Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales
Abstract Background Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome seque...
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| Format: | Article |
| Language: | English |
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BMC
2017-09-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4136-1 |
| _version_ | 1818047144796356608 |
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| author | Hariprasath Prakash Shivaprakash Mandya Rudramurthy Prasad S. Gandham Anup Kumar Ghosh Milner M. Kumar Chandan Badapanda Arunaloke Chakrabarti |
| author_facet | Hariprasath Prakash Shivaprakash Mandya Rudramurthy Prasad S. Gandham Anup Kumar Ghosh Milner M. Kumar Chandan Badapanda Arunaloke Chakrabarti |
| author_sort | Hariprasath Prakash |
| collection | DOAJ |
| description | Abstract Background Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism. Results The whole genome of A. variabilis NCCPF 102052 was sequenced and the genomic structure of A. variabilis was compared with already available genome structures of A. elegans, A. trapeziformis and other medically important Mucorales. The total size of genome assembly of A. variabilis was 39.38 Mb with 12,764 protein-coding genes. The transposable elements (TEs) were low in Apophysomyces genome and the retrotransposon Ty3-gypsy was the common TE. Phylogenetically, Apophysomyces species were grouped closely with Phycomyces blakesleeanus. OrthoMCL analysis revealed 3025 orthologues proteins, which were common in those three pathogenic Apophysomyces species. Expansion of multiple gene families/duplication was observed in Apophysomyces genomes. Approximately 6% of Apophysomyces genes were predicted to be associated with virulence on PHIbase analysis. The virulence determinants included the protein families of CotH proteins (invasins), proteases, iron utilisation pathways, siderophores and signal transduction pathways. Serine proteases were the major group of proteases found in all Apophysomyces genomes. The carbohydrate active enzymes (CAZymes) constitute the majority of the secretory proteins. Conclusion The present study is the maiden attempt to sequence and analyze the genomic structure of A. variabilis. Together with available genome sequence of A. elegans and A. trapeziformis, the study helped to indicate the possible virulence determinants of pathogenic Apophysomyces species. The presence of unique CAZymes in cell wall might be exploited in future for antifungal drug development. |
| first_indexed | 2024-12-10T10:01:07Z |
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| id | doaj.art-992f5439555a47668fc7aff1158298aa |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T10:01:07Z |
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| spelling | doaj.art-992f5439555a47668fc7aff1158298aa2022-12-22T01:53:21ZengBMCBMC Genomics1471-21642017-09-0118111310.1186/s12864-017-4136-1Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important MucoralesHariprasath Prakash0Shivaprakash Mandya Rudramurthy1Prasad S. Gandham2Anup Kumar Ghosh3Milner M. Kumar4Chandan Badapanda5Arunaloke Chakrabarti6Department of Medical Microbiology, Postgraduate Institute of Medical Education and ResearchDepartment of Medical Microbiology, Postgraduate Institute of Medical Education and ResearchMicrobial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial TechnologyDepartment of Medical Microbiology, Postgraduate Institute of Medical Education and ResearchDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of TechnologyDepartment of Biotechnology, OPJS UniversityDepartment of Medical Microbiology, Postgraduate Institute of Medical Education and ResearchAbstract Background Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism. Results The whole genome of A. variabilis NCCPF 102052 was sequenced and the genomic structure of A. variabilis was compared with already available genome structures of A. elegans, A. trapeziformis and other medically important Mucorales. The total size of genome assembly of A. variabilis was 39.38 Mb with 12,764 protein-coding genes. The transposable elements (TEs) were low in Apophysomyces genome and the retrotransposon Ty3-gypsy was the common TE. Phylogenetically, Apophysomyces species were grouped closely with Phycomyces blakesleeanus. OrthoMCL analysis revealed 3025 orthologues proteins, which were common in those three pathogenic Apophysomyces species. Expansion of multiple gene families/duplication was observed in Apophysomyces genomes. Approximately 6% of Apophysomyces genes were predicted to be associated with virulence on PHIbase analysis. The virulence determinants included the protein families of CotH proteins (invasins), proteases, iron utilisation pathways, siderophores and signal transduction pathways. Serine proteases were the major group of proteases found in all Apophysomyces genomes. The carbohydrate active enzymes (CAZymes) constitute the majority of the secretory proteins. Conclusion The present study is the maiden attempt to sequence and analyze the genomic structure of A. variabilis. Together with available genome sequence of A. elegans and A. trapeziformis, the study helped to indicate the possible virulence determinants of pathogenic Apophysomyces species. The presence of unique CAZymes in cell wall might be exploited in future for antifungal drug development.http://link.springer.com/article/10.1186/s12864-017-4136-1Apophysomyces variabilisCotH proteinsProteasesTransposonsGenome structureSequence analysis |
| spellingShingle | Hariprasath Prakash Shivaprakash Mandya Rudramurthy Prasad S. Gandham Anup Kumar Ghosh Milner M. Kumar Chandan Badapanda Arunaloke Chakrabarti Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales BMC Genomics Apophysomyces variabilis CotH proteins Proteases Transposons Genome structure Sequence analysis |
| title | Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales |
| title_full | Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales |
| title_fullStr | Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales |
| title_full_unstemmed | Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales |
| title_short | Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales |
| title_sort | apophysomyces variabilis draft genome sequence and comparison of predictive virulence determinants with other medically important mucorales |
| topic | Apophysomyces variabilis CotH proteins Proteases Transposons Genome structure Sequence analysis |
| url | http://link.springer.com/article/10.1186/s12864-017-4136-1 |
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