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Figure 8 | BMC Evolutionary Biology

Figure 8

From: Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family

Figure 8

The phylogenetic tree obtained from the alignment of a total of 7 and 108 IRK AA sequences of tunicates (underlined) and vertebrates, respectively. (A) illustrates the upper part of the tree and (B) does the lower part. a and a, b and b', c and c', and d and d' indicate the continuation of branches from the upper part to the lower. The outgroup were seven bacterial IRK genes. Except for Halocynthia data, AA sequences are inferred from the established genome data bases, JGI, NCBI and GenBank, and Ensembl. Alignment was carried out by the ClustalX1.83 program. The gaps within nonpreserved regions were carefully deleted manually by the BioEdit program. The phylogenetic tree derived from the aligned data was then made by the Neighbor Joining Method in the Mega3 v3.1 program, using the Amino Poisson correction model with Gamma-distributed Rates among sites (Gamma parameter 2.0) and Bootstrap as the test of inferred branches (Repetition 500), including 270 sites with a pairwise deletion of Gaps/Missing Data. The character of the same color indicates the proximity of the chromosomal location of gene pairs between two subbranches. The closure by an interrupted line indicated that the chromosomal location between paired genes was very close in the order of 10 to 200 Kbp. The closure by dotted line indicates that linkage is weak. The Hox name in the parentheses indicates the equivalence of the chromosomal locations among different taxa by the presence of the specific Hox gene group. See also Additional file 5, chromosomal locations of genes. [see Additional file 5]

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