Corresponding author: Ting-Jing Li (
Academic editor: A. Köhler
To date, only one mitochondrial genome (mitogenome) in the
Zhang Q-H, Huang P, Chen B, Li T-J (2018) The complete mitochondrial genome of
Animal mitochondrial genomes (mitogenomes) have been widely used in studies of molecular evolution, population genetic structure, and phylogeny because of their stable gene content, rapid evolutionary rate, relatively conserved gene arrangement, maternal inheritance, and infrequent recombination (
In the present study, the complete mitogenome of
The information of
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17972 | 38 |
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This study |
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16953 | 41 |
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16616 | 34 |
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14741 | 34 |
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16619 | 37 |
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16342 | 33 |
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15779 | 37 |
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15902 | 37 |
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16937 | 35 |
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16475 | 37 |
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16101 | 37 |
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17137 | 37 |
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16752 | 37 |
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The specimens of
The Illumina TruSeq library was constructed from the gDNA with the average length of the inserted fragment of 480 bp. The library was sequenced on a full run of Illumina Hiseq 2500 with 500 cycles and paired-end sequencing (250 bp reads). High-quality reads were used in
Eleven known mitogenome sequences in the family
The complete mitogenome of
The mitochondrial genome of
Mitochondrial genome annotation of
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F | 1–63 | 63 | 30–32 GAT | |||
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F | 63–127 | 65 | 93–95 CAT | -1 | ||
non-coding region | 1946 | ||||||
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R | 2074–2138 | 65 | 2108–2110 TTG | 0 | ||
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F | 2142–2208 | 67 | 2173–2175 CAT | 3 | ||
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F | 2209–3234 | 1026 | ATC | TAA | 0 | |
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F | 3249–3315 | 67 | 3280–3282 TCA | 14 | ||
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R | 3308–3374 | 67 | 3342–3344 GCA | -8 | ||
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R | 3383–3447 | 65 | 3416–3418 GTA | 8 | ||
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F | 3446–4981 | 1536 | TTG | TAA | -2 | |
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F | 5006–5073 | 68 | 5035–5037 TAA | 24 | ||
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F | 5074–5752 | 679 | ATC | T- | 0 | |
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F | 5753–5824 | 72 | 5785–5787 CTT | 0 | ||
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F | 5824–5893 | 70 | 5858–5860 GTC | -1 | ||
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F | 5894–6049 | 156 | ATC | TAA | 0 | |
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F | 6049–6720 | 672 | ATG | TAA | -1 | |
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F | 6742–7525 | 784 | ATG | T- | 21 | |
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F | 7526–7593 | 68 | 7556–7558 TCC | 0 | ||
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F | 7594–7947 | 354 | ATT | TAA | 0 | |
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F | 7947–8011 | 65 | 7977–7979 TGC | -1 | ||
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F | 8011–8074 | 64 | 8038–8040 TCG | -1 | ||
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F | 8078–8147 | 70 | 8108–8110 GTT | 3 | ||
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F | 8147–8206 | 60 | 8168–8170TCT | -1 | ||
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F | 8214–8277 | 64 | 8244–8246 TTC | 7 | ||
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R | 8277–8342 | 66 | 8307–8309 GAA | -1 | ||
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R | 8344–10032 | 1689 | ATT | TAA | 1 | |
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R | 10033–10096 | 64 | 10065–10067 GTG | 0 | ||
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R | 10097–11402 | 1306 | ATA | T- | 0 | |
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R | 11399–11677 | 279 | ATT | TAA | -4 | |
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F | 11726–11789 | 64 | 11756–11758 TGT | 48 | ||
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R | 11789–11858 | 70 | 11823–11825 TGG | -1 | ||
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F | 11860–12399 | 540 | ATG | TAA | 1 | |
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F | 12403–13534 | 1132 | ATG | T- | 3 | |
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F | 13544–13612 | 69 | 13572–13574 TGA | 9 | ||
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R | 13640–13707 | 68 | 13676–13678 TAG | 27 | ||
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R | 13708–14676 | 969 | ATA | TAA | 0 | |
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R | 14682–16044 | 1363 | 5 | |||
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R | 16043–16106 | 64 | 16074–16076 TAC | -2 | ||
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R | 16107–16894 | 788 | 0 | |||
Control region | 16895–17972 | 1078 | 0 |
The gene order of 13
Mitochondrial gene arrangement of 12 species of
To date, the nucleotide compositions of ten complete mitogenomes have been reported in the family
Nucleotide composition of different regions in all complete
Species | Regions | Size(bp) | A% | T% | G% | C% | (A+T)% | AT-skew | GC-skew |
---|---|---|---|---|---|---|---|---|---|
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Whole genome | 17972 | 39.53 | 39.9 | 8.06 | 12.51 | 79.43 | -0.005 | -0.216 |
Protein coding genes | 11122 | 33.15 | 45.12 | 10.02 | 11.72 | 78.27 | -0.153 | -0.078 | |
tRNA genes | 1525 | 42.69 | 40.72 | 9.25 | 7.34 | 83.41 | 0.024 | 0.115 | |
rRNA genes | 2151 | 41.89 | 42.4 | 10.79 | 4.93 | 84.29 | -0.006 | 0.373 | |
Control region | 1078 | 39.8 | 44.9 | 6.49 | 8.81 | 84.69 | -0.06 | -0.152 | |
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Whole genome | 16953 | 39.55 | 41.05 | 6.02 | 13.38 | 80.61 | -0.019 | -0.38 |
Protein coding genes | 11305 | 35.2 | 43.48 | 10.12 | 11.21 | 78.67 | -0.105 | -0.051 | |
tRNA genes | 1787 | 44.66 | 38.84 | 8.95 | 7.55 | 83.49 | 0.07 | 0.085 | |
rRNA genes | 2180 | 43.62 | 38.35 | 5.14 | 12.89 | 81.97 | 0.064 | 0.43 | |
Control region | 308 | 43.83 | 46.1 | 1.3 | 8.77 | 89.94 | -0.025 | -0.742 | |
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Whole genome | 16616 | 41.97 | 41.45 | 5.8 | 10.79 | 83.41 | 0.006 | -0.301 |
Protein coding genes | 10852 | 36.77 | 46.61 | 8.11 | 8.51 | 83.38 | -0.118 | -0.024 | |
tRNA genes | 1318 | 44.76 | 42.64 | 6.98 | 5.61 | 87.4 | 0.024 | 0.108 | |
rRNA genes | 2257 | 43.95 | 41.25 | 4.3 | 10.5 | 85.2 | 0.032 | 0.419 | |
Control region | 1096 | 39.05 | 46.53 | 6.84 | 7.57 | 85.58 | -0.087 | -0.051 | |
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Whole genome | 14741 | 43.09 | 41.65 | 5.32 | 9.95 | 84.73 | 0.017 | -0.303 |
Protein coding genes | 10852 | 36.77 | 46.61 | 8.11 | 8.51 | 83.38 | -0.118 | -0.024 | |
tRNA genes | 1258 | 47.22 | 41.02 | 6.52 | 5.25 | 88.24 | 0.07 | 0.108 | |
rRNA genes | 1932 | 43.27 | 43.22 | 9.16 | 4.35 | 86.49 | 0.001 | 0.356 | |
Control region | * | * | * | * | * | * | * | * | |
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Whole genome | 16619 | 43.39 | 39.55 | 5.91 | 11.15 | 82.94 | 0.046 | -0.307 |
Protein coding genes | 11022 | 35.48 | 45.16 | 9.54 | 9.82 | 80.65 | -0.12 | -0.015 | |
tRNA genes | 1486 | 44.01 | 42.13 | 7.67 | 6.19 | 86.14 | 0.022 | 0.107 | |
rRNA genes | 2176 | 40.3 | 45.96 | 9.38 | 4.37 | 86.26 | -0.066 | 0.365 | |
Control region | 1316 | 42.25 | 46.05 | 5.17 | 6.53 | 88.3 | -0.043 | -0.117 | |
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Whole genome | 15779 | 40.32 | 39.8 | 5.8 | 14.08 | 80.12 | 0.006 | -0.417 |
Protein coding genes | 11159 | 34.32 | 43.46 | 10.36 | 11.86 | 77.78 | -0.118 | -0.067 | |
tRNA genes | 1487 | 45.46 | 40.15 | 8.14 | 6.25 | 85.61 | 0.062 | 0.131 | |
rRNA genes | 2299 | 44.58 | 39.58 | 11.44 | 4.39 | 84.17 | 0.059 | 0.445 | |
Control region | 166 | 46.99 | 45.78 | 0 | 7.23 | 92.77 | 0.013 | -1 | |
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Whole genome | 15902 | 38.88 | 40.51 | 6.07 | 14.53 | 79.39 | -0.021 | -0.41 |
Protein coding genes | 11119 | 33.73 | 43.37 | 10.56 | 12.35 | 77.09 | -0.125 | -0.078 | |
tRNA genes | 1505 | 45.12 | 40.47 | 8.37 | 6.05 | 85.58 | 0.054 | 0.161 | |
rRNA genes | 1569 | 43.91 | 39.64 | 12.11 | 4.33 | 83.56 | 0.051 | 0.473 | |
Control region | 200 | 49 | 39.5 | 0.5 | 11 | 88.5 | 0.107 | -0.913 | |
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Whole genome | 16475 | 40.3 | 41.44 | 5.43 | 12.83 | 81.74 | -0.014 | -0.406 |
Protein coding genes | 11197 | 34.99 | 44.75 | 9.42 | 10.83 | 79.74 | -0.122 | -0.07 | |
tRNA genes | 1514 | 44.58 | 41.35 | 8.12 | 5.94 | 85.93 | 0.038 | 0.155 | |
rRNA genes | 2319 | 45.11 | 40.06 | 10.52 | 4.31 | 85.17 | 0.059 | 0.419 | |
Control region | 132 | 50.76 | 41.67 | 0 | 7.58 | 92.42 | 0.098 | -1 | |
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Whole genome | 16101 | 40.65 | 40.3 | 5.86 | 13.19 | 80.95 | 0.004 | -0.384 |
Protein coding genes | 10653 | 34.5 | 44.08 | 9.74 | 11.68 | 78.58 | -0.122 | -0.09 | |
tRNA genes | 1481 | 45.51 | 40.51 | 7.97 | 6.01 | 86.02 | 0.058 | 0.14 | |
rRNA genes | 2079 | 43.67 | 39.15 | 11.5 | 5.68 | 82.83 | 0.055 | 0.339 | |
Control region | 60 | 48.33 | 41.67 | 8.33 | 1.67 | 90 | 0.074 | 0.667 | |
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Whole genome | 17136 | 42.8 | 41.81 | 5.39 | 10 | 84.61 | 0.012 | -0.3 |
Protein coding genes | 11276 | 35.82 | 46.78 | 8.78 | 8.62 | 82.6 | -0.133 | 0.009 | |
tRNA genes | 1506 | 45.88 | 40.44 | 7.9 | 5.78 | 86.32 | 0.063 | 0.155 | |
rRNA genes | 2126 | 43.7 | 40.87 | 10.68 | 4.75 | 84.57 | 0.033 | 0.384 | |
Control region | 586 | 67.24 | 32.42 | 0 | 0.34 | 99.66 | 0.349 | -1 |
*
Two other parameters, AT-skew and GC-skew, have been widely used to measure the nucleotide compositional behaviors of mitogenome in addition to the A + T content (
Among the
Nucleotide composition of all 13
In the 13
There is a total of 3697 codons in
Relative synonymous codon usage (RSCU) in
There are 23 tRNAs found in
Secondary structures of 23 tRNAs of
The length of
The
The best fitting model GTR + G + I was selected for
The phylogenetic relationships were established by the 13
According to nine complete mitogenomes reported in the family
We are very grateful to James M. Carpenter and Rogério Lopes for their critical comments. This study was funded by the National Natural Science Foundation of China (Nos: 31772490, 31372247, 31000976, 31372265), Young Talent Incubation Program of Chongqing Normal University (14CSDG07), and the Par-Eu Scholars Program.