Limits...
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.

Show MeSH

Related in: MedlinePlus

Physical map of the mitochondrial genome of M. mycetomatis.All genes are located on the plus-strand and are shown in the outer ring of the circle, they are transcribed counterclockwise. On the plus-strand the following genes are encountered: rnl, rns, 11 genes encoding subunits of respiratory chain complexes (cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), 2 ATP synthase subunits (atp6 and atp8), 5 hypothetical proteins (x1, x2, x3, x4 and x5) and 6 intronic proteins including the ribosomal protein rps3 are shown. The introns are shown as blue boxes in the middle ring underneath the genes in which they are located. The intronic proteins are shown as pink boxes in the inner ring underneath the introns and the genes in which they are located. The exact starting en ending positions of each gene, intron and tRNA are shown in table 1.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3368884&req=5

pone-0038654-g001: Physical map of the mitochondrial genome of M. mycetomatis.All genes are located on the plus-strand and are shown in the outer ring of the circle, they are transcribed counterclockwise. On the plus-strand the following genes are encountered: rnl, rns, 11 genes encoding subunits of respiratory chain complexes (cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), 2 ATP synthase subunits (atp6 and atp8), 5 hypothetical proteins (x1, x2, x3, x4 and x5) and 6 intronic proteins including the ribosomal protein rps3 are shown. The introns are shown as blue boxes in the middle ring underneath the genes in which they are located. The intronic proteins are shown as pink boxes in the inner ring underneath the introns and the genes in which they are located. The exact starting en ending positions of each gene, intron and tRNA are shown in table 1.

Mentions: The mitochondrial genome of M. mycetomatis is a typical circular DNA molecule with a length of 45,590 bp. This mitochondrial genome size is small in comparison with the published mitochondrial genomes belonging to the order of the Sordariales. These genomes range from 64,840 nt (Neurospora crassa as stated by the Broad Institute)) to 127,206 nt (Chaetomium thermophilum) [14], [27], [28], [29]. This difference in genome size is due to the variation in intergenetic regions and the presence of hypothetical proteins. In overall, the mitochondrial genome of M. mycetomatis is highly compact, with 80% of the genome encoding for structural genes. The genome encodes 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 and 6 intronic proteins including the ribosomal protein rps3 (Figure 1, table 1). All genes and tRNAs are found on the plus-strand of the mitochondrial genome, as was also found for mitochondria of most other ascomycetes although for some ascomycetes such as Mycosphaerella graminicola genes were located both strands of the mitochondrial genome. [11], [13], [14], [27], [30], [31]. The M. mycetomatis mitochondrial genome is AT-rich, with an overall G+C content of only 26.8%. The regions of the encoding RNA genes, have a slightly higher G+C content, namely 28.8%. This is in agreement with values found for other fungal mitochondria [10].


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)

Physical map of the mitochondrial genome of M. mycetomatis.All genes are located on the plus-strand and are shown in the outer ring of the circle, they are transcribed counterclockwise. On the plus-strand the following genes are encountered: rnl, rns, 11 genes encoding subunits of respiratory chain complexes (cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), 2 ATP synthase subunits (atp6 and atp8), 5 hypothetical proteins (x1, x2, x3, x4 and x5) and 6 intronic proteins including the ribosomal protein rps3 are shown. The introns are shown as blue boxes in the middle ring underneath the genes in which they are located. The intronic proteins are shown as pink boxes in the inner ring underneath the introns and the genes in which they are located. The exact starting en ending positions of each gene, intron and tRNA are shown in table 1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368884&req=5

pone-0038654-g001: Physical map of the mitochondrial genome of M. mycetomatis.All genes are located on the plus-strand and are shown in the outer ring of the circle, they are transcribed counterclockwise. On the plus-strand the following genes are encountered: rnl, rns, 11 genes encoding subunits of respiratory chain complexes (cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), 2 ATP synthase subunits (atp6 and atp8), 5 hypothetical proteins (x1, x2, x3, x4 and x5) and 6 intronic proteins including the ribosomal protein rps3 are shown. The introns are shown as blue boxes in the middle ring underneath the genes in which they are located. The intronic proteins are shown as pink boxes in the inner ring underneath the introns and the genes in which they are located. The exact starting en ending positions of each gene, intron and tRNA are shown in table 1.
Mentions: The mitochondrial genome of M. mycetomatis is a typical circular DNA molecule with a length of 45,590 bp. This mitochondrial genome size is small in comparison with the published mitochondrial genomes belonging to the order of the Sordariales. These genomes range from 64,840 nt (Neurospora crassa as stated by the Broad Institute)) to 127,206 nt (Chaetomium thermophilum) [14], [27], [28], [29]. This difference in genome size is due to the variation in intergenetic regions and the presence of hypothetical proteins. In overall, the mitochondrial genome of M. mycetomatis is highly compact, with 80% of the genome encoding for structural genes. The genome encodes 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 and 6 intronic proteins including the ribosomal protein rps3 (Figure 1, table 1). All genes and tRNAs are found on the plus-strand of the mitochondrial genome, as was also found for mitochondria of most other ascomycetes although for some ascomycetes such as Mycosphaerella graminicola genes were located both strands of the mitochondrial genome. [11], [13], [14], [27], [30], [31]. The M. mycetomatis mitochondrial genome is AT-rich, with an overall G+C content of only 26.8%. The regions of the encoding RNA genes, have a slightly higher G+C content, namely 28.8%. This is in agreement with values found for other fungal mitochondria [10].

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