Research Article |
Corresponding author: Wentao Niu ( wentaoniu@tio.org.cn ) Academic editor: Bert W. Hoeksema
© 2022 Peng Tian, Zhiyu Jia, Bingbing Cao, Wei Wang, Jiaguang Xiao, Wentao Niu.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Tian P, Jia Z, Cao B, Wang W, Xiao J, Niu W (2022) Complete mitochondrial genome sequences of Physogyra lichtensteini (Milne Edwards & Haime, 1851) and Plerogyra sinuosa (Dana, 1846) (Scleractinia, Plerogyridae): characterisation and phylogenetic analysis. ZooKeys 1114: 21-34. https://doi.org/10.3897/zookeys.1114.85028
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In this study, the whole mitochondrial genomes of Physogyra lichtensteini and Plerogyra sinuosa have been sequenced for the first time. The length of their assembled mitogenome sequences were 17,286 bp and 17,586 bp, respectively, both including 13 protein-coding genes, two tRNAs, and two rRNAs. Their mitogenomes offered no distinct structure and their gene order were the same as other typical scleractinians. Based on 13 protein-coding genes, a maximum likelihood phylogenetic analysis showed that Physogyra lichtensteini and Plerogyra sinuosa are clustered in the family Plerogyridae, which belongs to the “Robust” clade. The 13 tandem mitogenome PCG sequences used in this research can provide important molecular information to clarify the evolutionary relationships amongst stony corals, especially at the family level. On the other hand, more advanced markers and more species need to be used in the future to confirm the evolutionary relationships of all the scleractinians.
Evolutionary relationships, mitogenome data, Plerogyridae, “Robust” clade
The order Scleractinia (Cnidaria, Anthozoa), including numerous reef-building coral species, is important as the constructors of coral reefs as an ecosystem. The mitogenome data of cnidarians contain important phylogenetic information for understanding their evolutionary history (
In Scleractinia, three main clades have been defined based on molecular analyses, “Complex”, “Robust”, and “Basal” (
Physogyra lichtensteini (Milne Edwards & Haime, 1851) and Plerogyra sinuosa (Dana, 1846) are covered by round to irregularly bifurcating vesicles during the day and active, open polyps at night (
In this research, the complete mitochondrial genomes of Physogyra lichtensteini and Plerogyra sinuosa are sequenced and their genome structures are analysed for the first time. The phylogenetic analyses of these two species, based on 13 protein coding genes (PCGs) of the mitogenome, in combination with another 42 species of other genera of Scleractinia and two species of Corallimorphidae Hertwig 1882 (order Corallimorpharia) as outgroups, because they are closely related to Scleractinia in evolutionary terms. This helps determine their phylogenetic status and facilitate further study on stony coral evolutionary and phylogenetic relationships.
Samples of Physogyra lichtensteini (Fig.
In this study, two methods were used to obtain the mitogenomes of Physogyra lichtensteini and Plerogyra sinuosa, respectively. The complete mitogenome of Plerogyra sinuosa was obtained through a PCR approach using the primer pairs designed by
The phylogenetic positions of Physogyra lichtensteini and Plerogyra sinuosa were inferred using 13 tandem mitogenome PCG sequences (ND5 + ND1 + Cytb + ND2 + ND6 + ATP6 + ND4 + COIII + COII + ND4L + ND3 + ATP8 + COI) (
Species | Family | Mitogenome length (bp) | GenBank accession number | |
1 | Physogyra lichtensteini | Plerogyridae | 17,286 | MW970409 |
2 | Plerogyra sinuosa | Plerogyridae | 17,586 | MW936598 |
3 | Acropora horrida | Acroporidae | 18,480 | NC_022825 |
4 | Alveopora japonica | Acroporidae | 18,144 | MG851913 |
5 | Astreopora explanata | Acroporidae | 18,106 | KJ634269 |
6 | Isopora palifera | Acroporidae | 18,725 | KJ634270 |
7 | Montipora cactus | Acroporidae | 17,887 | NC_006902 |
8 | Agaricia fragilis | Agariciidae | 18,667 | KM051016 |
9 | Agaricia humilis | Agariciidae | 18,735 | NC_008160 |
10 | Pavona clavus | Agariciidae | 18,315 | NC_008165 |
11 | Pavona decussata | Agariciidae | 18,378 | KP231535 |
12 | Desmophyllum pertusum | Caryophylliidae | 16,150 | FR821799 |
13 | Solenosmilia variabilis | Caryophylliidae | 15,968 | KM609293 |
14 | Dendrophyllia arbuscula | Dendrophylliidae | 19,069 | KR824937 |
15 | Tubastraea coccinea | Dendrophylliidae | 19,094 | KX024566 |
16 | Duncanopsammia peltata | Dendrophylliidae | 18,966 | NC_024671 |
17 | Fimbriaphyllia ancora | Euphylliidae | 18,875 | NC_015641 |
18 | Galaxea fascicularis | Euphylliidae | 18,751 | NC_029696 |
19 | Colpophyllia natans | Faviidae | 16,906 | NC_008162 |
20 | Mussa angulosa | Faviidae | 17,245 | DQ643834 |
21 | Fungiacyathus stephanus | Fungiacyathidae | 19,381 | JF825138 |
22 | Gardineria hawaiiensis | Gardineriidae | 19,430 | MT376619 |
23 | Echinophyllia aspera | Lobophylliidae | 17,697 | MG792550 |
24 | Dipsastraea rotumana | Merulinidae | 16,466 | MH119077 |
25 | Hydnophora exesa | Merulinidae | 17,790 | MH086217 |
26 | Orbicella faveolata | Merulinidae | 16,138 | AP008978 |
27 | Platygyra carnosa | Merulinidae | 16,463 | JX911333 |
28 | Letepsammia formosissima | Micrabaciidae | 19,048 | MT705247 |
29 | Letepsammia superstes | Micrabaciidae | 19,073 | MT706035 |
30 | Rhombopsammia niphada | Micrabaciidae | 19,542 | MT706034 |
31 | Madrepora oculata | Oculinidae | 15,841 | JX236041 |
32 | Plesiastrea versipora | Plesiastreidae | 15,320 | MH025639 |
33 | Pocillopora eydouxi | Pocilloporidae | 17,422 | EF526303 |
34 | Seriatopora hystrix | Pocilloporidae | 17,059 | EF633600.2 |
35 | Madracis mirabilis | Pocilloporidae | 16,951 | NC_011160 |
36 | Stylophora pistillata | Pocilloporidae | 17,177 | NC_011162 |
37 | Goniopora columna | Poritidae | 18,766 | JF825141 |
38 | Porites fontanesii | Poritidae | 18,658 | NC_037434 |
39 | Porites lobata | Poritidae | 18,647 | KU572435 |
40 | Porites rus | Poritidae | 18,647 | NC_027526 |
41 | Psammocora profundacella | Psammocoridae | 16,274 | MT576637 |
42 | Astrangia poculata | Astrangiidae | 14,853 | NC_008161 |
43 | Pseudosiderastrea tayami | Siderastreidae | 19,475 | KP260633 |
44 | Siderastrea radians | Siderastreidae | 19,387 | NC_008167 |
45 | Corallimorphus profundus | Corallimorphidae | 20,488 | KP938440 |
46 | Corynactis californica | Corallimorphidae | 20,715 | NC_027102 |
The mitochondrial genome sizes of Physogyra lichtensteini and Plerogyra sinuosa are 17,286 bp and 17,586 bp, respectively, both including 13 PCGs, two tRNA (tRNAMet, tRNATrp), and two rRNA genes (Tables
Gene | Position | Length (bp) | Anticodon | Codon | Intergenic nucleotides* | Strand† | ||
---|---|---|---|---|---|---|---|---|
From | To | Start | Stop | |||||
tRNAMet | 1 | 72 | 72 | CAU | 1228 | H | ||
16S rRNA | 270 | 1967 | 1698 | 197 | H | |||
ND5 5’ | 1998 | 2708 | 711 | ATG | 30 | H | ||
ND1 | 2817 | 3764 | 948 | ATG | TAG | 108 | H | |
Cytb | 3767 | 4906 | 1140 | ATG | TAA | 2 | H | |
ND2 | 5124 | 6218 | 1095 | TTA | TAA | 217 | H | |
ND6 | 6219 | 6779 | 561 | ATG | TAA | 0 | H | |
ATP6 | 6779 | 7453 | 675 | ATG | TAA | −1 | H | |
ND4 | 7453 | 8892 | 1440 | ATG | TAG | −1 | H | |
12S rRNA | 8890 | 9800 | 911 | −3 | H | |||
COIII | 9794 | 10573 | 780 | ATG | TAA | −7 | H | |
COII | 10576 | 11283 | 708 | ATG | TAG | 2 | H | |
ND4L | 11265 | 11564 | 300 | ATG | TAG | −19 | H | |
ND3 | 11567 | 11908 | 342 | GTG | TAA | 2 | H | |
ND5 3’ | 11996 | 13099 | 1104 | TAG | 87 | H | ||
tRNATrp | 13098 | 13166 | 69 | UCA | −2 | H | ||
ATP8 | 13170 | 13367 | 198 | ATG | TAA | 3 | H | |
COI 5’ | 13385 | 14095 | 711 | ATT | 17 | H | ||
COI 3’ | 15173 | 16057 | 885 | TAG | 1077 | H |
Gene | Position | Length (bp) | Anticodon | Codon | Intergenic nucleotides* | Strand† | ||
---|---|---|---|---|---|---|---|---|
From | To | Start | Stop | |||||
tRNAMet | 1 | 72 | 72 | CAU | 1581 | H | ||
16S rRNA | 272 | 1969 | 1698 | 199 | H | |||
ND5 5’ | 2000 | 2710 | 711 | ATG | 30 | H | ||
ND1 | 2819 | 3766 | 948 | ATG | TAG | 108 | H | |
Cytb | 3769 | 4908 | 1140 | ATG | TAA | 2 | H | |
ND2 | 5125 | 6219 | 1095 | TTA | TAA | 216 | H | |
ND6 | 6220 | 6780 | 561 | ATG | TAA | 0 | H | |
ATP6 | 6780 | 7454 | 675 | ATG | TAA | −1 | H | |
ND4 | 7451 | 8893 | 1443 | ATG | TAG | −4 | H | |
12S rRNA | 8891 | 9797 | 907 | −3 | H | |||
COIII | 9795 | 10574 | 780 | ATG | TAA | −3 | H | |
COII | 10577 | 11284 | 708 | ATG | TAG | 2 | H | |
ND4L | 11266 | 11565 | 300 | ATG | TAG | −19 | H | |
ND3 | 11568 | 11909 | 342 | GTG | TAA | 2 | H | |
ND5 3’ | 11997 | 13100 | 1104 | TAG | 87 | H | ||
tRNATrp | 13099 | 13167 | 69 | UCA | −2 | H | ||
ATP8 | 13171 | 13368 | 198 | ATG | TAA | 3 | H | |
COI 5’ | 13368 | 14270 | 903 | ATG | −1 | H | ||
COI 3’ | 15336 | 16004 | 669 | TAA | 1065 | H |
Nucleotide composition in different regions of mitogenomes of Physogyra lichtensteini (P. l.) and Plerogyra sinuosa (P. s.).
Gene/Region | T (%) | C (%) | A (%) | G (%) | A+T (%) | Size (bp) | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
P. l. | P. s. | P. l. | P. s. | P. l. | P. s. | P. l. | P. s. | P. l. | P. s. | P. l. | P. s. | |
ND5 | 46.56 | 46.61 | 12.07 | 12.01 | 21.71 | 21.76 | 19.67 | 19.61 | 68.27 | 68.37 | 1815 | 1815 |
ND1 | 43.35 | 43.46 | 14.14 | 14.03 | 19.20 | 19.09 | 23.31 | 23.42 | 62.55 | 62.55 | 948 | 948 |
Cytb | 44.91 | 44.82 | 13.68 | 13.68 | 20.88 | 20.88 | 20.53 | 20.61 | 65.79 | 65.70 | 1140 | 1140 |
ND2 | 47.31 | 47.31 | 12.79 | 12.60 | 20.00 | 20.09 | 19.91 | 20.00 | 67.31 | 67.40 | 1095 | 1095 |
ND6 | 44.56 | 44.56 | 13.37 | 13.55 | 22.28 | 22.28 | 19.79 | 19.61 | 66.84 | 66.84 | 561 | 561 |
ATP6 | 46.81 | 46.37 | 13.19 | 13.33 | 22.22 | 22.22 | 17.78 | 18.07 | 69.03 | 68.59 | 675 | 675 |
ND4 | 45.35 | 45.56 | 13.54 | 13.47 | 19.86 | 19.86 | 21.25 | 21.11 | 65.21 | 65.42 | 1440 | 1443 |
COIII | 42.69 | 42.69 | 15.38 | 15.51 | 19.74 | 19.62 | 22.18 | 22.18 | 62.43 | 62.31 | 780 | 780 |
COII | 39.69 | 39.55 | 13.28 | 13.28 | 24.01 | 23.87 | 23.02 | 23.31 | 63.70 | 63.42 | 708 | 708 |
ND4L | 44.33 | 44.33 | 12.00 | 12.00 | 24.67 | 24.67 | 19.00 | 19.00 | 69.00 | 69.00 | 300 | 300 |
ND3 | 47.08 | 46.78 | 9.94 | 9.94 | 17.84 | 17.84 | 25.15 | 25.44 | 64.92 | 64.62 | 342 | 342 |
ATP8 | 43.43 | 43.43 | 12.12 | 12.12 | 29.29 | 29.29 | 15.15 | 15.15 | 72.72 | 72.72 | 198 | 198 |
COI | 40.41 | 39.31 | 15.10 | 15.78 | 22.12 | 22.20 | 22.37 | 22.71 | 62.53 | 61.51 | 1596 | 1572 |
PCGs | 44.35 | 44.20 | 13.42 | 13.50 | 21.25 | 21.25 | 20.98 | 21.06 | 65.60 | 65.45 | 11598 | 11574 |
1st | 35.59 | 35.56 | 13.63 | 13.69 | 21.99 | 21.90 | 28.79 | 28.85 | 57.58 | 57.47 | 3866 | 3858 |
2nd | 47.31 | 47.15 | 18.65 | 18.61 | 17.93 | 18.01 | 16.11 | 16.23 | 65.24 | 65.16 | 3866 | 3858 |
3rd | 50.16 | 49.90 | 7.99 | 8.19 | 23.82 | 23.82 | 18.03 | 18.09 | 73.98 | 73.72 | 3866 | 3858 |
tRNA | 24.82 | 24.82 | 23.40 | 23.40 | 27.66 | 27.66 | 24.11 | 24.11 | 52.48 | 52.48 | 141 | 141 |
rRNA | 31.70 | 31.67 | 12.50 | 12.48 | 35.19 | 35.12 | 20.62 | 20.73 | 66.89 | 66.79 | 2609 | 2605 |
Overall | 40.17 | 39.96 | 13.32 | 13.16 | 24.75 | 24.87 | 21.75 | 22.01 | 64.92 | 64.83 | 17286 | 17586 |
The lengths of all 13 protein-coding genes (PCGs) are 11,598 bp and 11,574 bp for Physogyra lichtensteini and Plerogyra sinuosa, respectively. In both species, the ND5 gene and COI gene have intron insertions, and the start and stop codon of all 13 PCGs are exactly the same except for the COI gene. Their shortest gene is in both ATP8, and their longest gene is ND5 (Tables
The encoding genes 12S and 16S rRNA in Physogyra lichtensteini are 911 bp and 1,698 bp in size, and in Plerogyra sinuosa they are 907 bp and 1,698 bp in size. The base composition of rRNA in Physogyra lichtensteini was 35.19% A, 12.5% C, 20.62% G, and 31.7% T, and in Plerogyra sinuosa it was 35.12% A, 12.48% C, 20.73% G, and 31.67% T. The two tRNA encoding genes, tRNAMet (72 bp) and tRNATrp (69 bp), are exactly the same in Physogyra lichtensteini and Plerogyra sinuosa (Tables
There are three distinct clades of Scleractinia in our ML tree, including “Complex”, “Robust”, and “Basal” clade. The ML topology tree of all the 47 species shows that Physogyra lichtensteini and Plerogyra sinuosa are clustered in family Plerogyridae which belong to the “Robust” clade with high bootstrap support (Fig.
The complete mitochondrial genomes of Physogyra lichtensteini and Plerogyra sinuosa were sequenced for the first time. Their mitogenomes show a similar gene order and composition with other typical Scleractinia. Our phylogenetic analysis of Physogyra lichtensteini and Plerogyra sinuosa, based on their 13 tandem mitochondrial protein-coding genes and including another 42 species of Scleractinia and two species of Corallimorpharia, help us to understand the evolutionary relationships amongst stony corals and facilitate further studies on stony coral evolutionary and phylogenetic relationships.
This study was funded by the National Natural Science Foundation of China (grant number 42106143; 42006128); National key research and development program(021YFC3100503); the Scientific Research Foundation of Third Institute of Oceanography, Ministry of Natural Resources (grant number 2022024; 2020006); and Nansha Islands Coral Reef Ecosystem National Observation and Research Station (NSICR). PT and WN conceived, designed, and performed the study. ZJ, BC, JX, and WW processed and analysed the data. All authors contributed to the preparation of the manuscript.