Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics

Additional file 1:

The 45 families of metazoan bHLH defined by our phylogenetic analyses. Families have been named as in our previous studies, i.e. according to the name (or its common abbreviation) of the first discovered or best-known member of the family [4,11]. The number of members per family in each of the different analysed genomes is reported. Each family has been tentatively assigned to the previously defined higher-order groups [2,4,11,17]. The number of 'orphan genes' is shown as a range due to the uncertainty in the allocation of some bHLHs to a given family. These uncertainties are indicated by '?' in the table. Explanations about all these uncertainties can be found in the additional files 4 to 15. In the cases of Amphimedon queenslandica, Nematostella vectensis and Hydra magnipapillata, additional explanations can be found in the main text and in Figures 2 and 3. The data from Ciona intestinalis come from [12] and have not been reanalysed in this study. Species abreviations: H. sap = Homo sapiens; C. int = Ciona intestinalis; B. flo = Branchiostoma floridae; S. purp = Strongylocentrotus purpuratus; D. mel = Drosophila melanogaster; T. cas = Tribolium castaneum; D. pul = Daphnia pulex; C. ele = Caenorhabditis elegans; L. gig = Lottia gigantea; C. sp = Capitella sp. I; N. vec = Nematostella vectensis; H. mag = Hydra magnipapillata; A. que = Amphimedon queenslandica.

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Additional file 2:

Information about the species used in this study. Abbreviations are those we used in the figures and the other additional files. Taxonomy is according to the NCBI web site.

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Additional file 3:

List of all the sequences used in our study in fasta format. For the identification of the sequences, we preferentially use, when available, the accession number of the proteins. In the cases where no protein sequences have been reported, i.e. most of the bHLHs we identified from whole genome shotgun traces, we indicate the identification of one of the trace sequences that encode the bHLH domain (the other trace identifications and the contigs we made are available upon request). In some cases, the bHLH was also found in ESTs and, in these cases, we also indicate the accession number(s) of the corresponding EST(s). For Nematostella vectensis and Branchiostoma floridae, we also indicate the identification of the transcripts models as determined using their genome assemblies.

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Additional file 4:

The bHLHs found in the genome of Homo sapiens. In this and the 11 following tables (additional files 4 to 15), we report all the bHLHs found in the indicated species, the family to which each of these metazoan orthologs bHLHs belong to, and the statistical support for their inclusion in a given family. For neighbour-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML), the indicated numbers are bootstrap support values; for Bayesian inference (BI), the numbers are posterior probabilities. Details about the phylogenetic methods can be found in the Methods section. «?» indicate bHLHs that cannot be confidently assigned to any family (they are reported as 'orphan' genes in additional file 1). In this table (bHLHs from Homo sapiens), the phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster and Branchiostoma floridae.

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Additional file 5:

The bHLHs found in the genome of Branchiostoma floridae. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster and Branchiostoma floridae.

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Additional file 6:

The bHLHs found in the genome of Strongylocentrotus purpuratus. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster and Strongylocentrotus purpuratus.

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Additional file 7:

The bHLHs found in the genome of Drosophila melanogaster. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster and Branchiostoma floridae.

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Additional file 8:

The bHLHs found in the genome of Tribolium castaneum. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster, Daphnia pulex and Tribolium castaneum.

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Additional file 9:

The bHLHs found in the genome of Daphnia pulex. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster, Tribolium castaneum and Daphnia pulex.

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Additional file 10:

The bHLHs found in the genome of Caenorhabditis elegans. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster, and Caenorhabditis elegans.

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Additional file 11:

The bHLHs found in the genome of Lottia gigantea. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster and Lottia gigantea.

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Additional file 12:

The bHLHs found in the genome of Capitella sp. I. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster and Capitella sp I.

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Additional file 13:

The bHLHs found in the genome of Nematostella vectensis. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster, Hydra magnipapillata and Nematostella vectensis.

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Additional file 14:

The bHLHs found in the genome of Hydra magnipapillata. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster, Hydra magnipapillata and Nematostella vectensis.

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Additional file 15:

The bHLHs found in the genome of Amphimedon queenslandica. The phylogenetic studies have been done on a multiple alignment with all bHLHs from Homo sapiens, Drosophila melanogaster and Amphimedon queenslandica.

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Additional file 16:

Gene assemblies for the bHLHs from Amphimedon queenslandica. Nucleotide sequences of the contigs we assembled for each bHLH gene are shown together with the corresponding predicted proteins using Genscan and Geneid. In some cases, we also report additional sequences from EST data and from PCR products.

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Additional file 17:

Summary of the study of putative physical linkages between bHLH genes from Nematostella vectensis. In this table, we report the different bHLH genes that are physically linked, the families and the genomic scaffolds to which they belong, as well as their position in these scaffolds.

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Additional file 18:

The bHLHs in fungi. In this table, we report the list of the studied species, their taxonomy and the total number of bHLHs found in each species.

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