Mechanisms of intron gain and loss in Cryptococcus

Thomas J Sharpton¹ , Daniel E Neafsey² , James E Galagan² and John W Taylor¹

¹Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA

²Microbial Analysis Group Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA

author email corresponding author email

Genome Biology 2008, 9:R24doi:10.1186/gb-2008-9-1-r24


Published:	30 January 2008

Subject areas: Molecular biology, Evolution, Bioinformatics

Additional files

Additional data file 1:

Consecutive intron loss events.

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Additional data file 2:

Introns are binned according to the position (in base-pairs) of their occurrence in a coding sequence divided by the coding sequence length.

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Additional data file 3:

Intron loss in regard to intron order within the gene is well distributed, not requiring the 3'-most intron to be lost.

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Additional data file 4:

The large number of off-center, parallel lines illustrates this gene's highly repetitive sequence.

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Additional data file 5:

The strain relationships are designated in Additional data file 6. Positions with a sequence of 'X' designate the boundaries of D1 annotated introns.

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Additional data file 6:

The strain phylogeny is determined based on the history of strain synthesis as described in Results. The corresponding aligned CNN00420 ortholog for each strain is graphically represented in the cartoon next to each strain identifer. Horizontal bars correspond to sequence alignment positions: red lines indicate nucleotide sequence while white gaps indicate indels. Vertical blue bars correspond to annotated D1 introns. The phylogeny and the presence of unique sequence in the alignment corresponding to introns 3 and 5 in D1, its sibling JEC20, and parent B3502, suggest the gain of introns 3 and 5 in D1.

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Additional data file 7:

Exons (black lines) and introns (gold lines) are synthesized in the daughter strand during DNA replication. Repetitive sequences (red boxes) may create a looping out of the daughter strand and subsequent re-synthesis of the looped out region (here, an intron). After meiosis, the result is an allele with an extra repeat copy and, subsequently, an extra (acquired) intron.

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Additional data file 8:

Mathematica source code for the sojourn time density approximation.

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