Limits...
The evolutionary history of cytochrome P450 genes in four filamentous Ascomycetes.

Deng J, Carbone I, Dean RA - BMC Evol. Biol. (2007)

Bottom Line: To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans.MG experienced more genes and clans gains compared to the other fungi.The exception was the NC lineage, which exhibited pure P450 gene loss.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA. dengj@email.unc.edu <dengj@email.unc.edu>

ABSTRACT

Background: The Cytochrome P450 system is important in fungal evolution for adapting to novel ecological niches. To elucidate the evolutionary process of cytochrome P450 genes in fungi with different life styles, we studied the patterns of gene gains and losses in the genomes of four filamentous Ascomycetes, including two saprotrophs (Aspergillus nidulans (AN) and Neurospora crassa (NC)) and two plant pathogens (Fusarium graminearum (FG) and Magnaporthe grisea (MG)).

Results: A total of 376 P450 genes were assigned to 168 families according to standard nomenclature. On average, only 1 to 2 genes per family were in each genome. To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans. Subsequently a novel approach based on parsimony was developed to build the evolutionary models. Based on these analyses, a core of 30 distinct clans of P450s was defined. The core clans experienced contraction in all four fungal lineages while new clans expanded in all with exception of NC. MG experienced more genes and clans gains compared to the other fungi. Parsimonious analyses unanimously supported one species topology for the four fungi.

Conclusion: The four studied fungi exhibit unprecedented diversity in their P450omes in terms of coding sequence, intron-exon structures and genome locations, suggesting a complicated evolutionary history of P450s in filamentous Ascomycetes. Clan classification and a novel strategy were developed to study evolutionary history. Contraction of core clans and expansion of novel clans were identified. The exception was the NC lineage, which exhibited pure P450 gene loss.

Show MeSH

Related in: MedlinePlus

Gene gains and losses on each branch of the species cladogram within 30 clans that were present in LCA. The column marked "Presence" shows the number of genes of each clan present in each fungus. For the remaining columns, filled rectangles represent gene gains and unfilled rectangles represent gene losses. The number following each rectangle represents the number of gains or losses. For colour codes, see Figure 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1828051&req=5

Figure 4: Gene gains and losses on each branch of the species cladogram within 30 clans that were present in LCA. The column marked "Presence" shows the number of genes of each clan present in each fungus. For the remaining columns, filled rectangles represent gene gains and unfilled rectangles represent gene losses. The number following each rectangle represents the number of gains or losses. For colour codes, see Figure 2.

Mentions: The number of duplication and loss events within individual clans that occurred on all branches of the species cladogram was inferred as described in Methods. Twenty-seven clans appeared to have had at least one duplication event before AN split from the LCA (Figure 4), independent of gain or loss model, suggesting that the LCA genome contained more than one member of these clans. In total, genes from these 27 clans accounted for 103 P450 genes in the LCA genome. In particular, clans containing larger numbers of genes were usually present in the LCA. For 28 clans which contained 4 genes or more, 24 of them were unambiguously inferred to be present in the LCA. Furthermore, we found a positive relationship (correlation coefficient = 0.7) between the number of genes within a current clan and the inferred number of ancestral genes of the clan present in the LCA genome. However, one obvious exception was clan CYP68, the third largest clan. It contained 20 P450 genes from the four fungi. However, only 2 CYP68 ancestral genes were inferred to be present in the LCA genome. Thus, it appeared that clan 68 must have experienced considerable expansion after the AN split. Our data suggest that there were 5 duplication events on branch 1, 4 in branch A, 2 in branch F and 3 in branch M (Figure 4). Therefore, clan 68 is a clear example of an orthologous group of genes that resulted from filamentous fungal lineage specific expansion.


The evolutionary history of cytochrome P450 genes in four filamentous Ascomycetes.

Deng J, Carbone I, Dean RA - BMC Evol. Biol. (2007)

Gene gains and losses on each branch of the species cladogram within 30 clans that were present in LCA. The column marked "Presence" shows the number of genes of each clan present in each fungus. For the remaining columns, filled rectangles represent gene gains and unfilled rectangles represent gene losses. The number following each rectangle represents the number of gains or losses. For colour codes, see Figure 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1828051&req=5

Figure 4: Gene gains and losses on each branch of the species cladogram within 30 clans that were present in LCA. The column marked "Presence" shows the number of genes of each clan present in each fungus. For the remaining columns, filled rectangles represent gene gains and unfilled rectangles represent gene losses. The number following each rectangle represents the number of gains or losses. For colour codes, see Figure 2.
Mentions: The number of duplication and loss events within individual clans that occurred on all branches of the species cladogram was inferred as described in Methods. Twenty-seven clans appeared to have had at least one duplication event before AN split from the LCA (Figure 4), independent of gain or loss model, suggesting that the LCA genome contained more than one member of these clans. In total, genes from these 27 clans accounted for 103 P450 genes in the LCA genome. In particular, clans containing larger numbers of genes were usually present in the LCA. For 28 clans which contained 4 genes or more, 24 of them were unambiguously inferred to be present in the LCA. Furthermore, we found a positive relationship (correlation coefficient = 0.7) between the number of genes within a current clan and the inferred number of ancestral genes of the clan present in the LCA genome. However, one obvious exception was clan CYP68, the third largest clan. It contained 20 P450 genes from the four fungi. However, only 2 CYP68 ancestral genes were inferred to be present in the LCA genome. Thus, it appeared that clan 68 must have experienced considerable expansion after the AN split. Our data suggest that there were 5 duplication events on branch 1, 4 in branch A, 2 in branch F and 3 in branch M (Figure 4). Therefore, clan 68 is a clear example of an orthologous group of genes that resulted from filamentous fungal lineage specific expansion.

Bottom Line: To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans.MG experienced more genes and clans gains compared to the other fungi.The exception was the NC lineage, which exhibited pure P450 gene loss.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA. dengj@email.unc.edu <dengj@email.unc.edu>

ABSTRACT

Background: The Cytochrome P450 system is important in fungal evolution for adapting to novel ecological niches. To elucidate the evolutionary process of cytochrome P450 genes in fungi with different life styles, we studied the patterns of gene gains and losses in the genomes of four filamentous Ascomycetes, including two saprotrophs (Aspergillus nidulans (AN) and Neurospora crassa (NC)) and two plant pathogens (Fusarium graminearum (FG) and Magnaporthe grisea (MG)).

Results: A total of 376 P450 genes were assigned to 168 families according to standard nomenclature. On average, only 1 to 2 genes per family were in each genome. To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans. Subsequently a novel approach based on parsimony was developed to build the evolutionary models. Based on these analyses, a core of 30 distinct clans of P450s was defined. The core clans experienced contraction in all four fungal lineages while new clans expanded in all with exception of NC. MG experienced more genes and clans gains compared to the other fungi. Parsimonious analyses unanimously supported one species topology for the four fungi.

Conclusion: The four studied fungi exhibit unprecedented diversity in their P450omes in terms of coding sequence, intron-exon structures and genome locations, suggesting a complicated evolutionary history of P450s in filamentous Ascomycetes. Clan classification and a novel strategy were developed to study evolutionary history. Contraction of core clans and expansion of novel clans were identified. The exception was the NC lineage, which exhibited pure P450 gene loss.

Show MeSH
Related in: MedlinePlus