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. 2017 May 30;7(13):4951–4962. doi: 10.1002/ece3.3067

The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep‐sea environment

Bo Zhang 1,2, Yan‐Hong Zhang 1, Xin Wang 1,2, Hui‐Xian Zhang 1, Qiang Lin 1,✉
PMCID: PMC5496520  PMID: 28690821

Abstract

The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.

Keywords: adaptation, Bolocera sp, deep‐sea sea anemone, mitochondrial genome

1. INTRODUCTION

The deep sea is the part of the ocean below the continental shelves, and it is the most extensive ecosystem on earth (Rex, 1981). The organisms living there survive in an extremely harsh environment, tolerating hundreds of bars of pressure, small amounts of oxygen, very little food, constant darkness, and low temperature (Sanders & Hessler, 1969). Because of the sparseness of animal life and the technical difficulties in sampling the deep‐sea benthos, our knowledge of deep‐sea organisms is based almost entirely on morphological distinctions at the species level (Etter, Rex, Chase, & Quattro, 1999). There is little information about the adaptive molecular mechanisms of the organisms living in the deep‐sea environment (Sanders & Hessler, 1969).

As the powerhouse of the cell, mitochondria generate energy by oxidative phosphorylation (OXPHOS) (Luo et al., 2008) and play important roles in energy metabolism and various biosynthetic pathways (Green & Reed, 1998; Newmeyer & Ferguson‐Miller, 2003). Mitochondria, with their own genetic material, are present in nearly all eukaryotic cells (Bernt, Braband, Schierwater, & Stadler, 2013), and they are autonomously replicated and transcribed (Boore, 1999). Mitogenomes have been widely used for studies of population genetics, phylogeography, phylogeny, and species identification (Brown, Brooke, Fordyce, & McCracken, 2011; Feng, Li, Kong, & Zheng, 2011; Gvoždík, Moravec, Klütsch, & Kotlik, 2010; Keskin & Can, 2009; Lei et al., 2010; Ma et al., 2013). The mitogenome, especially the 13 energy pathway protein‐coding genes, represents a particularly useful genetic marker for investigating the molecular basis of organismal adaptation to an extreme environment (Yu, Wang, Ting, & Zhang, 2011). In recent years, several mitochondrial genes have been shown to contain signatures of adaptive evolution, including the cytochrome b gene of alpacas (da Fonseca, Johnson, O'Brien, Ramos, & Antunes, 2008), the cytochrome c oxidase gene of plateau pikas (Luo et al., 2008), the NADH dehydrogenase six gene of domestic horses (Ning, Xiao, Li, Hua, & Zhang, 2010), and the ATP synthase genes of Caprinae (Hassanin, Ropiquet, Couloux, & Cruaud, 2009).

Most metazoan mitogenomes are circle molecules, between 14 and 18 kb in length that encode 37 genes (13 protein‐coding genes, 22 transfer RNA genes, and two ribosomal RNA genes) as well as a putative control region (Boore, 1999; Wolstenholme, 1992). As sea anemones are primitive animals (Putnam et al., 2007), their mitogenomes exhibit some differences. Similar to most metazoan mitogenomes, the typical sea anemone mitogenome is a circular molecule, 16–20 kb in length and encodes 13 energy pathway protein‐coding genes and two ribosomal RNA genes (Beagley, Okimoto, & Wolstenholme, 1998; Emblem et al., 2014; Osigus, Eitel, Bernt, Donath, & Schierwater, 2013). However, some distinctive features have been identified in these mitogenomes. Only 2 of the 22 essential transfer RNAs (tRNAs) are present, one or two genes are interrupted by a group I intron, the open reading frames (ORFs) encode unknown proteins, and there is a very slow nucleotide substitution rate (Beagley, Okada, & Wolstenholme, 1996; Beagley & Wolstenholme, 2013; Emblem et al., 2011; Johansen et al., 2010; Nielsen & Johansen, 2009; Osigus et al., 2013).

Although several complete or partial mitogenomes of sea anemones have been sequenced in recent years, the members of these genera are highly diverse (Emblem et al., 2014), and the information regarding these mitogenomes remains incomplete. For deep‐water species from extreme environments in particular, little mitochondrial data have been reported. To evaluate the variation in deep‐sea sea anemone gene structures and their adaptations to the deep‐sea environment, this study determined the complete mitogenome of a deep‐sea sea anemone (Bolocera sp.), identified its mitochondrial gene structures and arrangements, and elucidated their evolutionary characteristics.

2. MATERIALS AND METHODS

2.1. Specimens and DNA extraction

The specimen was collected on December 15, 2014, from a seamount on the Pacific Ocean (137.44˚E/8.52˚N) at a depth of 1106 m, fixed in 99% ethanol, and stored at 4°C. DNA was extracted using a Genomic DNA Kit (Tiangen Co. Beijing, China) according to the manufacturer's instructions. The specimen was not an endangered or protected species, and no specific permits were required for our collection process.

2.2. PCR and sequencing

To identify the subspecies of the specimen, two conserved genes (COI and cytb) were sequenced. The complete mitogenomes of closely related species were downloaded from the NCBI Entrez Database and amplified to search for conserved regions where primers for the complete mitogenome clone were designed. The complete mitogenome was amplified by overlapping PCR. All PCRs were performed in a 50 μl volume, which included 1 μl template DNA (approximately 100 ng), each primer at a concentration of 0.3 μmol/L, 5 μl of 10 × LA Taq buffer (Mg2+ plus), 5 μl of dNTP Mix (2.5 mmol/L), and 1 U of LA Taq (TaKaRa, Japan). The PCR amplifications used the following procedure: one cycle of denaturation for 5 min at 94°C; 35 cycles of 40 s at 94°C, 40 s at the primer‐specific annealing temperature, and 5 min at 72°C; and finally a 10‐min extension at 72°C. After purification, the PCR products were directly sequenced in both directions three times with the PCR primers. Sequencing was performed by ThermoFisher Scientific (Guangzhou, China).

2.3. Complete mitogenome analysis

The sequence alignment was conducted using Clustal X. The protein‐coding genes and rRNA genes were determined by BLAST and the NCBI Entrez Database and by comparison with the mitogenome sequences of homologous species. The tRNA genes and their secondary structures were predicted by the Web‐based tRNAscan‐SE 1.21 (Lowe & Eddy, 1997). The skew in nucleotide composition was calculated by AT skew and GC skew and measured according to the following formulae: AT skew = (A − T)/(A + T) and GC skew = (G − C)/(G + C) (Perna & Kocher, 1995), where A, T, C, and G are the occurrences of the corresponding bases. Codon usage was calculated by the Codon Usage Database (http://www.kazusa.or.jp/codon/). The gene map of the complete mitogenome was depicted by OGDRAW (http://ogdraw.mpimp-golm.mpg.de/).

2.4. Phylogenetic analysis

To illustrate the phylogenetic relationships among sea anemone, the complete mitogenomes of 23 Anthozoa species were downloaded from the GenBank database, including Aiptasia pulchella (HG423148), Alicia sansibarensis (KR051001), Antholoba achates (KR051002), Bolocera tuediae (HG423145), Halcampoides purpurea (KR051003), Hormathia digitata (HG423146), Isosicyonis striata (KR051006), Metridium senile (HG423143), Nematostella sp. (DQ643835), Sagartia ornata (KR051008), Urticina eques (HG423144), Chrysopathes formosa (NC_008411), Myriopathes japonica (NC_027667), Stichopathes lutkeni (NC_018377), Savalia savaglia (NC_008827), Acropora aculeus (KT001202), Acropora tenuis (NC003522), Pocillopora damicornis (EF526302), Siderastrea radians (DQ643838), Heliopora coerulea (NC_020375), Dendronephthya suensoni (NC_022809), Renilla muelleri (NC_018378), and Stylatula elongata (JX023275). Geodia neptuni (AY320032) (Demospongiae) was selected as the out‐group. The concatenated nucleotide sequences of 13 energy pathway protein‐coding genes were aligned using Clustal X with the default settings. The maximum likelihood (ML) method was employed to analyze the phylogenetic tree. The GTR + I + G model was selected as the best nucleotide substitution model by ModelTest 3.7 (Posada & Crandall, 1998). The ML analysis was performed by MEGA 5.1 with 1,000 bootstrap replicates.

2.5. Positive selection analysis

The selective pressure imposed on the mitogenomes of sea anemones was evaluated using CODEML from the PAML package. Two different tree‐building methods were used because the CODEML likelihood analysis is sensitive to tree topology. The two‐ratio and free‐ratio model (M1 model) was used in the mitogenome analysis. The branch‐site model was used to determine whether these genes have undergone positive selection in the foreground lineage. Bayes Empirical Bayes (BEB) analysis was used to calculate the Bayesian posterior probability of the positively selected sites.

3. RESULTS AND DISCUSSION

3.1. Genome organization

Similar to most metazoan mitogenomes, the mitogenome of Bolocera sp. is a circular molecule. The complete mitochondrial DNA of Bolocera sp. contained 19,463 bp. It shared the highest overall similarity (96.43%) with the B. tuediae mitochondrial DNA sequence (Emblem et al., 2014). In addition to the common individual base composition differences, the alignment of the two complete mitogenomes also showed several insertions or deletions of genetic fragments. Therefore, we speculated that Bolocera sp. was a new subspecies of Bolocera. Similar to those of other anthozoan species, the mitogenome of Bolocera sp. showed a different evolution pattern than most metazoans (Shearer, Van Oppen, Romano, & Wörheide, 2002). It encoded 16 protein‐coding genes (13 energy pathway protein‐coding genes, a heg gene, and two unknown ORFs), two tRNA genes, and two rRNA genes (Figure 1, Table 1). All of the genes were coded by the same strand (the H‐strand) and transcribed in the same direction. The gene order and orientation were identical to other sequenced actiniarians. In all the mitogenomes studied, no gene overlaps were observed, and the intergenic spacers varied. Several typical anthozoan mitogenome features (Beagley & Wolstenholme, 2013; Beagley et al., 1998; Emblem et al., 2014) were also observed in Bolocera sp., including the presence of two group I introns, two tRNA genes, and large intergenic spacers. In addition, two noncanonical protein‐coding genes (ORFC and ORFD) were observed. A genetic fragment similar to the control region (CR) of metazoans was also observed, which was first reported in sea anemones. The complete mitochondrial DNA sequence was deposited in the GenBank database under the accession number KU507297.

Figure 1.

Figure 1

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Graphical map of complete mitogenome of Bolocera sp. Different genes are represented by different boxes in different colors. tRNAs are displayed according to the one‐letter code. Genes encoded by the heavy strand are shown outside the circle, and those encoded by the light strand are shown inside. The direction of the arrows shows the direction of transcription. The inner ring shows the GC content of the mitogenome

Table 1.

Gene structure of the mitogenome of Bolocera sp

Feature Position numbers Size Codon Intergenic nucleotides Strand
Nucleotides Amino acid Start Stop
ND5 1–717,
3,115–4,230 		1,833 610 ATG TAG 18 H
ND1 941–1,924 984 327 ATG TAA 223 H
ND3 1,969–2,325 357 118 ATG TAA 44 H
tRNA Trp 4,544–4,613 70 313 H
ND2 4,729–6,111 1,383 460 ATG TAG 115 H
srRNA 6,161–7,215 1,055 49 H
COII 7,269–8,015 747 248 ATG TAA 53 H
ND4 8,021–9,496 1,476 491 ATG TAA 5 H
ND6 9,501–10,109 609 202 ATG TAA 4 H
cytb 10,137–11,288 1,152 383 ATG TAG 27 H
ORFD 11,371–11,505 135 44 ATG TAG 82 H
tRNA Met 11,549–11,619 71 43 H
lrRNA 11,620–13,835 2,216 0 H
COIII 13,904–14,692 789 262 ATG TAA 68 H
ORFC 14,946–15,146 201 66 ATG TAG 253 H
COI 15,253–16,142,
16,996–17,677 		1,572 523 ATG TAA 106 H
heg 16,297–16,986 690 229 GTG TAA 154 H
ND4L 18,182–18,481 300 99 ATG TAA 504 H
ATP8 18,506–18,721 216 71 ATG TAA 24 H
ATP6 18,755–19,444 690 229 ATG TAA 33 H
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3.2. Group I introns and unknown ORFs

In addition to the standard set of 13 energy pathway protein‐coding genes, an additional heg gene and two group I introns as well as two unknown ORFs were identified in the Bolocera sp. mitogenome (Figures 1 and 2, Table 1). Group I introns are genetic insertion elements that are extremely rare in metazoans and have only been identified within the mitogenomes of hexacorals and some sponges (Boore, 1999). In Lophelia pertusa (a scleractinian coral), a complex group I intron is inserted in the ND5 gene to host seven essential mitochondrial protein genes and a rRNA gene (Emblem et al., 2011). In this study, two group I introns were detected (ND5 intron and CO I intron). Both of the group I introns contained the same gene components as those in other hexacorallian species except for scleractinians (Figure 2). A gene structure analysis of hexacorallians showed that the ND5 intron absorbed more genes but that the CO I intron lost the heg gene. The reason for this difference might be that the scleractinian ancestor had a different evolutionary pathway than other hexacorallian suborder species before significant mitogenome rearrangement, which is supported by the opinion of Mónica (Medina, Collins, Takaoka, Kuehl, & Boore, 2006).

Figure 2.

Figure 2

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Linearized schemes of mitochondrial gene arrangements in anthozoans. (a) Linearized mitochondrial gene arrangements in actiniarians, Stichopathes lutkeni (Antipatharia) as outgroups. (b) Linearized mitochondrial gene arrangements in different suborders of anthozoa. Lengths of the genes correspond to relative lengths of the genomes in a. tRNAs are displayed according to the one‐letter code. Species names and NCBI accession numbers are given under each of the linearized schemes

Emblem et al. (2014) observed two ORFs (orfA‐51 and orfB‐26) of unknown function in the mitogenome of the cold‐water sea anemone U. eques, and a truncated version of orfA was also found in tropical reef A. pulchella and cold‐water H. digitate mitogenome. Foox, Brugler, Siddall, & Rodríguez (2016) also observed homologous ORFs in other actinioidean species, but no obvious similarity was noted within the ORFs. Instead of the ORFs described above, two new truncated ORFs (ORFC and ORFD) were observed in the Bolocera sp. mitogenome. Consistent with previous studies, no obvious similarity was detected. Flot & Tillier (2007) strongly suggested that the ORFs are expressed proteins, and Emblem even identified the ORFs to be functional elements (Emblem et al., 2014). The ORFs appear to be evolving under some selection relative to other protein‐coding genes (Emblem et al., 2014). The patterns (gained, lost, or truncated) exhibited by these noncanonical ORFs are consistent with transposon‐like elements (Winckler, Szafranski, & Glöckner, 2005). The ORFs detected in this study showed the same characteristics as the ORFs above, so they may play similar roles. Transposable elements can influence neighboring genes by altering splicing and polyadenylation patterns, or by functioning as enhancers or promoters (Girard & Freeling, 1999; Slotkin & Martienssen, 2007; Waterland & Jirtle, 2003). They have been demonstrated to play essential roles in the host response to stress and in facilitating the adaptation of populations (Blot, 1994; Casacuberta & González, 2013; Chénais, Caruso, Hiard, & Casse, 2012). Considering the common features of the species that carry noncanonical ORFs and the particular characteristics of the environment in which they live, the ORFs identified in this study may play important roles in adjusting mitochondrial energy metabolism.

3.3. Genome composition and skewness

In metazoan mitogenomes, the frequency of each nucleotide utilized varies among different taxa. The mitogenome of metazoans usually has a strand‐specific bias in nucleotide composition (Alexandre, Nelly, & Jean, 2005). The A + T content of the mitogenome is extremely high in insects and nematodes and lower in vertebrates (Saccone, Giorgi, Gissi, Pesole, & Reyes, 1999). In the anthozoan mitogenome, the A + T content ranges from 54.9% to 68.1% (Brugler & France, 2007; Foox et al., 2016). The nucleotide composition of the H‐strand in Bolocera sp. was biased toward A and T, and the overall A + T content was 60.51%. Similar results have also been observed in other actiniarian mitogenomes (Foox et al., 2016; Zhang & Zhu, 2016). As is commonly found in metazoan mitogenomes, the A + T content varied in different regions (Table 2). The CR‐like element presented the highest A + T content (66.16%), and the lowest content was found in the 2 tRNA genes (49.65%).

Table 2.

Genomic characteristics of the mitogenome of Bolocera sp

Species GenBank accession NO. H‐strand 13 energy pathway protein‐coding genesa lrRNA gene srRNA gene 2 tRNA genes
Length (bp) A + T (%) AT‐skew GC‐skew NO. of amino acid A + T (%) Length (bp) A + T (%) Length (bp) A + T (%) Length (bp) A + T (%)
Bolocera sp. KU507297 19,463 60.51 −0.127 0.108 4,023 61.25 2,216 58.35 1,055 54.50 141 49.65
Bolocera tuediae HG423145 19,143 60.28 −0.123 0.109 4,023 61.32 2,209 58.22 1,082 54.71 141 49.65
Aiptasia pulchella HG423148 19,790 62.43 −0.104 0.110 4,090 62.76 2,178 60.42 1,065 57.00 141 47.52
Alicia sansibarensis KR051001 19,575 61.01 −0.126 0.110 3,893 61.55 2,200 59.73 1,074 57.36 141 48.23
Antholoba achates KR051002 17,816 61.89 −0.130 0.122 4,023 62.68 2,084 59.21 1,056 53.69 141 50.36
Halcampoides purpurea KR051003 18,038 57.88 −0.108 0.083 3,933 58.67 2,192 57.48 1,082 55.27 141 51.06
Hormathia digitata HG423146 18,754 61.79 −0.132 0.113 4,033 62.81 2,189 59.21 1,082 55.45 141 49.65
Isosicyonis striata KR051006 19,001 60.28 −0.121 0.108 3,984 61.30 2,212 58.27 1,055 54.50 141 51.77
Metridium senile HG423143 17,444 61.86 −0.129 0.112 3,953 62.67 2,188 59.37 1,082 55.27 141 51.06
Nematostella sp. DQ643835 16,389 60.86 −0.117 0.090 3,945 61.42 602 56.81 693 57.29 141 49.65
Sagartia ornata KR051008 17,446 62.21 −0.126 0.114 3,962 63.11 2,201 59.29 1,082 55.73 141 51.06
Urticina eques HG423144 20,458 59.32 −0.118 0.094 3,956 60.47 2,214 57.50 1,057 53.93 141 49.65
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a

The heg gene and two ORFs do not counted in the 13 energy pathway protein‐coding genes.

The AT skew was negative (−0.127), whereas the GC skew was positive (0.108) in Bolocera sp. In all sequenced actiniarian mitogenomes, the trends were the same, and the AT‐skew and GC‐skew values were similar (Table 2). This result indicated that actiniarian mitogenomes favor Ts and Gs. Similar nucleotide skew patterns have also been observed in the mitogenomes of other hexacorallian subclasses (Brugler & France, 2007; van Oppen et al., 2000).

3.4. Protein‐coding genes

In this study, 16 protein‐coding genes (13 energy pathway protein‐coding genes, a heg gene, and two unknown ORFs) were identified (Table 1). All of these genes were coded by the same strand (the H‐strand) and transcribed in the same direction. In metazoans, most of the mitochondrial protein‐coding genes start with an ATN codon (Liao et al., 2010; Ma et al., 2014; Wang, Chao, Fang, & Yu, 2016). In the present study, except for the inserted heg gene, which is considered to be a selfish genetic element (Edgell, 2009), all of the genes were initiated by typical ATG codons. This pattern of initiation codon usage has also been observed in other basal metazoans (Beagley et al., 1998; Boore & Brown, 1995; Pont‐Kingdon et al., 1998).

In metazoan mitogenomes, stop codons are frequently incomplete (Clary & Wolstenholme, 1985; Okimoto, Macfarlane, & Wolstenholme, 1990) and are presumed to be completed by post transcriptional polyadenylation (Ojala, Montoya, & Attardi, 1981). However, in this study, all of the protein‐coding genes were terminated by complete TAA (11) and TAG (5) termination codons. This situation has also been observed in some sequenced cnidaria (Flot & Tillier, 2007; Kayal & Lavrov, 2008). The typical initiation codons and completed termination codons indicated a near standard genetic code, which is rare in metazoan mitogenomes. This result indicated that Bolocera sp. might retain some features of its cnidarian ancestor.

No significant difference in codon usage was detected among the sequenced actiniarians, and the A + T contents of the 13 energy pathway protein‐coding genes were 61.25% in Bolocera sp. In the 13 protein‐coding genes, UUA (Leu, 7.21%), UUU (Phe, 6.21%), and AUU (Ile, 4.56%) were the most frequently utilized codons in Bolocera sp., and the third position of the codons showed relatively high percentage of A and T bases (A, 26.58% and T, 38.06%). These features reflected codon usage with A and T biases at the third codon position, which is similar to the biases observed in most metazoans (Liao et al., 2010; Ma et al., 2014; Miller, Murphy, Burridge, & Austin, 2005; Wang et al., 2016).

3.5. Transfer RNA genes

In most cnidarian mitogenomes, only two tRNAs (tRNATrp and tRNAMet) were detected (except for octocorallians, in which only one tRNAMet was detected) (Beagley et al., 1998; Beaton, Roge, & Cavalier‐Smith, 1998; Kayal & Lavrov, 2008). A study by Beagley and Wolstenholme (2013) showed that nuclear DNA‐encoded functional tRNAs were detected in mitochondria, and the missing tRNAs are believed to be encoded in the nucleus and later imported into the mitochondrion (Schneider & Maréchal‐Drouard, 2000). In this study, the mitogenome of Bolocera sp. contained two tRNAs (tRNATrp and tRNAMet) (Figure 3). Both tRNAs could fold into a clover‐leaf secondary structure, and the anticodon usage was identical to most of the observed sea anemone species. One mismatched base pair (C‐A) was detected in tRNA Met. Interestingly, the unmatched base pair occurred on the amino acid acceptor arm. Such stem mismatches seem to be a common phenomenon for mitochondrial tRNAs in many species (Jiang et al., 2013; Liao et al., 2010; Miller et al., 2005; Wang et al., 2016) and are probably corrected by a post RNA‐editing mechanism (Lavrov, Brown, & Boore, 2000).

Figure 3.

Figure 3

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Inferred secondary structure of tRNAs in mitogenome of Bolocera sp.

3.6. Noncoding regions

A total of 22 noncoding regions (ranging from 4 to 789 bp) were identified in the Bolocera sp. mitogenome. The longest noncoding region (789 bp) was located between the ND3 gene and the second exon of the ND5 gene. The nucleotide content of the 789‐bp noncoding region was 238 As (30.16%), 284 Ts (36.00%), 130 Cs (16.48%), and 137 Gs (17.36%). The A + T content (66.16%) of the 789‐bp noncoding region was higher than that of other regions in the mitogenome. In addition, several special TTTT and AAA repeats and T + A‐rich regions were observed (Figure 4).

Figure 4.

Figure 4

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The CR‐like sequences of Bolocera sp. The T + A‐rich regions were underlined, and the “G(A)nT” motifs were marked with box

The CR in the mitogenome is essential for transcription and replication in vertebrates (Fernández‐Silva, Enriquez, & Montoya, 2003). As it was not constrained in the same way as the protein‐coding genes, the mitochondrial CR is usually considered to be the most variable portion of the mitogenome (Marshall & Baker, 1997), showing the highest variation in the whole mitogenome (Aquadro & Greenberg, 1983). The structure of the CR has been intensively investigated in vertebrates, but not in invertebrates. Generally, in vertebrates, the mitochondrial CR is divided into three domains, including the extended terminal associated sequences (ETAS), the central conserved sequence blocks (CSB‐F, CSB‐E, and CSB‐D), and the conserved sequence blocks (CSB‐1, CSB‐2, and CSB‐3) (Pesole, Gissi, Chirico, & Saccone, 1999; Sbisà, Tanzariello, Reyes, Pesole, & Saccone, 1997). However, the nucleotide sequence, length, and number of each motif all vary considerably among vertebrate classes and even within a class (Rand, 1993; Ruokonen & Kvist, 2002; Shaffer & McKnight, 1996). In invertebrates, especially in anthozoans, similar CR structures are not clearly defined, but some similar features have been observed. In A. tenuis, the candidate mitochondrial CR contains repetitive elements and has the potential to form the typical secondary structures of vertebrate D–loops (van Oppen et al., 2000). In Pocillopora, the candidate mitochondrial CR exhibits three characteristics: large size, variability in nucleotide composition, and tandemly arranged repeated sequences (Flot & Tillier, 2007). With the exception of the repeated sequences, the rest of these characteristics were all observed in the 789‐bp noncoding region identified here. In addition, the special CR “G(A)nT” motif that is present in S. gregaria and C. parallelus (Zhang, Szymura, & Hewitt, 1995) was also observed in the 789‐bp noncoding region (Figure 4). In all organisms except primates, A + T > G + C in the CR domains (Sbisà et al., 1997), which was also observed in the 789‐bp noncoding region. Replication of mitogenome has been shown to initiate near hairpin structures (Clayton, 2000). In Drosophila, the origin of replication is located near a conserved stem‐loop structure (Saito, Tamura, & Aotsuka, 2005). In this study, the secondary structure of the 789‐bp noncoding fragment presented several similar stem‐loop structures (Figure 5), which is a characteristic feature of O L in vertebrates (Clayton, 1991). In short, while no repetitive elements were observed, the 789‐bp noncoding region exhibited typical CR structures observed in other invertebrates. Considering the primitiveness of sea anemones in evolution, there must be some primitive features maintained. Therefore, we concluded that the 789‐bp noncoding sequence was a candidate CR (that we defined as “CR‐like”) that has not been reported in other actiniarians. This would be a unique and/or primitive mitogenomic feature for Bolocera sp., which is in agreement with the CR differences observed within invertebrates. As no other obvious adjusting elements were detected in the Bolocera sp. mitogenome, this special CR‐like element may play an important role in regulating the transcription and replication of the mitogenome in the extreme environment of the deep sea.

Figure 5.

Figure 5

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The potential stem‐loop structures in the 789‐bp noncoding “CR‐like” sequence of Bolocera sp.

3.7. Phylogenetic analyses

To investigate the relationships among anthozoan, we performed phylogenetic analysis based on the nucleotide datasets of the 13 mitochondrial energy pathway protein‐coding genes (Figure 6). All of the topologies showed a high support value. The phylogenetic tree of Anthozoa in this study showed that Bolocera sp. was clustered in the Actiniaria clade and had the closest relationship with Bolocera tuediae. The Actiniaria represented a monophyletic group and together with the sister groups Zoanthidea, Antipatharia, and Scleractinia clustered with the Hexacorallia group, which supported the classification of anthozoan (Daly, Fautin, & Cappola, 2003). Based on seven mitochondrial protein‐coding genes, Brugler and France (2007) found that zoanthid was at the base of the hexacoral clade, and the antipatharian clade had high support as a sister‐taxon to the scleractinian clade. However, in this study, based on the 13 protein‐coding genes, the antipatharians were a sister‐group to zoanthids, with a closer relationship to actiniarians, while scleractinians were located at the base of the hexacoral clade, which was identical to results obtained based on 18 S rRNA (Berntson, France, & Mullineaux, 1999). These findings also corroborated earlier studies of sea anemone phylogenetic relationships based on short mitochondrial and nucleotide sequences (Daly, Chaudhuri, Gusmão, & Rodríguez, 2008; Emblem et al., 2014).

Figure 6.

Figure 6

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Phylogenetic tree of species of Anthozoa based on ML analysis of the nucleotide datasets. Geodia neptuni was selected as outgroup. Bootstrap support values are shown on the nodes

3.8. Positive selection analysis

The selective pressures imposed on the mitogenomes of sea anemones were evaluated using CODEML from the PAML package (Table 3). Two different tree‐building methods were used because the CODEML likelihood analysis is sensitive to tree topology. There were no significantly different ω ratios between branches of genus Bolocera and other species when we set the genus Bolocera as a foreground branch using the two‐ratio model (p > .05). In the analyses of individual genes, we found that three positive selection sites (31 L and 42 N in ATP6, 570 S in ND5) showed BEB values >0.95 using branch‐site models.

Table 3.

Selective pressure analyses of the mitochondrial genes of sea anemones

Gene Branch‐site model Model compared 2△lnL LRT p‐value Positive sites
Model ln L Estimates of parameters
ATP6 Model A −3,368.2077 Site class 0.0000 1.0000 2a 2b Model A versus Model A null 2.1423 .1433 31 L 0.994**
42 N 0.991**
Proportion 0.0000 0.0000 0.9291 0.0709
Background ω 0.0719 1.0000 0.0719 1.0000
Foreground ω 0.0719 1.0000 999.0000 999.0000
Model A null −3,369.2788
ND5 Model A −9,573.8530 Site class 0.0000 1.0000 2a 2b Model A versus Model A null 0.3829 .5360 570 S 0.978*
Proportion 0.0000 0.0000 0.9074 0.0926
Background ω 0.0815 1.0000 0.0815 1.0000
Foreground ω 0.0815 1.0000 26.8046 26.8046
Model A null −9,574.0445
Trees Branch model Model compared 2△ln L LRT p‐value
Model ln L Estimates of parameters
NJ Model 1 −58,898.9152 Model 1 versus Model 0 477.4924 .0000
Two‐ratio −59,137.6137 ω0=0.0968 ω1=0.0795 Two‐ratio versus Model 0 0.0954 .9534
Model 0 −59,137.6614 ω=0.0968
ML Model 1 −58,898.6539 Model 1 versus Model 0 478.0150 .0000
Two‐ratio −59,137.6137 ω0=0.0968 ω1=0.0796 Two‐ratio versus Model 0 0.0954 .9534
Model 0 −59,137.6614 ω=0.0968
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*posterior probability >95%; **posterior probability >99%.

The NADH dehydrogenase complex, which likely functions as a proton pump (da Fonseca et al., 2008) and influences metabolic performance (Hassanin et al., 2009), has been considered important in the adaptive evolution of the mammalian mitogenome (da Fonseca et al., 2008; Xu et al., 2007). ND2 and ND6 were found to be under positive selection pressure in a mitogenome analysis of Chinese snub‐nosed monkeys, which is suggestive of adaptive changes related to high altitude and cold weather stress (Yu et al., 2011). ND6 was found to be under positive selection pressure in Tibetan horses living at high altitude (Ning et al., 2010). ATP synthase is directly associated with the produce of ATP (Mishmar et al., 2003; Weiss, Friedrich, Hofhaus, & Preis, 1991; Zhou, Shen, Irwin, Shen, & Zhang, 2014). It has been suggested that variation in ATPase proteins could result in significant variation in mitochondrial adaptation to different environments (Mishmar et al., 2003; Wallace, 2007). Members of the Caprini tribe that live in high‐altitude mountain regions show higher levels of adaptive evolution in the ATP synthase complex (Hassanin et al., 2009). The positive selection of ATP6 and ND5 observed in the present study could help us to better understand the adaptation of organisms to the deep‐sea environment.

4. CONCLUSION

This study characterized the complete mitogenome of a deep‐sea benthos species, Bolocera sp., which was speculated to be a new species of Bolocera. The study provided the following conclusions about deep‐sea organisms: (1) These organisms have monophyletic genome characteristics similar to those of shallow sea organisms: The basic gene content, order, and orientation of the species were identical to most of those reported homologous species, and phylogenetic analyses indicated that Bolocera sp. is closely related to Bolocera tuediae and belongs to the Actiniidae family. (2) Several genes experienced positive selection: Residues 31 L and 42 N in ATP6 and 570 S in ND5 were inferred to be positively selected sites for the branch of Bolocera sp. and B. tuediae, which may indicate that the genes were under positive selection pressure. (3) Novel genetic structures appeared: Some novel/unique gene features were observed in the mitogenomes of deep‐sea organisms compared with those of shallow sea species. In the mitogenome of Bolocera sp., two transposon‐like noncanonical ORFs and a CR‐like structure were detected. These novel genetic structures of Bolocera sp. may provide some clues regarding the adaptation to deep‐sea conditions. This study may shed light on the mitogenomic adaptation of sea anemones that inhabit the deep‐sea environment.

CONFLICT OF INTEREST

The authors report no conflict of interests. The authors alone are responsible for the content and the writing of the article.

ACKNOWLEDGMENTS

This work was financially supported by the Special Fund for Strategic Pilot Technology Chinese Academy of Sciences (Grant No. XDA11030203‐2), the National Science Fund for Excellent Young Scholars (Grant No. 41322038); the National Natural Science Foundation of China (Grant/Award Number: 41576145, 41606170); and GuangDong Oceanic and Fisheries Science and Technology Foundation of (A201601D03).

Zhang B, Zhang Y‐H, Wang X, Zhang H‐X, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep‐sea environment. Ecol Evol. 2017;7:4951–4962. https://doi.org/10.1002/ece3.3067

Funding information

This research was supported by Special Fund for Strategic Pilot Technology Chinese Academy of Sciences (Grant/Award Number: XDA11030203‐2); National Science Fund for Excellent Young Scholars (Grant/Award Number: 41322038); the National Natural Science Foundation of China (Grant/Award Number: 41576145, 41606170); and Guangdong Oceanic and Fisheries Science and Technology Foundation (A201601D03)

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