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Open Access Highly Accessed Research article

De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs

Musa A Hassan1, Mariane B Melo1, Brian Haas2, Kirk D C Jensen1 and Jeroen P J Saeij1*

Author Affiliations

1 Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

2 Genome Annotation Research and Development, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA

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BMC Genomics 2012, 13:696  doi:10.1186/1471-2164-13-696

Published: 12 December 2012

Additional files

Additional file 1:

Nucleotide sequences of all the PASA transcripts.

Format: GZ Size: 7.1MB Download file

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Additional file 2:

A bed file with the genome coordinates of all the PASA transcripts.

Format: BED Size: 1.2MB Download file

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Additional file 3:

Sequences for Trinity contigs having invalid genome alignment in PASA but aligning to the ME49 genome in Blast.

Format: XLS Size: 90KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

The classes of transcripts obtained at different stages of our analysis pipeline.

Format: FASTA Size: 1.2MB Download file

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Additional file 5:

Blast search results of Trinity contigs rejected in PASA against ME49 known genes.)

Format: XLS Size: 370KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 6:

Evidence from ToxoDB showing splice junction tracks supporting the fusion of TGME49_005240 and TGME49_005230.

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Additional file 7:

Identities of PASA transcripts and the ME49 genes they overlap in addition to the average read coverage.

Format: XLS Size: 3.9MB Download file

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Additional file 8:

A figures showing the correlation between ability to reconstruct full transcripts of Toxoplasma genes and (A) expression (represented as reads per kilobase) and (B) RNA-seq read coverage. We binned the transcripts based on their RPK or raw read coverage values and we show the fractions of fully assembled transcripts in each bin (from a total of 2073 fully assembled genes). For this figure, fully assembled transcripts were defined as those producing ORFs that matched the ToxoDB proteins both in length and sequence (2073 total).

Format: PDF Size: 1.1MB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 9:

Table showing novel ME49 genes.

Format: DOCX Size: 14KB Download file

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Additional file 10:

Identities of PASA transcripts supporting alternative splicing classes and their relative expression values in 27 sequenced samples.

Format: DOCX Size: 14KB Download file

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