Fig 1.
The simple de novo mitochondrial genome assembly pipeline for the Taiwanese macaque mitochondrial genome.
Fig 2.
Illustration of checking for boundary overlap to finish the mitochondrial genome.
Circular mitochondrial DNA was assembled to scaffolds in linear form each of which exhibited overlapped regions at the ends.
Table 1.
Library statistics of quality reads and coverage information.
Table 2.
Comparison of mitochondrial size between macaque species.
Fig 3.
The organization of the mitogenome of M. cyclopis.
The outer and the inner circles represent the H- and L-strands, respectively. The tRNA, rRNA, protein-coding genes and control region are represented in green, red, blue and gray, respectively.
Table 3.
Summary of the mitochondrial genome organization of M. cyclopis.
Table 4.
Characteristics of the D-loop/control region of macaque species.
Table 5.
Results of sequence alignment of the complete M. cyclopis mitochondrial genome against the three existing datasets of M. cyclopis partial mitochondrial fragments.
Table 6.
List of sequenced fragments of M. cyclopis mitochondrial genome.
Fig 4.
Phylogenetic analysis based on whole mitochondrial genome sequence.
The evolutionary history was inferred by MrBayes. The scale is 1.0 expected changes per site. The outgroup for evolutionary analysis is Homo sapiens mitochondrion with GenBank acc. NC_012920.
Table 7.
Pair-wise sequence similarity between macaques by LAGAN.
Fig 5.
Insertion in tRNA-Tyr of the WANCY tRNA-gene cluster.
Multiple sequence alignment of the WANCY tRNA-gene cluster identified a 17 bp insertion at the 3’-end of tRNA-Tyr specific to M. sylvanus and a 24 bp insertion at the 3’-end of tRNA-Tyr specific to M. mulatta. The red box showed the overlap region between tRNA-Tyr and COX1. The blue line showed the 3’-end boundary of tRNA-Tyr while checking with tRNAscan-SE and MITOS.
Fig 6.
COX2/tRNA-Lys intergenic region.
A short CT repeat region in red box is present in the fascicularis group but absent in species of the sinica group. The blue line represents the boundary of COX2 and tRNA-Lys respectively. In sequence alignment, * (asterisk) character indicates positions which are fully conserved.
Fig 7.
The less conserved region (red box) in the 3’-end of tRNA-Lys was explored by multiple sequence alignment. The blue line represents the boundary of 5’-end and 3’-end of tRNA-Lys respectively. In sequence alignment, * (asterisk) character indicates positions which are fully conserved.
Table 8.
Comparison of start and stop codons of protein-coding genes of seven species/subspecies of macaques.