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Each sequenced sample was prepared according to the Illumina protocols.

Furthermore, the error rate needs to be <1 in 100 000 bases, the coverage at least 98%, and the cost no more than $10 000 for each sequenced genome [10].

Custom BLAST databases of each sequenced commensal were compiled to use for further analysis.

We mapped the Illumina mate-paired reads to these 454-Titanium contigs to define the "true" insert length of each sequenced insert.

Multiple representatives from each sequenced amoebozoan lineage were included to deeply sample the molecular diversity available within Amoebozoa and to assess congruence with other amoebozoan phylogenies.

Each sequenced molecule is referred to as a "tag".

Each sequenced sample was prepared using Illumina protocols.

Breed and population information is provided for each sequenced animal in Additional file 1.

Samples T3 and N1 were each sequenced over two different Illumina flow cells.

An average of 19.4 M reads from each sequenced sample successfully aligned to its corresponding transcriptome.

Positive clones were selected to sequence in both directions and each sequenced twice independently.

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