Abstract
In present study, the complete mitogenome sequence of the Antarctic stalked jellyfish, Haliclystus antarcticus Pfeffer (Staurozoa: Stauromedusae) has been sequenced by next-generation sequencing method. The assembled mitogenome comprises of 15,766 bp including 13 protein coding genes, 7 transfer RNAs, and 2 ribosomal RNA genes. The overall base of Antarctic stalked jellyfish constitutes of 26.5% for A, 19.6% for C, 19.8% for G, 34.1% for T and show 90% identity to Sessile Jelly, Haliclystus sanjuanensis, in the northeastern Pacific Ocean. The complete mitogenome of the Antarctic stalked jellyfish, contributes fundamental and significant DNA molecular data for further phylogeography and evolutionary analysis for seahorse phylogeny. The complete sequence was deposited in DBBJ/EMBL/GenBank under accession number KU947038.
Keywords: Antarctic stalked jellyfish, Mitogenome, Mt genome, Genetics
| Organism | Haliclystus antarcticus Pfeffer, 1889 |
| Sequencer or array type | Complete mitochondrial genome |
| Data format | Raw |
| Experimental factors | N/A |
| Experimental features | Whole genome analysis of Antarctic stalked jellyfish |
| Consent | On request |
| Sample source location | Catalog number NMMBCR84. Locality: King George Island, Antarctic (longitude 58°54′10.1″W and latitude 62°11′11.3″S) |
1. Direct link to deposited data
2. Introduction
The Antarctic stalked jellyfish, Haliclystus antarcticus Pfeffer, 1889, is a member of the medusa order Stauromedusae, a small benthic creature, which is commonly found attaching themselves on algae or rocky shoreline in Antarctic region off Antarctic Peninsula, Argentina and Chile [1]. The differences between H. antarcticus Pfeffer and Haliclystus kerguelensis (Antarctic congener) are small anchors and short calyx [2]. In South Georgia Island, the main food for large size Antarctic stalked jellyfishes are calanoid copepods whereas small size individuals consume amphipods [3]. In the present study, the complete mitochondrial genome of the Antarctic stalked jellyfish from the nearshore of King George Island, Antarctic in December 2014 (longitude 58°54′10.1″W and latitude 62°11′11.3″S) was sequenced. The voucher (NMMBCR84) was deposited at the National Museum of Marine Biology and Aquarium.
3. Results and discussion
3.1. Main features of the mt genome of H. antarcticus
Samples of Antarctic stalked jellyfishes were collected from the nearshore of King George Island, Antarctic in December 2014 (longitude 58°54′10.1″W and latitude 62°11′11.3″S). Their genomic DNA was extracted from muscle by using Genomic DNA Purification Kit (GeneMark, Taichung, Taiwan). The methods for genomic DNA extraction, library construction and next generation sequencing were described in previous publication [4]. The raw next generation sequencing reads were de novo assembled by Geneious Version 9.0 (Auckland, New Zealand) to construct a single, circular form of complete mitogenome with about an average 109.7 X coverage (6415 out of 3,142,022, 0.002%). The complete mitochondrial genome of Antarctic stalked jellyfish was 15,766 bp (GenBank: KU947038) consisting of 13 protein coding genes, 7 transfer RNAs, and 2 ribosomal RNAs genes (Table 1). The overall base of Antarctic stalked jellyfish has 26.5% of A, 19.6% of C, 19.8% of G, 34.1% of T and matches 90% identity to Sessile Jelly, Haliclystus sanjuanensis, in the northeastern Pacific Ocean.
Table 1.
Mitochondrial genome of the Antarctic stalked jellyfish, Haliclystus antarcticus Pfeffer, 1889.
| Name | Minimum | Maximum | Direction | Type | Length | # Intervals |
|---|---|---|---|---|---|---|
| D-Loop | 1225 | 1951 | None | D-Loop | 727 | 1 |
| 12S rRNA | 11,208 | 12,124 | Forward | rRNA | 917 | 1 |
| 16S rRNA | 1952 | 3782 | Reverse | rRNA | 1831 | 1 |
| ATP6 | 6473 | 7180 | Forward | Gene | 708 | 1 |
| ATP8 | 6276 | 6479 | Forward | Gene | 204 | 1 |
| COB | 1 | 1143 | Forward | Gene | 1143 | 1 |
| COX1 | 3783 | 5360 | Reverse | Gene | 1578 | 1 |
| COX2 | 5455 | 6201 | Forward | Gene | 747 | 1 |
| COX3 | 7191 | 7976 | Forward | Gene | 786 | 1 |
| NAD1 | 13,350 | 14,301 | Forward | Gene | 952 | 1 |
| NAD2 | 8051 | 9397 | Forward | Gene | 1347 | 1 |
| NAD3 | 12,702 | 13,019 | Forward | Gene | 318 | 1 |
| NAD4 | 14,307 | 15,696 | Forward | Gene | 1390 | 1 |
| NAD4L | 13,033 | 13,320 | Forward | Gene | 288 | 1 |
| NAD5 | 9496 | 11,182 | Forward | Gene | 1687 | 1 |
| NAD6 | 12,121 | 12,619 | Forward | Gene | 499 | 1 |
| trnD(gtc) | 5419 | 5480 | Forward | tRNA | 62 | 1 |
| trnF(gaa) | 12,625 | 12,687 | Reverse | tRNA | 63 | 1 |
| trnI(gat) | 12,996 | 13,060 | Forward | tRNA | 65 | 1 |
| trnL2(taa) | 1157 | 1224 | Reverse | tRNA | 68 | 1 |
| trnM(cat) | 7982 | 8050 | Forward | tRNA | 69 | 1 |
| trnS1(gct) | 15,690 | 15,749 | Reverse | tRNA | 60 | 1 |
| trnW(tca) | 6205 | 6275 | Forward | tRNA | 71 | 1 |
The protein coding and tRNA genes of Antarctic stalked jellyfish mitogenome were predicted by using DOGMA [5], ARWEN [6] and MitoAnnotator [7] tools. Some ambiguous annotation sites are manual checked. All protein-coding genes were encoded on H-strand with exception for COX1. All tRNA genes were encoded on H-strand with exception for tRNA-Ser, tRNA-Leu, and tRNA-Phe. All the 13-mitochondrial protein-coding genes share the start codon ATG, except for NAD3 and NAD4L (Both with ATA start codon). It also important to note that NAD2, NAD3, NAD4L, COX1, COX3, ATP6, and ATP8 all have the same stop codon (TAA), while others are terminated with codons of T– (NAD1, NAD4, NAD5 and NAD6) and TAG (COX2).
In all protein coding genes, NAD5 gene is the longest one with 1687 bp whereas ATP8 gene is the shortest one with 204 bp. The two ribosomal RNA genes, 12S rRNA gene (917 bp) is located between NAD5 and NAD6 genes and 16S rRNA gene (1831 bp) is located between D-Loop and COX1 gene. The present finding is expected to phenogenically reveal the prospective differences in species of jellyfish.
To validate the phylogenetic position of H. antarcticus, we used MEGA6 [8] software to construct a Maximum likelihood tree (with 500 bootstrap replicates) containing complete mitogenomes of 6 Cnidaria species. Hydra oligactis derived from Hydrozoa was used as outgroup for tree rooting. Result shows H. antarcticus can be grouped with H. sanjuanensis and Craspedacusta sowerbyi in a monophyly with high bootstrap value supported (Fig. 1). In conclusion, the complete mitogenome of H. antarcticus was decoded for the first time in this study and provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for jellyfish.
Fig. 1.
Molecular phylogeny of Haliclystus antarcticus and other Cnidaria species based on complete mitogenome. The complete mitogenomes is downloaded from GenBank and the phylogenic tree is constructed by maximum likelihood method with 500 bootstrap replicates. The gene's accession number for tree construction is listed as follows: Hydra oligactis (NC_010214), Craspedacusta sowerbyi (JN593332), Haliclystus sanjuanensis (JN700944), Haliclystus antarcticus (KU947038), Aurelia aurita (NC_008446), Cassiopea frondosa (NC_016466) and Chrysaora quinquecirrha (NC_020459).
Conflict of interest
Authors declare no conflicts of interest in this study. The authors are responsible for the published content and manuscript compellation.
Acknowledgments
This study was financially supported by the National Museum of Marine Biology & Aquarium. We thank our former directors, Drs. L.-S. Fang and W.-S. Wang, for various support, WeThinkBio Co., Taiwan for technical support, and members of the 31st Chinese National Antarctic Research Expedition for help in collecting the samples.
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