proteins and candidate effector proteins, respectively. Comparative genomic analysis showed that the CAZyme-coding genes and secondary metabolite biosynthesis genes of FCN23 were similar to those of other Ascomycetes. Additionally, the transcriptome of FCN23 during infection of lotus was analyzed and 7,013 differentially expressed genes were identified. Eight putative effectors that were upregulated in the infection stage were cloned. Among them, F23a002499 exhibited strong hypersensitive response after transiently expressed in Nicotiana benthamiana leaves. Our results provide a valuable genetic basis for understanding the molecular mechanism of the interaction between F. commune and aquatic plants. IMPORTANCE Fusarium commune is an important soilborne pathogen with a wide range of hosts and can cause Fusarium wilt of land plants. However, there are few studies on Fusarium wilt of aquatic plants. Lotus rhizome rot mainly caused by F. commune is a devastating disease that causes extensive yield and quality losses in China. Here, we obtained high-quality genomic information of the FCN23 using Illumina NovaSeq and the third-generation sequencing technology PacBio Sequel II. Compared to the reference genome F. oxysporum f. sp. lycopersici strain 4287, it contains 11 core and 3 lineage-specific chromosomes. Many differentially expressed genes associated with pathogenicity were identified by RNA sequencing. The genome and transcriptome sequences of FCN23 will provide important genomic information and insights into the infection mechanisms of F. commune on aquatic plants.
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Affiliation(s)
- Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lianhu Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lifang Ye
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jian Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xugen Shi
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yachun Lin
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaotang Sun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ruqiang Cui
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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