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Yew SM, Chan CL, Kuan CS, Toh YF, Ngeow YF, Na SL, Lee KW, Hoh CC, Yee WY, Ng KP. The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions. BMC Genomics 2016; 17:91. [PMID: 26842951 PMCID: PMC4738786 DOI: 10.1186/s12864-016-2409-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/21/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Ochroconis mirabilis, a recently introduced water-borne dematiaceous fungus, is occasionally isolated from human skin lesions and nails. We identified an isolate of O. mirabilis from a skin scraping with morphological and molecular studies. Its genome was then sequenced and analysed for genetic features related to classification and biological characteristics. RESULTS UM 578 was identified as O. mirabilis based on morphology and internal transcribed spacer (ITS)-based phylogeny. The 34.61 Mb assembled genome with 13,435 predicted genes showed less efficiency of this isolate in plant cell wall degradation. Results from the peptidase comparison analysis with reported keratin-degrading peptidases from dermatophytes suggest that UM 578 is very unlikely to be utilising these peptidases to survive in the host. Nevertheless, we have identified peptidases from M10A, M12A and S33 families that may allow UM 578 to invade its host via extracellular matrix and collagen degradation. Furthermore, the lipases in UM 578 may have a role in supporting the fungus in host invasion. This fungus has the potential ability to synthesise melanin via the 1,8-dihydroxynaphthalene (DHN)-melanin pathway and to produce mycotoxins. The mating ability of this fungus was also inspected in this study and a mating type gene containing alpha domain was identified. This fungus is likely to produce taurine that is required in osmoregulation. The expanded gene family encoding the taurine catabolism dioxygenase TauD/TdfA domain suggests the utilisation of taurine under sulfate starvation. The expanded glutathione-S-transferase domains and RTA1-like protein families indicate the selection of genes in UM 578 towards adaptation in hostile environments. CONCLUSIONS The genomic analysis of O. mirabilis UM 578 provides a better understanding of fungal survival tactics in different habitats.
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Affiliation(s)
- Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chai Ling Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chee Sian Kuan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yue Fen Toh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yun Fong Ngeow
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, 43000, Kajang, Selangor Darul Ehsan, Malaysia.
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kok Wei Lee
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor Darul Ehsan, Malaysia.
| | - Chee-Choong Hoh
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor Darul Ehsan, Malaysia.
| | - Wai-Yan Yee
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor Darul Ehsan, Malaysia.
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Cunha SMPRM, Guedes da Silva MFC, Fraústo da Silva JJR, Pombeiro AJL. Cyanoimide‐Bridged, Bi‐ and Trinuclear, Heterometallic Complexes with an NCN–Mo–NCN Phosphinic Core. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sónia M. P. R. M. Cunha
- Centro de Química Estrutural, Complexo Interdisciplinar, Instituto Superior Técnico, TU Lisbon, Av. Rovisco Pais, 1049‐001 Lisboa, Portugal
| | - M. Fátima C. Guedes da Silva
- Centro de Química Estrutural, Complexo Interdisciplinar, Instituto Superior Técnico, TU Lisbon, Av. Rovisco Pais, 1049‐001 Lisboa, Portugal
- Universidade Lusófona de Humanidades e Tecnologias, ULHT Lisbon, Campo Grande 376, 1749‐024, Lisboa, Portugal
| | - João J. R. Fraústo da Silva
- Centro de Química Estrutural, Complexo Interdisciplinar, Instituto Superior Técnico, TU Lisbon, Av. Rovisco Pais, 1049‐001 Lisboa, Portugal
| | - Armando J. L. Pombeiro
- Centro de Química Estrutural, Complexo Interdisciplinar, Instituto Superior Técnico, TU Lisbon, Av. Rovisco Pais, 1049‐001 Lisboa, Portugal
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Sundar IK, Sakthivel N. Advances in selectable marker genes for plant transformation. JOURNAL OF PLANT PHYSIOLOGY 2008; 165:1698-716. [PMID: 18789557 DOI: 10.1016/j.jplph.2008.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Accepted: 08/04/2008] [Indexed: 05/22/2023]
Abstract
Plant transformation systems for creating transgenics require separate process for introducing cloned DNA into living plant cells. Identification or selection of those cells that have integrated DNA into appropriate plant genome is a vital step to regenerate fully developed plants from the transformed cells. Selectable marker genes are pivotal for the development of plant transformation technologies because marker genes allow researchers to identify or isolate the cells that are expressing the cloned DNA, to monitor and select the transformed progeny. As only a very small portion of cells are transformed in most experiments, the chances of recovering transgenic lines without selection are usually low. Since the selectable marker gene is expected to function in a range of cell types it is usually constructed as a chimeric gene using regulatory sequences that ensure constitutive expression throughout the plant. Advent of recombinant DNA technology and progress in plant molecular biology had led to a desire to introduce several genes into single transgenic plant line, necessitating the development of various types of selectable markers. This review article describes the developments made in the recent past on plant transformation systems using different selection methods adding a note on their importance as marker genes in transgenic crop plants.
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