Abstract
The complete mitochondrial genome of Tethya sp. was studied. This is the second complete mitochondrial report on the family Tethyidae. The mitochondrial genome of Tethya sp. is 20,582 bp in length, containing 14 protein-coding genes and 25 tRNA genes, with 2 rRNA genes. Our phylogenetic result suggested that Tethya sp. converged well with Tethya actinia, which further verified the morphological result. We anticipate our study to shed light on future molecular studies of demosponges.
Keywords: Demosponge, mitogenome, sponge, Tethya sp.
Sponge systematics is a long-standing issue due to vulnerability to environmental modification which enhancing the difficulty in taxonomy. As a supplementary measure for morphological taxonomy, studies have applied the mitochondrial genome of metazoa as a marker to resolve taxonomic controversies (Gissi et al. 2008). Little information is known about the evolution of sponges. Currently, only one complete mitogenome of Tethya actinia has been reported for the genus Tethya (Lavrov et al. 2005). In this study, we concentrated on exploring an approach of aligning mitochondrial genome with other demosponges to describe the molecular relationships among them.
Tethya sp. was sampled from Gulei Peninsula, Fujian Province, China (117.5928E 23.8015N), in May 2014 and deposited in the Museum of Marine Science and Technology, Xiamen University with the number XMU02001 079. DNA was extracted using guanidinium isothiocyanate with the method adapted from Wilson and Carson (2001) and sequenced with MPS (massive parallel sequencing) Illumina technology. The sample was constructed in a paired-end library with an insert size of 420 bp and was sequenced using a Hiseq2500 (Beijing, China) by PE125 strategy. Sequencing and annotation was performed at Beijing Novogene Bioinformatics Technology Co. Ltd. Clean reads were assembled by SOAPdenovo (Li et al. 2008, 2010) to produce a single circular form of the complete mitochondrial genome. A whole genome Blast (Altschul et al. 1990) search (E-value ≤1e − 5, minimal alignment length percentage≥ 40%) against 6 databases, KEGG (Kanehisa 1997; Kanehisa et al. 2004; Kanehisa et al. 2006), COG (Tatusov et al. 1997; Tatusov et al. 2003), NR, Swiss-Prot (Magrane & Consortium 2011), GO (Ashburner et al. 2000) and TrEMBL (Magrane & Consortium 2011), was conducted. An alignment of the assembled scaffold for Tethya sp. demonstrated that mitogenome of Tethya actinia (GenBank number: AY320033.1) shared many similarities (86% identity) with our sample. We took the homological mitogenome as reference using the mitochondrial genome annotation (MITOS) server (Bernt et al. 2013) for annotation and BLASTX to improve results. Subsequently, we obtained annotated coding DNA sequences (CDS), transfer RNA genes (tRNA) and ribosomal RNA (rRNA) genes.
The complete genome of Tethya sp. is 20,582 bp long with 14 protein-coding genes, 25 tRNA genes and 2 rRNA subunits. The base composition of the mitogenome is A (29.79%), T (35.22%), C (11.93%), and G (23.07%), with a GC content of 35.38% (Table 1). The annotated mitogenome has been submitted to NCBI (GenBank accession number KU748128).
Table 1.
Mitochondrial genome organization of Tethya sp.
| Name | From | To | Direction | Length (bp) |
|---|---|---|---|---|
| trnF (gaa) | 35 | 107 | + | 73 |
| rrnS | 111 | 1363 | + | 1253 |
| trnG (tcc) | 1458 | 1529 | + | 72 |
| trnV (tac) | 1648 | 1719 | + | 72 |
| rrnL | 1739 | 4392 | + | 2654 |
| trnE (ttc) | 4505 | 4576 | + | 72 |
| nad6 | 4580 | 5131 | + | 552 |
| trnY (gta) | 5161 | 5232 | + | 72 |
| trnM (cat) | 5300 | 5371 | + | 72 |
| cox2 | 5424 | 6086 | + | 663 |
| trnL (taa) | 6134 | 6216 | + | 83 |
| trnK (ttt) | 6313 | 6384 | + | 72 |
| atp8 | 6447 | 6599 | + | 153 |
| atp6 | 6897 | 7418 | + | 522 |
| trnR (tct) | 7463 | 7535 | + | 73 |
| cox3 | 7548 | 9330 | + | 783 |
| trnN (gtt) | 8361 | 8432 | + | 72 |
| cob | 8520 | 9653 | + | 1134 |
| trnS (gct) | 9682 | 9755 | + | 74 |
| trnI (gat) | 9789 | 9861 | + | 73 |
| trnQ (ttg) | 9915 | 9986 | + | 72 |
| trnW (tca) | 10,036 | 10,106 | + | 71 |
| atp9 | 10,245 | 10,478 | + | 234 |
| nad4 | 10,675 | 11,958 | + | 1284 |
| trnH (gtg) | 12,048 | 12,120 | + | 73 |
| trnD (gtc) | 12,159 | 12,230 | + | 72 |
| nad3 | 12,334 | 12,663 | + | 330 |
| trnR (tcg) | 12,797 | 12,867 | + | 71 |
| nad4l | 12,907 | 13,158 | + | 252 |
| cox1 | 13,299 | 14,840 | + | 1542 |
| trnS (tga) | 14,991 | 15,071 | + | 81 |
| nad1 | 15,187 | 16,149 | + | 963 |
| trnP (tgg) | 16,230 | 16,302 | + | 73 |
| trnL (tag) | 16,463 | 16,536 | + | 74 |
| trnC (gca) | 16,602 | 16,673 | + | 72 |
| trnT (tgt) | 16,685 | 16,757 | + | 73 |
| trnM (cat) | 16,840 | 16,910 | + | 71 |
| nad2 | 17,268 | 18,179 | + | 912 |
| nad5 | 18,522 | 20,282 | + | 1761 |
| trnA (tgc) | 20,322 | 20,394 | + | 73 |
| trnM (cat) | 20,445 | 20,516 | + | 72 |
Direction: “+” stands for 5′ to 3′, “−” stands for 3′ to 5′.
In Tethya sp., the arrangement of protein-coding genes and gene contents was completely identical to that of T. actinia. After multiple sequence alignment with other mitogenomes of demosponges by MAFFT (Katoh & Standley 2013), we constructed a phylogenetic tree (Figure 1) using Maximum Likelihood (ML) method in MEGA 6.06 (Tamura et al. 2013). The phylogenetic result indicated that Tethya sp. converged well with Tethya actinia, which further verified the morphological result. In conclusion, mitogenome studies of sponges may contribute to a better phylogenetic understanding of demosponges, subsequently influencing the knowledge of molecular evolution of metazoa.
Figure 1.
The consensus phylogenetic relationship of Tethya sp. and the other species of Demospongiae as well as Aurelia aurita (a kind of jellyfish) from Maximum Likelihood (ML) analysis with 1000 bootstrap. The number on the branches are the bootstrap values for ML. The Genbank accession numbers of each species are shown in the brackets.
Acknowledgements
We would like to thank Mr. Huilong Ou, Dr. Jing Zhao and all the members from sponge laboratory of Xiamen University for sample collection and intellectual advice.
Disclosure statement
The authors alone are responsible for the content and writing of the paper and have no conflict of interest.
Funding information
This work was funded by the frontier project of China Ocean Mineral Resources R & D Association (DY125-22-QY-18) and Scientific Research Project of Xiamen Southern Ocean Center (grant: 13GYY002NF07, 14CZP039HJ13).
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