Research Article |
Corresponding author: Wentao Niu ( wentaoniu@tio.org.cn ) Academic editor: Bert W. Hoeksema
© 2018 Wentao Niu, Shuangen Yu, Peng Tian, Jiaguang Xiao.
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:
Niu W, Yu S, Tian P, Xiao J (2018) Complete mitochondrial genome of Echinophyllia aspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning. ZooKeys 793: 1-14. https://doi.org/10.3897/zookeys.793.28977
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Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coral Echinophyllia aspera (Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows that E. aspera clustered closely with Sclerophyllia maxima (Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome of E. aspera provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.
Daya Bay, gene order, next-generation sequence, phylogeny
Reef-building coral species of the order Scleractinia play an important role in shallow tropical seas by providing an environmental base for the ecosystem (
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 (
Echinophyllia aspera (Ellis & Solander, 1786), commonly known as the chalice coral, is a stony coral species with large polyps in the scleractinian family Lobophylliidae. It is native to the western and central Indo-Pacific (
Samples (voucher no. DYW15) of Echinophyllia aspera (Figure
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 E. aspera within the Scleractinia, the complete mitogenome sequences of an additional ten representative scleractinian species (Table
Representative Scleractinia species included in this study for comparison.
Species | Family | Distribution | Length (bp) | GenBank accession number |
---|---|---|---|---|
Echinophyllia aspera | Lobophylliidae | Indo-Pacific | 17,697 | MG792550 |
Sclerophyllia maxima | Lobophylliidae | Indo-Pacific | 18,168 | FO904931 |
Platygyra carnosa | Merulinidae | Indo-Pacific | 16,463 | NC_020049 |
Favites abdita | Merulinidae | Indo-Pacific | 17,825 | NC_035879 |
Favites pentagona | Merulinidae | Indo-Pacific | 18,006 | NC_034916 |
Orbicella faveolata | Merulinidae | West Atlantic | 16,138 | AP008978 |
Orbicella franksi | Merulinidae | West Atlantic | 16,138 | AP008975 |
Orbicella annularis | Merulinidae | West Atlantic | 16,138 | AP008974 |
Mussa angulosa | Mussidae | West Atlantic | 17,245 | NC_008163 |
Colpophyllia natans | Mussidae | West Atlantic | 16,906 | NC_008162 |
Madrepora oculata | Oculinidae | West Atlantic | 15,841 | NC_018364 |
The complete mitogenome of E. aspera was 17,697 bp in size (GenBank accession number: MG792550) including unique 13 protein-coding genes (PCGs), two transfer RNA genes (tRNA-Met, tRNA-Trp) and two ribosomal RNA genes (Figure
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 b | 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 |
Nucleotide composition in different regions of mitochondrial genome of Echinophyllia aspera.
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 b | 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 |
PCGs | 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 PCGs was 11,576 bp in size, and its base composition was 21.6% for A, 13.4% for C, 20.5% for G and 44.5% for T. The ND5 had a 10,136 bp intron insertion, and COI had a 1,075bp intron insertion. According to
The genes encoding the small and large ribosomal RNA subunits (12S rRNA and 16S rRNA) were identified in E. aspera, which were 912 bp and 1,696 bp in length, respectively. The total ribosomal RNA was 2,608 bp in size, and its base composition was 35.43% for A, 12.65% for C, 20.17% for G and 31.75% for T. The two transfer RNAs were 72 bp for tRNA-Met and 71 bp for tRNA-Trp in length respectively. They can be folded into the typical cloverleaf structure, the typical cloverleaf structure contained amino acid accept stem, TψC stem, anticodon stem, and DHU stem (Figure
ML and BI analyses were performed with the concatenated PCG nucleotide data. The topological relationships of two phylogenetic analyses remained consistent, and all analyses provided high support values for all internodes (Figure
Limited data are available on the mitogenomes of Lobophylliidae, so the mitochondrial genome of Echinophyllia aspera was completed using NGS in the present study. The mitogenome of E. aspera was found to be 17,697 bp in length and showed a similar composition in size, low GC content and gene order to mitogenomes already available in Scleractinia. In conclusion, the complete mitogenome of E. aspera sequenced and analysed in this study provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses for scleractinian phylogeny.
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.