Corresponding author: Wentao Niu (
Academic editor: B.W. Hoeksema
Lack of mitochondrial genome data of
Niu W, Yu S, Tian P, Xiao J (2018) Complete mitochondrial genome of
Reef-building coral species of the order
The unique characters of mitochondrial genome DNA (mitogenome), which include small size, fast evolutionary rate, simple structure, maternal inheritance, and high informational content, suggest that the constituting loci could be powerful markers for resolving ancient phylogenetic relationships (
Samples (voucher no. DYW15) of
Example of
We used next generation sequencing to perform low-coverage whole-genome sequencing according to the protocol (
The assembled consensus sequence was further annotated and analyzed. Preliminary annotation using DOGMA (
To validate the phylogenetic position of
Representative
Species | Family | Distribution | Length (bp) | GenBank accession number |
---|---|---|---|---|
|
|
Indo-Pacific | 17,697 |
|
|
|
Indo-Pacific | 18,168 |
|
|
|
Indo-Pacific | 16,463 |
|
|
|
Indo-Pacific | 17,825 |
|
|
|
Indo-Pacific | 18,006 |
|
|
|
West Atlantic | 16,138 |
|
|
|
West Atlantic | 16,138 |
|
|
|
West Atlantic | 16,138 |
|
|
|
West Atlantic | 17,245 |
|
|
|
West Atlantic | 16,906 |
|
|
|
West Atlantic | 15,841 |
|
The complete mitogenome of
The mitochondrial genome of
Organization of the mitochondrial genome of
Gene | Position | Length (bp) | Anticodon | Codon | Intergenic nucleotides* | Strand | ||
---|---|---|---|---|---|---|---|---|
From | To | Start | Stop | |||||
tRNAMet | 1 | 72 | 72 | UAC | 140 | H | ||
16S rRNA | 210 | 1905 | 1696 | 137 | H | |||
ND5 5’ | 1991 | 2701 | 711 | ATG | 85 | H | ||
ND1 | 2813 | 3760 | 948 | ATG | TAG | 111 | H | |
Cyt |
3763 | 4902 | 1140 | ATG | TAA | 2 | H | |
ND2 | 5111 | 6214 | 1104 | ATT | TAA | 208 | H | |
ND6 | 6216 | 6776 | 561 | ATG | TAA | 1 | H | |
ATP6 | 6776 | 7453 | 678 | ATG | TAA | -1 | H | |
ND4 | 7453 | 8892 | 1440 | ATG | TAG | -1 | H | |
12S rRNA | 9085 | 9996 | 912 | 192 | H | |||
COIII | 10127 | 10906 | 780 | ATG | TAG | 130 | H | |
COII | 11448 | 12155 | 708 | ATG | TAA | 541 | H | |
ND4L | 12137 | 12436 | 300 | ATG | TAA | -19 | H | |
ND3 | 12439 | 12780 | 342 | ATG | TAA | 2 | H | |
ND5 3’ | 12838 | 13941 | 1104 | TAG | 57 | H | ||
tRNATrp | 13940 | 14010 | 71 | ACU | -2 | H | ||
ATP8 | 14014 | 14211 | 198 | ATG | TAA | 3 | H | |
COI 5’ | 14920 | 15650 | 731 | ATG | 708 | H | ||
COI 3’ | 16726 | 17556 | 831 | TAG | 1075 | H |
Notes: * Data are number of nucleotides between the given gene and its previous gene, negative numbers indicate overlapping nucleotides.
Codon usage bias in different regions of mitochondrial genome of
Nucleotide composition in different regions of mitochondrial genome of
Gene/Region | T(%) | C(%) | A(%) | G(%) | A+T(%) | Size (bp) |
---|---|---|---|---|---|---|
ND5 | 46.12 | 12.51 | 21.60 | 19.78 | 67.72 | 1815 |
ND1 | 43.88 | 13.50 | 20.57 | 22.05 | 64.45 | 948 |
Cyt |
46.05 | 13.51 | 20.88 | 19.56 | 66.93 | 1140 |
ND2 | 46.74 | 13.04 | 20.29 | 19.93 | 67.03 | 1104 |
ND6 | 47.06 | 13.19 | 20.86 | 18.89 | 67.92 | 561 |
ATP6 | 46.46 | 14.01 | 20.65 | 18.88 | 67.11 | 678 |
ND4 | 44.65 | 14.24 | 20.00 | 21.11 | 64.65 | 1440 |
COIII | 41.40 | 15.60 | 20.60 | 22.30 | 62.00 | 780 |
COII | 39.41 | 12.57 | 25.71 | 22.32 | 65.12 | 708 |
ND4L | 43.67 | 10.67 | 27.33 | 18.33 | 71.00 | 300 |
ND3 | 49.71 | 9.06 | 18.71 | 22.51 | 68.42 | 342 |
ATP8 | 43.43 | 10.60 | 33.33 | 12.63 | 76.76 | 198 |
COI | 41.42 | 14.53 | 22.60 | 21.45 | 64.02 | 1562 |
|
44.50 | 13.40 | 21.60 | 20.50 | 66.10 | 11576 |
1st | 36.70 | 14.20 | 22.10 | 27.00 | 58.80 | 3859 |
2st | 47.90 | 18.00 | 18.20 | 15.90 | 66.10 | 3859 |
3st | 48.90 | 8.00 | 24.50 | 18.60 | 73.40 | 3858 |
tRNA | 25.17 | 20.28 | 32.87 | 21.68 | 58.04 | 143 |
rRNA | 31.75 | 12.65 | 35.43 | 20.17 | 67.18 | 2608 |
Overall | 40.57 | 13.43 | 25.35 | 20.65 | 65.92 | 17697 |
The
The
The PCG-codons use frequency of mitochondrial genome of
The genes encoding the small and large ribosomal RNA subunits (12S rRNA and 16S rRNA) were identified in
Putative secondary structures of two tRNA of
Inferred phylogenetic relationships based on the concatenated nucleotide sequences of 13 mitochondrial protein-coding genes using Bayesian inference (
Limited data are available on the mitogenomes of
This work was supported by the National Key Research and Development Plan under grant No. 2017YFA0604902 and the National Natural Science Foundation of China under grant No.41406161.