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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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Related in: MedlinePlus

Maximum likelihood phylogenetic tree based on amino acid sequences of conserved mitochondrial proteins of various fungal species.Amino acid sequences of the genes atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 were used to construct this tree using the maximum likelihood algorithm of MEGA 5.05. Bootstrap support was calculated from 1000 replicates using the same program. GenBank sequences used were: V. lecanni (NC_004514), B. bassiana (NC_010652), H. jecorina (NC_NC003388), G. zeae (NC_009493), S. macrospora (CABT01004783), P. anserina (NC_001329), C. thermophilum (NC­_015893), P. nodorum (NC_009746), T. rubrum (NC_012824), E. floccosum (NC_007394), M. canis (NC_012832), P. marneffei (NC_005256), A. tubingensis (NC_007597), A. niger (NC_007445), P. brasiliensis (NC_007935), P. pastoris (NC_015384), C. albicans (NC_002653). Protein sequences of N. crassa mtDNA was downloaded from supercontig 10.21 from the Broad institute.
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pone-0038654-g002: Maximum likelihood phylogenetic tree based on amino acid sequences of conserved mitochondrial proteins of various fungal species.Amino acid sequences of the genes atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 were used to construct this tree using the maximum likelihood algorithm of MEGA 5.05. Bootstrap support was calculated from 1000 replicates using the same program. GenBank sequences used were: V. lecanni (NC_004514), B. bassiana (NC_010652), H. jecorina (NC_NC003388), G. zeae (NC_009493), S. macrospora (CABT01004783), P. anserina (NC_001329), C. thermophilum (NC­_015893), P. nodorum (NC_009746), T. rubrum (NC_012824), E. floccosum (NC_007394), M. canis (NC_012832), P. marneffei (NC_005256), A. tubingensis (NC_007597), A. niger (NC_007445), P. brasiliensis (NC_007935), P. pastoris (NC_015384), C. albicans (NC_002653). Protein sequences of N. crassa mtDNA was downloaded from supercontig 10.21 from the Broad institute.

Mentions: With the exception of the group of yeast that are lacking NADH genes, all other fungal mtDNAs contain the same essential functional genes [11]. Therefore, the sequences of these 14 conserved protein encoding genes, as well as the mitochondrial organization of these genes can be used tpone.0038654.g001.tifo determine the relations between different fungal species. Amino acid sequence of 14 protein coding genes in the mitochondrial genomes of M. mycetomatis and 20 other fungi are used for phylogenetic tree construction (figure 2). Most nodes in this tree have high bootstrap values which indicate the robustness of the tree computed. As found by others, the mitochondrial genomes of the yeast species cluster apart from the mitochondrial genomes obtained from filamentous fungi [10]. As is seen in figure 2, M. mycetomatis clusters amongst other species of the order Sordariales with high bootstrap support. Placing M. mycetomatis in the order Sordariales is in line with previous observations based on the nuclear sequences SSU, ITS, betatubulin 2 and ribosomal binding protein 2 [3], [4]. Based on an extensive phylogenetic comparison of the SSU rDNA sequence of M. mycetomatis with that of 157 other members of the Ascomycota belonging to the orders Chaetothyriales, Diaporthales, Dothideales, Eurotiales, Halosphaeriales, Hypocreales, Lecanorales, Leotiales, Microascales, Onygenales, Ophiostomatales, Pezizales, Pleosporales, Sordariales, Taphrinales and Tuberales it appeared that M. mycetomatis clustered among the members of the order Sordariales while M. grisea clustered among the members of the order Pleosporales [3]. In order to determine the phylogenetic place of M. mycetomatis within the order Sordariales, the ITS, betatubulin 2 and ribosomal binding protein 2 were also sequenced and compared to 39 members of the order Sordariales. In this latter study it appeared that M. mycetomatis was most closely related to M. tropicana, M. pseudomycetomatis and M. fahalli, but that the genus Madurella itself was most closely related to the genus Chaetomium[4]. This close relatedness to the genus Chaetomium is confirmed in this study. Based on the phylogenetic comparisons made with the mitochondrial sequence, it appears that the closest relative of M. mycetomatis is C. thermophilum.


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)

Maximum likelihood phylogenetic tree based on amino acid sequences of conserved mitochondrial proteins of various fungal species.Amino acid sequences of the genes atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 were used to construct this tree using the maximum likelihood algorithm of MEGA 5.05. Bootstrap support was calculated from 1000 replicates using the same program. GenBank sequences used were: V. lecanni (NC_004514), B. bassiana (NC_010652), H. jecorina (NC_NC003388), G. zeae (NC_009493), S. macrospora (CABT01004783), P. anserina (NC_001329), C. thermophilum (NC­_015893), P. nodorum (NC_009746), T. rubrum (NC_012824), E. floccosum (NC_007394), M. canis (NC_012832), P. marneffei (NC_005256), A. tubingensis (NC_007597), A. niger (NC_007445), P. brasiliensis (NC_007935), P. pastoris (NC_015384), C. albicans (NC_002653). Protein sequences of N. crassa mtDNA was downloaded from supercontig 10.21 from the Broad institute.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3368884&req=5

pone-0038654-g002: Maximum likelihood phylogenetic tree based on amino acid sequences of conserved mitochondrial proteins of various fungal species.Amino acid sequences of the genes atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6 were used to construct this tree using the maximum likelihood algorithm of MEGA 5.05. Bootstrap support was calculated from 1000 replicates using the same program. GenBank sequences used were: V. lecanni (NC_004514), B. bassiana (NC_010652), H. jecorina (NC_NC003388), G. zeae (NC_009493), S. macrospora (CABT01004783), P. anserina (NC_001329), C. thermophilum (NC­_015893), P. nodorum (NC_009746), T. rubrum (NC_012824), E. floccosum (NC_007394), M. canis (NC_012832), P. marneffei (NC_005256), A. tubingensis (NC_007597), A. niger (NC_007445), P. brasiliensis (NC_007935), P. pastoris (NC_015384), C. albicans (NC_002653). Protein sequences of N. crassa mtDNA was downloaded from supercontig 10.21 from the Broad institute.
Mentions: With the exception of the group of yeast that are lacking NADH genes, all other fungal mtDNAs contain the same essential functional genes [11]. Therefore, the sequences of these 14 conserved protein encoding genes, as well as the mitochondrial organization of these genes can be used tpone.0038654.g001.tifo determine the relations between different fungal species. Amino acid sequence of 14 protein coding genes in the mitochondrial genomes of M. mycetomatis and 20 other fungi are used for phylogenetic tree construction (figure 2). Most nodes in this tree have high bootstrap values which indicate the robustness of the tree computed. As found by others, the mitochondrial genomes of the yeast species cluster apart from the mitochondrial genomes obtained from filamentous fungi [10]. As is seen in figure 2, M. mycetomatis clusters amongst other species of the order Sordariales with high bootstrap support. Placing M. mycetomatis in the order Sordariales is in line with previous observations based on the nuclear sequences SSU, ITS, betatubulin 2 and ribosomal binding protein 2 [3], [4]. Based on an extensive phylogenetic comparison of the SSU rDNA sequence of M. mycetomatis with that of 157 other members of the Ascomycota belonging to the orders Chaetothyriales, Diaporthales, Dothideales, Eurotiales, Halosphaeriales, Hypocreales, Lecanorales, Leotiales, Microascales, Onygenales, Ophiostomatales, Pezizales, Pleosporales, Sordariales, Taphrinales and Tuberales it appeared that M. mycetomatis clustered among the members of the order Sordariales while M. grisea clustered among the members of the order Pleosporales [3]. In order to determine the phylogenetic place of M. mycetomatis within the order Sordariales, the ITS, betatubulin 2 and ribosomal binding protein 2 were also sequenced and compared to 39 members of the order Sordariales. In this latter study it appeared that M. mycetomatis was most closely related to M. tropicana, M. pseudomycetomatis and M. fahalli, but that the genus Madurella itself was most closely related to the genus Chaetomium[4]. This close relatedness to the genus Chaetomium is confirmed in this study. Based on the phylogenetic comparisons made with the mitochondrial sequence, it appears that the closest relative of M. mycetomatis is C. thermophilum.

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