The first mitochondrial genome of Tetraclita japonica (Crustacea: Sessilia) from China: phylogeny within Cirripedia based on mitochondrial genes

Abstract

The first mitochondrial genome of Tetraclita japonica from China was presented. The mitochondrial genome of T. japonica CN is a circular DNA molecule containing 15,192 bp. It contains 13 protein-coding genes, two rRNAs genes and 22 tRNAs. Four PCGs, seven tRNAs, and two rRNAs are encoded on the light strand (trnF, nd5, trnH, nd4, nd4L, trnP, nd1, trnL1, lrRNA, trnV, srRNA, trnK, and trnQ), and the other nine PCGs are located on the heavy strand. The length of all non-coding regions is 667 bp and the longest one distributed between srRNA and trnK (263 bp). Interestingly, cox1 of T. japonica CN started with CGA, which is different from most other mitochondrial PCGs whose initiation codon is ATN. In comparison with the pancrustacean ground pattern, seven tRNAs (trnQ, trnI, trnP, trnT, trnS₁, trnE, and trnA) are translocated, and three tRNAs (trnK, trnC, and trnY) are inverted. Phylogenetic tree was constructed based on 13 mitochondrial PCGs. In the phylogenetic tree, T. japonica CN clustered with T. japonica JP into a branch (BP = 100). Tesseropora rosea clustered with T. japonica, and they grouped with T. rufotincta with high support (BP = 100). In the tree, T. divisa as the most distantly related species within Tetraclitidae. Moreover, phylogenetic analysis indicates that the two families (Balanidae and Archaeobalanidae) are non-monophyletic. More mitochondrial genomic data are urgently needed to reveal the deeper phylogeny within Cirripedia.

Keywords:

• Tetraclita japonica
• gene rearrangement
• mitochondrial genome
• phylogeny

Tetraclita (Crustacea: Cirripedia: Sessilia) is a common genus in coastal area, while Tetraclita japonica is found in the East China Sea, South China Sea, North Korea, and Japan sea, etc. (Liu and Ren 2007). Genetic diversity is a product of long-term evolution and is the premise of survival adaptation (Frankham 2005). Specimen of T. japonica was collected from Zhoushan (N: 30.71, E: 122.78), Zhejiang Province, China (T. japonica CN). DNA was extracted with the TIANamp DNA Kit (TIANGEN, Beijing, China) as directed by the manufacturer, which was stored at Marine Museum of Huaihai Institute of Technology (Accession number: Tjap-003). Referencing to sequencing of T. japonica Japan (JP), the extracted DNA was subjected to PCR amplification. DNA sequencing was carried out at MAP Biotech (Shanghai, China).

The mitochondrial genome of T. japonica CN is a circular DNA molecule containing 15,192 bp (GenBank accession number: MH119183). It contains 13 protein-coding genes, two rRNAs genes, and 22 tRNAs. Total A + T content of T. japonica CN is 66.1%. Four PCGs, seven tRNAs, and two rRNAs are encoded on the light strand (trnF, nd5, trnH, nd4, nd4L, trnP, nd1, trnL1, lrRNA, trnV, srRNA, trnK, and trnQ) and the other nine PCGs are located on the heavy strand. The length of all non-coding regions is 667 bp and the longest one distributed between srRNA and trnK (263 bp). Interestingly, cox1 of T. japonica CN started with CGA, which is different from most other mitochondrial PCGs whose initiation codons is ATN (Shen et al. 2009).

There are genes rearrangements in barnacles mitochondrial genomes compared with the pancrustacean ground pattern (Boore and Brown 1998; Tsang et al. 2017). In comparison with the pancrustacean ground pattern, seven conserved blocks were found in the mitochondrial genome of T. japonica CN (cox1- trnL₂- cox2, trnD- atp8- atp6- cox3- trnG- nd3, trnR- trnN, trnF- nd5- trnH- nd4- nd4L, nd6- cob- trnS₂, nd1- lrRNA- trnV- srRNA and trnM- nd2- trnW). While seven tRNAs (trnQ, trnI, trnP, trnT, trnS₁, trnE, and trnA) are translocated, and three tRNAs (trnK, trnC, and trnY) are inverted.

In order to investigate phylogenetic relationships of T. japonica CN with the other barnacles, the MEGA7.0 was used to constructed a maximum-likelihood tree based on 13 PCGs from complete mitochondrial genomes from Cirripedia (Wares 2015; Shen, Chan, et al. 2015, Shen, Tsang et al. 2015; Baek et al. 2016; Shen, Chan, et al. 2016; Shen, Chu, et al. 2016; Shen, Tsoi, et al. 2016; Shen et al. 2017). In the phylogenetic tree (Figure 1), T. japonica CN clustered with T. japonica JP into a branch (BP = 100). Tesseropora rosea clustered with T. japonica, and they grouped with T. rufotincta with high support (BP = 100). In the tree, T. divisa as the most distantly related species within Tetraclitidae, which was consistent with the previous results (Cai et al. 2018; Song et al. 2017). Moreover, phylogenetic analysis indicates that the two families (Balanidae and Archaeobalanidae) are non-monophyletic (Figure 1). However, more mitochondrial genomic data are urgently needed to reveal the deeper phylogeny within Cirripedia.

Figure 1. Maximum-likelihood phylogenetic tree based on 13 PCGs nucleotide acid sequences of Tetraclita japonica and other mitochondrial genomes from Cirripedia.

The accession numbers of the genomes used for comparison were NC_024636 (Megabalanus ajax), NC_006293 (Megabalanus volcano), NC_029168 (Acasta sulcata), NC_024525 (Amphibalanus amphitrite), NC_029167 (Armatobalanus allium), KJ754821 (Savignium sp. BKKC-2014), NC_023945 (Nobia grandis), NC_029169 (Chelonibia testudinaria), NC_029170 (T. divisa), NC_033393 (Epopella plicata), KY865100 (T. rufotincta), NC_029154 (T. serrata), KY865099 (T. rosea), MH119183(T. japonica CN), NC_008974 (T. japonica JP), NC_026730 (Chthamalus antennatus), NC_022716 (Notochthamalus scabrosus), KJ754820 (Octomeris sp. BKKC-2014), NC_005936 (Pollicipes polymerus), NC_025295 (Lepas australis), and NC_026576 (Lepas anserifera).

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by the National Nature Science Foundation of China [NSFC No. 41876147], and also funded by the Jiangsu Priority Academic Program Development (PAPD), Postgraduate graduate Research & Practice Innovation Programs [SJKY19_2442 and KYCX18_2570], Jiangsu Qinglan, Six Talent Peaks and Lianyungang 521 Talent Projects.