Computational protocol: Phylogenetic analysis of ionotropic L-glutamate receptor genes in the Bilateria, with special notes on Aplysia californica

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Protocol publication

[…] iGluR sequences for phylogenetic analysis were obtained from NCBI for all species except Branchiostoma belcheri (lancelet), which were obtained from the Chinese Lancelet Genome Project (). Sequences of all identified canonical iGluR proteins were aligned in MEGA7 [] using the MUSCLE (multiple sequence comparison by log-expectation) multiple aligner algorithm with default parameters []. Poorly aligned regions of the alignment were removed using trimAl [] with the –automated1 option to heuristically determine optimal trimming of the alignment, resulting in 473 positions used for phylogenetic analysis. Unrooted phylogenetic trees were then constructed in MEGA7 using maximum likelihood and 1000 bootstrap replicates with the LG amino acid substitution model [] with gamma distributed rates and five rate categories. The initial tree was obtained by applying the Neighbor-Joining algorithm to a matrix of pairwise distances estimated using a JTT model.Subtype specific trees were built to further clarify the relationships within orthologous groups using the same parameters as the full phylogeny, except 500 bootstrap replicates were performed. These same parameters were also used to build the Aplysia-only iGluR tree. Trees were visualized using FigTree (v1.4.2) []. Protein accessions for all sequences can be found in Additional file . […]

Pipeline specifications

Software tools MEGA, MUSCLE, trimAl, FigTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Aplysia californica
Chemicals N-Methylaspartate