Research
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
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* Corresponding authors: Jason E Stajich jason_stajich@berkeley.edu - Scott W Roy royscott@ncbi.nlm.nih.gov
1 Department of Molecular Genetics and Microbiology, Center for Genome Technology, Institute for Genome Science and Policy, Duke University, Durham, NC 27710, USA
2 Miller Institute for Basic Research and Department of Plant and Microbial Biology, 111 Koshland Hall #3102, University of California, Berkeley, CA 94720-3102, USA
3 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
Genome Biology 2007, 8:R223 doi:10.1186/gb-2007-8-10-r223
Published: 19 October 2007Additional files
Additional data file 1:
The left tree was built with a MrBayes using 30 orthologous proteins with the position of S. nodorum constrained based on previously published phylogenies. The tree on the right is the strict consensus tree of 116 MP trees built using Dollo parsimony and the matrix of presence or absence of intron positions. Nodes that are not present in all 116 trees are collapsed. Species groups are colored so that Euascomycota are in dark green, Hemiascomycota in red, archiascomycete S. pombe in yellow, Basidiomycota excluding U. maydis in blue, U. maydis in purple, zygomycete R. oryzae in orange, vertebrates in pink, and green plant A. thaliana in light green.
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Additional data file 2:
The phylogenetic tree used in the simulation data analysis.
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Additional data file 3:
Genomes and annotations used for this analysis with the source and version of the annotation indicated, with references for previously published annotations.
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Additional data file 4:
Not all methods reconstruct a value for the Crown ancestor as this requires an outgroup and additional assumptions.
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Additional data file 5:
Not all methods estimate gain and loss from Crown ancestor as this requires an outgroup and additional assumptions.
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Additional data file 6:
Summary statistics for intron length, intron frequency, total length per genome, total intron count, total length of coding sequence, and genome size.
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Additional data file 7:
The file also contains the customized software for running NYK and the RG intron calculations.
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Additional data file 8:
Introns are represented by numbers in the alignment indicating the phase of the intron (0,1,2) as defined by the position in the codon the intron falls within. Coding sequence alignments and unaligned sequences are available from the authors.
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