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BIOINF 16-018: Evolution of Fungal U3 snoRNAs: Structural Variation and Introns

Sebastian Canzler, Peter F. Stadler, Jana Hertel

Taxonomic Tree and Genome Information

An NCBI-based taxonomic classification of all 147 fungal organisms that were used in our publication can be found here:
Taxonomic Tree of Fungi, except of Pezizomycotina
Taxonomic Tree of Pezizomycotina

Machine readable information about the fungal organisms, such as genome sources and 3-letter abbreviations are given here:
Genome Information

Alignments

A summary file containing the total amount of detected U3 transcripts and intron-interrupted transcripts can be found here

Lineage specific fasta files, alignments, and gene structures of all U6 sequence that have been retrieved during our analysis can be accessed in the following table:

Kingdom Phylum Subphylum Class Precursor Fasta Precursor Alignment Mature Alignment Intron Fasta
Fungi Microsporidia fasta aln|stk -|- -|-
Fungi incertae sedis Mucoromycotina fasta aln|stk -|- -|-
Chytridiomycota fasta aln|stk -|- -|-
Blastocladiomycota fasta aln|stk -|- -|-
Basidiomycota fasta aln|stk aln|stk fasta
Ascomycota Taphrinomycotina fasta aln|stk -|- -|-
Saccharomycotina fasta aln|stk aln|stk fasta
Pezizomycotina Dothideomycetes fasta aln|stk aln|stk fasta
Eurotiomycetes fasta aln|stk aln|stk fasta
Leotiomycetes fasta aln|stk aln|stk fasta
Sordariomycetes fasta aln|stk aln|stk fasta

Intron Information

Machine readable information about all extracted introns, such as:
  • precise splice site position within the U3 precursor
  • intron length
  • distance of branch point adenosine to 3' splice site
  • 5' splice site sequence motif
  • branch site sequence motif
  • 3' splice site sequence motif
is provided here: U3_Introns

Intron Homology

To determine whether introns of different U6 transcripts are related the pairwise sequence identities of all intron pairs and was calculated intron positions were checked for similarities. Operationally, a set of introns is defined as homologous if each of its members share sequence identity of at least 65%. Naturally, the evolution of introns is not constrained very much, such that a signal of common origin may be lost already within a few million years. Thus, lower similarities cannot be interpreted as proof that sequences are not related by common descent.
Within this heatmap, three different cluster types are detectable: