PpMC1_alignment_iqtree.rar

Phylogenetic analysis

The dataset of 141 sequences of AAC, APC and distinct ATP mitochondrial carriers representing a range of eukaryotic taxa was obtained by BLAST search using human AAC1/APC1, yeast Aac2/Sal1p, A. thaliana AAC1/APC1, T. vaginalis HMP31 (homolog of distinct ADP/ATP carrier of T. gallinae) as a query. Additionally, the sequences of SCaMC-b, an APC lacking a regulatory domain found mainly in parasitic protists, the distinct ADP/ATP carrier of E. histolytica and A. locustae were included in the dataset. The sequences were aligned by MAFFT v7.453  using the L-INS-I algorithm and a maximum of 1,000 iterations. The obtained alignment was further trimmed by BMGE v1.12 with an entropy threshold stetted up to 0.7, resulting in an alignment of 254 positions. The maximum likelihood tree was generated by IQ-TREE v2.1.2 with the LG+F+R7 model suggested by ModelFinder. Branch supports were generated by ultra-fast bootstrap with 10,000 replicates. The tree with four P. pyriformis carriers and reference dataset (53 human carriers, 35 yeast carriers) was prepared in same way as described above. The alignment of 214 position was used to generated tree by LG+F+R6 model suggested by ModelFinder.