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Fig. 2 | Genome Biology

Fig. 2

From: Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Fig. 2

Duplications and repeats in mitoVGP assemblies. a Comparison of mitoVGP, NOVOPlasty, and RefSeq mitogenome assemblies for the sand lizard (Lacerta agilis). Duplicated genes missing from the reference and NOVOPlasty assemblies: MT-CYB, MT-TT, MT-TP (brown bar). Gray, read coverage: PacBio CLR 34× and Nanopore 46× mean coverage. b Golden eagle (Aquila chrysaetos), where the current RefSeq sequence (top) lacks a large fraction of a tandem repeat in the CR and 10 bp from the start of the MT-TF gene (brown bar). Mean CLR coverage 170×. c Kakapo (Strigops habroptilus), where the RefSeq sequence (top) lacks the entire CR. Mean coverage 99×. d Maguari stork (Ciconia maguari). Duplicated genes: MT-CYB, MT-TT, MT-TP, MT-ND6, and MT-TE (brown bar). Mean CLR coverage 209×. e Warty frogfish (Antennarius maculatus). Duplicated genes: MT-TV and MT-RNR2 (brown bar). Mean CLR coverage 21×. The rRNA genes are colored in red, tRNA genes in green, other genes in yellow, and the CR/intergenic region in blue. Homologous regions are highlighted in orange, tandem repeats in shades of blue, gaps as dashed lines and duplicated genes with brown bars. Long read coverage depth represented by the gray track. All labels in kbp. Coordinates relative to the PacBio mitoVGP assembly

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