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Phylogenetic analysis of the complete mitochondrial genome of Madurella mycetomatis confirms its taxonomic position within the order Sordariales.

van de Sande WW - PLoS ONE (2012)

Bottom Line: Analyses of the gene order showed that within the order Sordariales a similar gene order is found.Furthermore also the tRNA order seemed mostly conserved.Phylogenetic analyses of fungal mitochondrial genomes confirmed that M. mycetomatis belongs to the order of Sordariales and that it was most closely related to Chaetomium thermophilum, with which it also shared a comparable gene and tRNA order.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands. w.vandesande@erasmusmc.nl

ABSTRACT

Background: Madurella mycetomatis is the most common cause of human eumycetoma. The genus Madurella has been characterized by overall sterility on mycological media. Due to this sterility and the absence of other reliable morphological and ultrastructural characters, the taxonomic classification of Madurella has long been a challenge. Mitochondria are of monophyletic origin and mitochondrial genomes have been proven to be useful in phylogenetic analyses.

Results: The first complete mitochondrial DNA genome of a mycetoma-causative agent was sequenced using 454 sequencing. The mitochondrial genome of M. mycetomatis is a circular DNA molecule with a size of 45,590 bp, encoding for the small and the large subunit rRNAs, 27 tRNAs, 11 genes encoding subunits of respiratory chain complexes, 2 ATP synthase subunits, 5 hypothetical proteins, 6 intronic proteins including the ribosomal protein rps3. In phylogenetic analyses using amino acid sequences of the proteins involved in respiratory chain complexes and the 2 ATP synthases it appeared that M. mycetomatis clustered together with members of the order Sordariales and that it was most closely related to Chaetomium thermophilum. Analyses of the gene order showed that within the order Sordariales a similar gene order is found. Furthermore also the tRNA order seemed mostly conserved.

Conclusion: Phylogenetic analyses of fungal mitochondrial genomes confirmed that M. mycetomatis belongs to the order of Sordariales and that it was most closely related to Chaetomium thermophilum, with which it also shared a comparable gene and tRNA order.

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Mitochondrial gene order of 5 members of the order Sordariales.The gene order of the protein-encoding genes, atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 are shown for S. macrospora, N. crassa, M. mycetomatis, C. thermophilum and P. anserina. For the first four species, the positions of the tRNA genes are also depicted by using their one letter amino acid code.
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pone-0038654-g003: Mitochondrial gene order of 5 members of the order Sordariales.The gene order of the protein-encoding genes, atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 are shown for S. macrospora, N. crassa, M. mycetomatis, C. thermophilum and P. anserina. For the first four species, the positions of the tRNA genes are also depicted by using their one letter amino acid code.

Mentions: The relatedness amongst the order Sordariales is further studied by comparing the mitochondrial organizatiopone.0038654.g002.tifn of M. mycetomatis to the 4 complete fungal mtDNA sequences belonging to the order Sordariales. Comparable to the high similarity in amino-acid sequence and the uniform mtDNA genome organization found for dermatophytes belonging to the order Onygenales [10], the mitochondrial genome organization found for the order Sordariales is apparently also uniform (figure 3). The only exception is the mitochondrial genome organization of P. anserina, which differs from the genome organization of the other members of the order Sordariales (figure 3). This marked difference has been noted in the past, and led to the conclusion that the mitochondrial gene order in the order Sordariales was apparently quite diverse [11]. Here it is shown, that for most mitochondrial genomes in the order Sordariales this is not the case. More mitochondrial genomes are needed for the order Sordariales to determine if the gene order is indeed similar and that P. anserina is the exception, or that the gene orders are in overall more diverse within this order. When comparing the different genome organizations it appears that the genome organization of M. mycetomatis is most closely related to that of C. thermophilum (figures 3), which only differed in the presence of the gene atp9 between nad3 and cox2 in C. thermophilum and its absence in M. mycetomatis. Next to having the same gene order, the tRNA clustering in the order Sordariales is similar. Again the tRNA order of M. mycetomatis resembles that of C. thermophilum the most (figure 3). Combining the phylogenetic data, the gene order and the tRNA order it appears that the mitochondrial genome of M. mycetomatis is most closely related to the mitochondrial genome of C. thermophilum. Fungi belonging to the order Sordariales are mostly soil-, wood- and dung-inhabiting fungi [43]. N. crassa is usually found in or on burned vegetation and the soil, while het natural habitat of S. macrospora P. anserina and C. thermophilum, is mainly the soil and herbivore dung [15], [44], [45], [46]. Although DNA of M. mycetomatis has been shown to be present in soil and on thorns in the endemic area, nobody has been able to culture M. mycetomatis directly from these niches [47]. Therefore the natural habitat of M. mycetomatis still needs to be confirmed. Based on this and other studies, it is demonstrated that M. mycetomatis clusters within the order Sordariales, therefore the natural habitat of M. mycetomatis might be sought on similar substrates. To discover the natural niche of this fungus could lead to strategies in the prevention of this mutilating disease.


Phylogenetic analysis of the complete mitochondrial genome of Madurella mycetomatis confirms its taxonomic position within the order Sordariales.

van de Sande WW - PLoS ONE (2012)

Mitochondrial gene order of 5 members of the order Sordariales.The gene order of the protein-encoding genes, atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 are shown for S. macrospora, N. crassa, M. mycetomatis, C. thermophilum and P. anserina. For the first four species, the positions of the tRNA genes are also depicted by using their one letter amino acid code.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3368884&req=5

pone-0038654-g003: Mitochondrial gene order of 5 members of the order Sordariales.The gene order of the protein-encoding genes, atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 are shown for S. macrospora, N. crassa, M. mycetomatis, C. thermophilum and P. anserina. For the first four species, the positions of the tRNA genes are also depicted by using their one letter amino acid code.
Mentions: The relatedness amongst the order Sordariales is further studied by comparing the mitochondrial organizatiopone.0038654.g002.tifn of M. mycetomatis to the 4 complete fungal mtDNA sequences belonging to the order Sordariales. Comparable to the high similarity in amino-acid sequence and the uniform mtDNA genome organization found for dermatophytes belonging to the order Onygenales [10], the mitochondrial genome organization found for the order Sordariales is apparently also uniform (figure 3). The only exception is the mitochondrial genome organization of P. anserina, which differs from the genome organization of the other members of the order Sordariales (figure 3). This marked difference has been noted in the past, and led to the conclusion that the mitochondrial gene order in the order Sordariales was apparently quite diverse [11]. Here it is shown, that for most mitochondrial genomes in the order Sordariales this is not the case. More mitochondrial genomes are needed for the order Sordariales to determine if the gene order is indeed similar and that P. anserina is the exception, or that the gene orders are in overall more diverse within this order. When comparing the different genome organizations it appears that the genome organization of M. mycetomatis is most closely related to that of C. thermophilum (figures 3), which only differed in the presence of the gene atp9 between nad3 and cox2 in C. thermophilum and its absence in M. mycetomatis. Next to having the same gene order, the tRNA clustering in the order Sordariales is similar. Again the tRNA order of M. mycetomatis resembles that of C. thermophilum the most (figure 3). Combining the phylogenetic data, the gene order and the tRNA order it appears that the mitochondrial genome of M. mycetomatis is most closely related to the mitochondrial genome of C. thermophilum. Fungi belonging to the order Sordariales are mostly soil-, wood- and dung-inhabiting fungi [43]. N. crassa is usually found in or on burned vegetation and the soil, while het natural habitat of S. macrospora P. anserina and C. thermophilum, is mainly the soil and herbivore dung [15], [44], [45], [46]. Although DNA of M. mycetomatis has been shown to be present in soil and on thorns in the endemic area, nobody has been able to culture M. mycetomatis directly from these niches [47]. Therefore the natural habitat of M. mycetomatis still needs to be confirmed. Based on this and other studies, it is demonstrated that M. mycetomatis clusters within the order Sordariales, therefore the natural habitat of M. mycetomatis might be sought on similar substrates. To discover the natural niche of this fungus could lead to strategies in the prevention of this mutilating disease.

Bottom Line: Analyses of the gene order showed that within the order Sordariales a similar gene order is found.Furthermore also the tRNA order seemed mostly conserved.Phylogenetic analyses of fungal mitochondrial genomes confirmed that M. mycetomatis belongs to the order of Sordariales and that it was most closely related to Chaetomium thermophilum, with which it also shared a comparable gene and tRNA order.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands. w.vandesande@erasmusmc.nl

ABSTRACT

Background: Madurella mycetomatis is the most common cause of human eumycetoma. The genus Madurella has been characterized by overall sterility on mycological media. Due to this sterility and the absence of other reliable morphological and ultrastructural characters, the taxonomic classification of Madurella has long been a challenge. Mitochondria are of monophyletic origin and mitochondrial genomes have been proven to be useful in phylogenetic analyses.

Results: The first complete mitochondrial DNA genome of a mycetoma-causative agent was sequenced using 454 sequencing. The mitochondrial genome of M. mycetomatis is a circular DNA molecule with a size of 45,590 bp, encoding for the small and the large subunit rRNAs, 27 tRNAs, 11 genes encoding subunits of respiratory chain complexes, 2 ATP synthase subunits, 5 hypothetical proteins, 6 intronic proteins including the ribosomal protein rps3. In phylogenetic analyses using amino acid sequences of the proteins involved in respiratory chain complexes and the 2 ATP synthases it appeared that M. mycetomatis clustered together with members of the order Sordariales and that it was most closely related to Chaetomium thermophilum. Analyses of the gene order showed that within the order Sordariales a similar gene order is found. Furthermore also the tRNA order seemed mostly conserved.

Conclusion: Phylogenetic analyses of fungal mitochondrial genomes confirmed that M. mycetomatis belongs to the order of Sordariales and that it was most closely related to Chaetomium thermophilum, with which it also shared a comparable gene and tRNA order.

Show MeSH
Related in: MedlinePlus