{"title":"Whole genome sequencing and annotation of Pseudocercospora abelmoschi, a causal agent of black leaf mould of okra.","authors":"Shagun Sinha, Sudhir Navathe, Anjali, Shubham Vishwakarma, Priyanka Prajapati, Ramesh Chand, Ravindra Nath Kharwar","doi":"10.1007/s11274-025-04398-4","DOIUrl":null,"url":null,"abstract":"<p><p>Pseudocercospora abelmoschi causes black mould on the leaves of okra. The disease is prevalent post-rainy season when high moisture and warm temperatures prevail. Severe defoliation is observed during favourable environments, leading to a significant loss in productivity. Based on the importance of the pathogen agriculturally, the P. abelmoschi isolate Cer 86 - 18 (MCC:9491) was selected for genome sequencing. The genome assembly of P. abelmoschi resulted in a genome of 31.90 Mb with an overall GC content of 54.26%. Quantitative genome assessment using BUSCO (Benchmarking Universal Single-Copy Orthologs) identified 1,664 (97.53%) complete BUSCOs, reflecting a high representation of conserved genes with minimal duplication and strong orthologous uniqueness. Gene prediction analysis identified 11,325 protein-coding genes, of which 3,857 were annotated using the KEGG database. As per analyses, 410 genes were predicted to encode carbohydrate-active enzymes, whereas 369 genes were predicted to encode peptidases. Eighteen gene clusters involved in secondary metabolite biosynthesis were also identified. A total of 143 proteins were predicted to be effectors using the in-silico pipeline. This is the first report on the genome organisation of P. abelmoschi. This study was designed to address this gap by enhancing our understanding of the genome organisation of P. abelmoschi and gene annotation, thereby paving the way for functional genomics studies, such as identifying virulence genes to aid in resistance breeding. Also, this genome could be another addition to the available genomic resources of the genus Pseudocercospora and can provide valuable insights into host-pathogen interactions and evolutionary relationships.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"174"},"PeriodicalIF":4.0000,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"World journal of microbiology & biotechnology","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1007/s11274-025-04398-4","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Pseudocercospora abelmoschi causes black mould on the leaves of okra. The disease is prevalent post-rainy season when high moisture and warm temperatures prevail. Severe defoliation is observed during favourable environments, leading to a significant loss in productivity. Based on the importance of the pathogen agriculturally, the P. abelmoschi isolate Cer 86 - 18 (MCC:9491) was selected for genome sequencing. The genome assembly of P. abelmoschi resulted in a genome of 31.90 Mb with an overall GC content of 54.26%. Quantitative genome assessment using BUSCO (Benchmarking Universal Single-Copy Orthologs) identified 1,664 (97.53%) complete BUSCOs, reflecting a high representation of conserved genes with minimal duplication and strong orthologous uniqueness. Gene prediction analysis identified 11,325 protein-coding genes, of which 3,857 were annotated using the KEGG database. As per analyses, 410 genes were predicted to encode carbohydrate-active enzymes, whereas 369 genes were predicted to encode peptidases. Eighteen gene clusters involved in secondary metabolite biosynthesis were also identified. A total of 143 proteins were predicted to be effectors using the in-silico pipeline. This is the first report on the genome organisation of P. abelmoschi. This study was designed to address this gap by enhancing our understanding of the genome organisation of P. abelmoschi and gene annotation, thereby paving the way for functional genomics studies, such as identifying virulence genes to aid in resistance breeding. Also, this genome could be another addition to the available genomic resources of the genus Pseudocercospora and can provide valuable insights into host-pathogen interactions and evolutionary relationships.
期刊介绍:
World Journal of Microbiology and Biotechnology publishes research papers and review articles on all aspects of Microbiology and Microbial Biotechnology.
Since its foundation, the Journal has provided a forum for research work directed toward finding microbiological and biotechnological solutions to global problems. As many of these problems, including crop productivity, public health and waste management, have major impacts in the developing world, the Journal especially reports on advances for and from developing regions.
Some topics are not within the scope of the Journal. Please do not submit your manuscript if it falls into one of the following categories:
· Virology
· Simple isolation of microbes from local sources
· Simple descriptions of an environment or reports on a procedure
· Veterinary, agricultural and clinical topics in which the main focus is not on a microorganism
· Data reporting on host response to microbes
· Optimization of a procedure
· Description of the biological effects of not fully identified compounds or undefined extracts of natural origin
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All articles published in the Journal are independently refereed.