Apusomonadida genome sequences (Thecomonas trahens) were searched at http://www.broadinstitute.org/annotation/genome/multicellularity_project/.org/annotation/genome/multicellularity_project/
Additionally, genomes were searched at http://www.broadinstitute.org/annotation/genome/multicellularity_project/GenomesIndex.html, http://genome.jgi.doe.gov/and http://cyanophora.rutgers.edu/cyanophora/home.php.php
Cartilaginous fish elephant shark (Callorhinchus milii) was searched at http://esharkgenome.imcb.a-star.edu.sg/, and lamprey (Petromyzon marinus) at http://jlampreygenome.imcb.a-star.edu.sg/.sg/
Genomes of Hemichordates (Saccoglossus kowalevskii), Cnidaria (Hydra magnipapillata, Nematostella vectensis), Choanoflagellates (Monosiga brevicollis), and Placozoa (Trichoplax adhaerens) were searched at http://www.metazome.net/.net/
For Testudines and Archosauria, genomes of 48 bird species as well as genomes of alligator (Alligator mississippiensis) and green turtle (Chelonia mydas) were searched at http://phybirds.genomics.org.cn/index.jsp.jsp
Trypanosoma brucei 927 genome sequence data were searched at geneDB (http://www.genedb.org) [40].
Protist data were searched at JGI (http://genome.jgi-psf.org/), in particular Cryptophyta (Guillardia theta), Haptophyta (Emiliana huxleyii), Heterolobosea (Naegleria gruberi), and Stramenopiles (Thalassiosira pseudonana, Phytophtora ramorum).
The proteomes of other organisms were not analysed systematically, but were searched at GenBank, EuPATHdb http://eupathdb.org, or the Joint Genome Institute.
Second, the massively parallel signature sequencing (MPSS) database was searched at the rice MPSS project (http://mpss.udel.edu/rice/) for 20-base signatures from 22 mRNA libraries representing 18 different tissues/organs in rice expression evidence analysis.
