Fig. 4
Comparison between the C. blackwelliae mitogenome and the assembled transcripts. (A) BLASTN analysis of the mitogenome against the 34 transcripts assembled under the genome-guided mode of Trinity. Four transcripts representing transcription of almost all mitochondrial genes are indicated by arrows. Several independent transcripts corresponding to introns are indicated by black asterisks. (B) Comparison between the mitogenome (mt) and the four transcripts marked by arrows in Panel A. In the mitogenome map, different kinds of genes are colored using the same coloring schemes as Fig. 1. Only the seven intron-containing genes are marked, and other genes can be known by referring to Fig. 1 or Table 1. The four transcripts are manually connected with 10 N bases (for convenience of drawing the figure), and their actual connections are later verified by PCR assays as shown in Additional file 2: Fig. S5. Please also note that the 3rd exon of cox1 is extremely short (11 bp in length). Such a short exon cannot be shown by the genome comparison visualizer Easyfig, and hence we artificially add a brown line to indicate the position of the exon. By this way, all introns except nad4P505 are seen to be excised