Background: Many physiological processes are influenced by nicotinic acetylcholine receptors (nAChR), ranging from neuromuscular and parasympathetic signaling to modulation of the reward system and long-term memory. Due to the complexity of the nAChR family and variable evolutionary rates among its members, their evolution in vertebrates has been difficult to resolve. In order to understand how and when the nAChR genes arose, we have used a broad approach of analyses combining sequence-based phylogeny, chromosomal synteny and intron positions.
Results: Our analyses suggest that there were ten subunit genes present in the vertebrate predecessor. The two basal vertebrate tetraploidizations (1R and 2R) then expanded this set to 19 genes. Three of these have been lost in mammals, resulting in 16 members today. None of the ten ancestral genes have kept all four copies after 2R. Following 2R, two of the ancestral genes became triplicates, five of them became pairs, and three seem to have remained single genes. One triplet consists of CHRNA7, CHRNA8 and the previously undescribed CHRNA11, of which the two latter have been lost in mammals but are still present in lizards and ray-finned fishes. The other triplet consists of CHRNB2, CHRNB4 and CHRNB5, the latter of which has also been lost in mammals. In ray-finned fish the neuromuscular subunit gene CHRNB1 underwent a local gene duplication generating CHRNB1.2. The third tetraploidization in the predecessor of teleosts (3R) expanded the repertoire to a total of 31 genes, of which 27 remain in zebrafish. These evolutionary relationships are supported by the exon-intron organization of the genes. Conclusions: The tetraploidizations explain all gene duplication events in vertebrates except two. This indicates that the genome doublings have had a substantial impact on the complexity of this gene family leading to a very large number of members that have existed for hundreds of millions of years.
aLRT SH-like trees paralogon 1
Phylogenetic aLRT SH-like trees of the neighboring gene families included in analysis of nAChR paralogon 1. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
Table paralogon 1
Table containing information about the nAChR neighboring gene families included in the analysis of the nAChR paralogon 1. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
aLRT SH-like trees paralogon 3
Phylogenetic aLRT SH-like tree of the neighboring gene families included in analysis of nAChR paralogon 3. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
Table paralogon 3
Table containing information about the nAChR neighboring gene families included in the analysis of the nAChR paralogon 3. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
aLRT SH-like trees paralogon 5
Phylogenetic aLRT SH-like tree of the neighboring gene families included in analysis of nAChR paralogon 5. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
Table paralogon 5
Table containing information about the nAChR neighboring gene families included in the analysis of the nAChR paralogon 5. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
aLRT SH-like trees paralogon 1 in teleosts
Phylogenetic aLRT SH-like tree of the neighboring gene families included in analysis of nAChR paralogon 1 in relation to 3R in teleosts. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
Table paralogon 1 in teleosts
Table containing information about the nAChR neighboring gene families included in the analysis of nAChR paralogon 1 in relation to 3R event in teleosts. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
Maximum likelihood tree nAChR gene family
The phylogenetic maximum likelihood tree of the nAChR genes in nexus format. The tree topology is supported by a non-parametric Ultra-Fast Bootstrap (UFBoot) and approximate Likelihood-Ratio Test (aLRT) with 1000 replicates. For simplicity only UFBoot values are shown. The taxa ID contains the species, the localization of the gene (chromosome/scaffold/contig number) and a number indicating the order on the chromosome/scaffold/contig if several genes are located on the same one. The taxa ID of human and zebrafish genes with annotated HGNC or ZFIN names, respectively, also contain these names. The assigned taxa ID and sequence information details are provided in Additional file 4.
