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Determination and Analysis of the Complete Mitochondrial DNA Sequence of Octopus dollfusi (Mollusca: Cephalopoda: Octopodidae) from China

PJZ_50_2_463-472

 

 

Determination and Analysis of the Complete Mitochondrial DNA Sequence of Octopus dollfusi (Mollusca: Cephalopoda: Octopodidae) from China

Yunjun Yan, Zhenming Lü, Tianming Wang, Yongjiu Chen, Jingwen Yang, Baoying Guo, Lihua Jiang, Changwen Wu and Liqin Liu*

National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Sciences, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China

ABSTRACT

In this study, we have determined the complete nucleotide sequence of the mitochondrial genome of Octopus dollfusi (Robson, 1932) collected from the coast of Guangdong Province, China, and analyzed the phylogenetic relationship with other cephalopod species. The results show that the mitochondrial genome of O. dollfusi composed of 15843 nucleotide pairs and encodes 13 proteins, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a major long noncoding region (LNCR) of the mitochondrion’s own protein synthesizing system. Seven of thirteen proteins, eight tRNAs are encoded by the plus strand, while the other proteins and tRNAs, as well as two rRNAs are encoded by the minus strand. Two (ND4 and ND4L) of the 13 protein coding genes of O. dollfusi began with the unorthodox translation initiation codon ATA and all others use the standard ATG. Ten protein-coding genes use TAA as the termination codon and the rest share the termination codon TAG. There are five cases where tRNA genes appear to overlap. The LNCR of O. dollfusi was 926 nucleotides and no repeated sequences were found in this LNCR. Phylogenetic analysis of 24 cephalopoda species based on the complete mitochondrial genome showed that the O. dollfusi is most closely related to Amphioctopus aegina. These results seems to support the recent notion that O. dollfusi should be considered as synonym of Amphioctopus aegina. More morphologic and molecular evidences should be involved to resolve the taxonomic status of O. dollfusi in future’s studies.


Article Information

Received 07 June 2017

Revised 14 July 2017

Accepted 23 September 2017

Available online 25 January 2018

Authors’ Contribution

ZL, LL and YY designed the study and wrote the arctile. TW and YC helped to analyze the sequence data and submit to the Genbank. BG, LJ, and CW helped to sample and identify species.

Key words

Mitochondrial genome, Octopus dollfusi, Proteins, tRNAs, Phylogenetic relationship.

DOI: http://dx.doi.org/10.17582/journal.pjz/2018.50.2.463.472

* Corresponding author: liuliqin-666@163.com

0030-9923/2018/0002-0463 $ 9.00/0

Copyright 2018 Zoological Society of Pakistan



Introduction

 

Cephalopoda is the third largest molluscan class including a great number of families and more than 800 species have been identified with high commercial value as food sources (Lindgren et al., 2004; Boyle and Rodhouse, 2007). Octopus, one genus of cephalopod with four pairs of arms, more than 200 species have been recognized and play an increasing important role in the ocean fisheries in recent years (Lindgren et al., 2004). So far, the octopus scientific classification system are continuously in revision and consummation (Guzik et al., 2005). At present, more and more new genus were separated from traditional genus Octopus (Huffard and Hochberg, 2005; Norman and Hochberg, 2005). Although morphology has been successfully employed to identify differences between subspecies or species in most coleoids, there are still many disadvantages about the taxonomic classification of this species based on morphological differences (Roper and Hochberg, 1988; Voight, 1994; Herke and Foltz, 2001).

Analysis of metazoan mitochondrial (mt) genome is a valuable tool for resolving ancient phylogenetic relationships and subtle taxonomic classification between species (Boore and Brown, 1998). Mt genomes are typically circular duplex molecules ranging in size from 14 to 18 kilobases, consisting of 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs (Boore, 1999). The mitochondrial genome has now been extensively used for studying population structure, phylogeography and phylogenetic relationships at various taxonomic levels across animal taxa based on several valuable characteristics including its small size, fast evolutionary rate, relatively conserved gene content and organization, and limited recombination (Avise et al., 2003; Liu and Cui, 2011; Xu et al., 2011; Huang et al., 2017). Some studies on taxonomic classification by using mt genomes have been reported such as the genus Echinococcus and Sotalia (Caballero et al., 2007; Nakao et al., 2007). So far, most molluscan mt genomes reported have different gene organizations, and there are large differences in mt gene organization within each class (Kurabayashi and Ueshima, 2000; Grande et al., 2002; Tomita et al., 2002; Cheng et al., 2012). Regarding Octopus, complete mtDNAs have been sequenced from some species, such as O. vulgaris, O. bimaculatus, O. conispadiceus, O. minor and O. ocellatus, which provided useful information for the future research of genetic diversity and phylogenetics (Yokobori et al., 2004; Akasaki et al., 2006; Cheng et al., 2012; Dominguez-Contreras et al., 2015; Ma et al., 2016). Comparison of mtDNA gene sequences plays an important role in solving the evolutionary history especially those involving deep branching events (Boore and Staton, 2002; Helfenbein and Boore, 2004).

Octopus dollfusi, commonly called as “marbled octopus”, is one of the most economically marine cephalopods which belongs to Octopodidae, Incirratai, Coleoidea, Cephalopoda, animalia Mollusca (Dong, 1988; Sundaram and Sawant, 2010). It is distributed mainly along Indo-China and Hong Kong (Lei et al., 2006; Sundaram and Sawant, 2010). As a kind of important economic cephalopods, O. dollfusi is a seafood with higher protein and lower fat, very high protein nutritive value, more fatty acid and mineral elements (Lei et al., 2006). The total production of O. dollfusi is very high and consumed heavily by the consumers throughout the world each year. Nevertheless, for this species, there are a lot of debates regarding its taxonomic status, to dates. O. dollfusi was firstly discovered and named by Robson after an intensive examination of stored Cephalopod samples in British museum, in 1929 and was considered as valid species, as well as O. aegina (Robson, 1932). Voss and Wiliamson (1972) and Dong (1979) supported the valid species of both O. dollfusi and O. aegina, and described the difference, in detail, of the morphology and life history between these two species (Voss and Wiliamson, 1972; Dong, 1979). However, Norman and Hochberg (2005) removed the O. dollfusi from genus octopus and considered it invalid as a synonym of A. aegina (Norman and Hochberg, 2005). Nevertheless, Chen and some other authors still regarded O. dollfusi and O. aegina as two different species when they sampled in their researches (Chen et al., 2009; Herrero et al., 2012; Gestal et al., 2015). The mtDNAs genomic information is very helpful to understand the phylogenetic and taxonomic status of species. In this study, we present the complete sequence of the mtDNA genome of the octopus species O. dollfusi (GenBank accession number KX108697). The gene arrangement of O. dollfusi shows remarkable similarity to that of Octopodiformes. Phylogenetic analysis of 24 species cephalopoda (Supplementary Table I) based on the complete mitochondrial genome showed that the O. dollfusi is most closely related to A. aegina. This study will provide important information for taxonomic status of O. dollfusi.

 

Materials and methods

PCR amplification and sequencing of mitochondrial DNA

O. dollfusi were obtained from the Zhanjiang, Guangdong, China and identified based on both the morphologic features and the COX1. According to Dong’s research, the morphology of O. dollfusi is quite unique, with a smooth body surface, longitudinal pale stripe on dorsal mantle and pale stripe between eyes, which differed from that of O. aegina (Dong, 1979). Muscle Tissue samples were reserved in 95% ethanol for molecular analysis and stored at -20°C. Whole genomic DNA was extracted from muscle tissue of individual specimens using the phenol-chloroform method (Sambrook et al., 1989). Primers were designed according to the conserved regions of cephalopod mtDNA sequences present in GenBank. Primers were generated by Primer Premier 5 and listed in Supplementary Table II. Sequences were amplified by PCR with long and accuracy Taq (LA-Taq) DNA polymerase (Takara) following the manufacturer’s protocol. Then the PCR product sequencing was sequenced. Primer synthesis and PCR product were completed by Thermo Fisher Scientific Company. The complete mtDNA genome were assembled after the amplified regions were individually sequenced.

Gene annotation and analysis

Sequences were assembled using Geneious 4.5.3 (http://www.geneious.com). PCGs and rRNAs in mtDNA were identified based on a comparison with mtDNA sequences of O. vulgaris (Accession No. NC_006353.1), O. minor (Accession No. NC_015896.1), O. ocellatus (Accession No. NC_007896.1) and A. aegina (Accession No. NC_029702.1). tRNAs sequences were verified in sequences between protein and rRNA genes by their ability to fold into the typical cloverleaf structures characteristic of mt-tRNA genes, and from the trinucleotide in the anticodon position of these structures either using the tRNAscan-SE Search Server (http://lowelab.ucsc.edu/tRNAscan-SE/) and corrected through alignment with other cephalopod sequences. Sequence alignment was deduced by BioEdit 7.0 using ClustalW alignment. The complete nucleotide sequence has been submitted to GenBank (Accession number: KX108697).

Phylogenetic analysis

To estimate phylogenetic relationships, phylogenetic tree was constructed depending on the Neighbor-Joining (NJ) Method of Molecular Evolutionary Genetics Analysis (MEGA 6.0) based on the 24 complete mitochondrial genome sequences of cephalopods. The bootstrap value was repeated 1000 times to obtain the confidence value for the analysis (Kimura, 1980).

 

Table I.- Mitochondrial genome characteristics of O. dollfusi.

Gene

Position

Size(bp)

Codon

Intergenic nucleotidesa

Strand

From

To

Nucleotide

Amino acid

Initiation

Stop

COIII

1

780

780

259

ATG

TAA

0

L

tRNALys

790

855

66

 

 

 

9

L

tRNAAla

854

919

66

 

 

 

-2

L

tRNAArg

919

985

67

 

 

 

-1

L

tRNAAsn

986

1052

67

 

 

 

0

L

tRNAIle

1053

1119

67

 

 

 

0

L

ND3

1120

1470

351

116

ATG

TAA

0

L

tRNASer

1469

1537

69

 

 

 

-2

L

ND2

1538

2575

1038

345

ATG

TAA

0

L

COI

2547

4079

1533

510

ATG

TAA

-29

L

COII

4085

4771

687

228

ATG

TAA

5

L

tRNAAsp

4774

4840

67

 

 

 

2

L

ATP8

4842

4997

156

51

ATG

TAA

1

L

ATP6

4999

5691

693

230

ATG

TAG

1

L

tRNAPhe

5716

5783

68

 

 

 

24

H

ND5

5739

7475

1737

579

ATG

TAA

-45

H

tRNAHis

7476

7540

64

 

 

 

0

H

ND4

7544

8887

1344

447

ATA

TAA

3

H

ND4L

8884

9189

306

101

ATA

TAA

-4

H

tRNAThr

9184

9247

64

 

 

 

-6

L

tRNASer

9250

9315

66

 

 

 

2

H

CYTB

9315

10454

1140

379

ATG

TAA

-1

H

ND6

10447

10959

513

170

ATG

TAG

-8

H

tRNAPro

10961

11027

67

 

 

 

1

H

ND1

11031

11969

939

312

ATG

TAG

3

H

tRNALeu

11970

12040

71

 

 

 

0

H

tRNALeu

12040

12106

67

 

 

 

-1

H

16S rRNA

12105

13408

1304

 

 

 

-2

H

tRNAVal

13410

13478

69

 

 

 

1

H

12s rRNA

13480

14440

961

 

 

 

1

H

tRNAMet

14442

14509

68

 

 

 

1

H

tRNACys

14513

14577

65

 

 

 

3

H

tRNATyr

14576

14641

66

 

 

 

-2

H

tRNATrp

14642

14707

66

 

 

 

0

H

tRNAGln

14708

14775

68

 

 

 

0

H

tRNAGly

14779

14847

69

 

 

 

3

H

tRNAGlu

14846

14917

72

 

 

 

-2

H

Control region

14918

15843

926

 

 

 

0

H

aNumbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.

 

Results and discussion

Organization of the mitochondrial genome

Gene content and organization of the mtDNA molecule of O. dollfusi were given in Table I. Moreover, the mitochondrial gene map of O. dollfusi was also shown in Figure 1. The size of O. dollfusi molecule is 15843 nucleotide pairs, which is similar with that of the other octopuses (Cheng et al., 2012; Dominguez-Contreras et al., 2015; Zhang et al., 2015; Ma et al., 2016). As in almost all metazoan mtDNAs, the O. dollfusi mtDNA molecule contains 13 PCGs, 22 tRNAs, 2 rRNAs, and a major non-coding region (926 in length) of the mitochondrion’s own protein synthesizing system. The mitogenome base composition was A: 42.15%, T: 33.93%, C: 16.33%, and G: 7.59%, with A+T content (76.08%) was much higher than the G+C content, which is in common with other invertebrate mitogenomes (Zhang et al., 2015) (Supplementary Table III). 13 PCGs can be classified into two parts: COX3, ND3, ND2, COX1, COX2, ATP8, and ATP6 were encoded by the plus strand (light-strand), the rests including ND1, ND5, ND4, ND4L, CYTB and ND6 were encoded by the minus strand (heavy strand). The two rRNA genes, 16SrRNA (1304 bp) and 12SrRNA (960 bp), are located between tRNA-Leu and tRNA-Met and are separated by tRNA-Val gene. In addition, there are three nucleotide overlaps between ND2 and COI, ND4 and ND4L and Cytb and ND6, respectively. The largest overlap is 29 nucleotides, between ND4 and COI genes (Table I).

 

 

Table II.- Codon usage in the 13 mt-PCGs of O. dollfusi.

Phe

TTT

306

Ser2

TCT

82

Tyr

TAT

153

Cys

TGT

57

 

TTC

44

 

TCC

24

 

TAC

18

 

TGC

4

Leu1

TTA

375

 

TCA

121

TER

TAA

10

Trp

TGT

87

 

TTG

80

 

TCG

6

 

TAG

3

 

TGG

12

Leu2

CTT

35

Pro

CCT

63

His

CAT

58

Arg

CGT

14

 

CTC

9

 

CCC

14

 

CAC

17

 

CGC

0

 

CTA

53

 

CCA

46

Gln

CAA

52

 

CGA

33

 

CTG

2

 

CCG

0

 

CAG

7

 

CGG

5

Ile

ATT

325

Thr

ACT

57

Asn

AAT

150

Ser1

AGT

57

 

ATC

38

 

ACC

11

 

AAC

33

 

AGC

4

Met

ATA

280

 

ACA

60

Lys

AAA

88

 

AGA

58

 

ATG

43

 

ACG

4

 

AAG

14

 

AGG

26

Val

GTT

97

Ala

GCT

59

Asp

GAT

60

Gly

GGT

74

 

GTC

1

 

GCC

14

 

GAC

10

 

GGC

3

 

GTA

87

 

GCA

43

Glu

GAA

55

 

GGA

106

 

GTG

21

 

GCG

9

 

GAG

23

 

GGG

39

The number of occurrences of each codon in the 13 mt-PCGs of O. dollfusi is given. Assumed modifications relative to the standard genetic code are AGA and AGG specify serine; ATA specific methionine and TGA specific tryptophan.

 

So far, complete mtDNA sequences have been determined at least 30 species in cephalopods, a very small sampling compared to those available for molluscs. In recent two years, more and more cephalopod complete mtDNA sequences were revealed such as A. aegina, Allonautilus scrobiculatus, O. bimaculatus, Illex argentines, Loligo duvaucelii, Loliolus uyii, Sepiella maindroni (Domínguez-Contreras et al., 2015; Groth et al., 2015; Jiang et al., 2015, 2016; Zhang et al., 2015). The mtDNA of the O. dollfusi is fairly typical in many respects, with a size, gene content, and A+T-richness similar to those most common for animal mtDNAs. The mtDNA of O. dollfusi shares the same structure and characteristics with other cephalopods, which corresponds to the fact the structure and arrangement order of protein-coding genes and rRNAs of cephalopods are relatively conservative compared to other molluscs.

Codon usage of PCGs

Codon usage among the 13 PCGs was given in Tables I and II. All amino acids specifying codons and the two termination codons, TAA and TAG are used for O. dollfusi. Non-standard initiation codons are often used in mitochondrial genomes (Wolstenholme, 1992). As shown in Table I, ND4 and ND4L start with ATA as an initiation codon and the last protein-coding genes start with an ATG initiation codon. Except for Ten protein-coding genes (COX3, ND3, ND2, COX1, COX2, ATP8, ND4, ND4L, ND5 and CYTB) use TAA as the termination codon, the rest three protein-coding genes (ATP6, ND6, ND1,) share the termination codon TAG. Overlapping nucleotides in protein are commonly observed for mtDNAs, which are thought to be translated as a bicistron. For example, ND2 is inferred to overlap COI by 29 nucleotides; ND4L is inferred to overlap ND4 by 4 nucleotides and ND6 is inferred to overlap Cytb by 8 nucleotides.

The frequencies of nucleotides in codon third positions are higher for T (44.05%) and A (41.56%) and lower for G (7.86%) and C (6.53%). This differed obviously with the base content in the sense strands of the PCGs (T, 43.02%; A, 31.68%; G, 14.03%; C, 11.28%). The overall A +T content in the sense strands of the PCGs (74.70%) shows the obvious bias in the AT nucleotide composition. Statistics found that the A+T content in the sense strands of metazoan mt-PCGs is from 83.3% (Apis mellifera) to 54.9% (human) (Anderson et al., 1981; Crozier and Crozier, 1993). The A+T content in the sense strands of the PCGs (74.70%) of O. dollfusi is within the range of values.

As shown in Table II, the content of Arg is the lowest and there are 5 amino acids (from high to low: Leu, Ser, Ile, Phe, Met) used in a high frequency. In particular, the content of Leu is the highest, which is a common phenomenon in cephalopods. Some scholars suggested that Leu may effectively participate in transmembrane transport as hydrophobic amino acids since most of the proteins encoded by mt-PCGs are transmembrane proteins (Obuchi et al., 2001).

rRNA genes

The O. dollfusi mt-rRNA genes (16S and 12S) were identified from nucleotide sequence similarities to the corresponding genes in other cephalopod species. As in mammalian and some other mtDNAs, the two mt-rRNA genes are separated from each other by a single tRNA gene (Bibb et al., 1981; Clary and Wolstenholme, 1985). As shown in Table I and Figure 1, 16S and 12S genes are separated from each other by tRNA-Val in O. dollfusi mtDNA. The nucleotides adjacent to the tRNA-Leu and tRNA-Val are tentatively identified as the 5’ and 3’ ends of the 16S gene, and the nucleotides adjacent to the tRNA-Val and tRNA-Met are tentatively identified as the 5’ and 3’ ends of the mt-12S gene (Pont-Kingdon et al., 1994; Beagley et al., 1998). The 16S and 12S genes thus defined are 1304 and 961 ntp, respectively in O. dollfusi. Compared to other Octopodidae species, the length of O. dollfusi rRNAs are in the normal range and closest to A. aegina (Supplementary Table IV).

tRNA genes

Sequences were identified according to the potential secondary structures. The 22 O. dollfusi mt-tRNA genes vary in size from 64 nucleotides to 72 nucleotides (Table I). There is strict conservation of the size of the amino-acyl stem (7 ntp), the anticodon stem (5 ntp), and the anticodon loop (7 nucleotides) (Supplementary Fig. S1). The variable loop is 4 or 5 nucleotides lied between the anticodon and the TΨC arms (Supplementary Fig. S1). Within the TΨC arm, the stem varies from 3 to 6 ntp, and the loop varies from 3 to 10 nucleotides (Supplementary Fig. S1).

There are five cases where tRNA genes appear to overlap (Table I). As follows: tRNA-Ala appears to overlap tRNA-Lys by two nucleotides, GG; tRNA-Arg appears to overlap tRNA-Ala by one nucleotide, A; tRNA-leu (TAA) appears to overlap tRNA-leu (TAG) by one nucleotides, T; tRNA-Tyr appears to overlap tRNA-Cys by two nucleotides, CC; tRNA-Glu appears to overlap tRNA-Gly by two nucleotides, AT. It appears for each case that cleavage to form a complete downstream tRNA followed by polyadenylation of the upstream tRNA would yield fully formed, well-paired structures for all (Yokobori and Pääbo, 1995).

 

 

Except for at the junctions of ND2/COI, COI/COII, ATP8/ATP6, ND4/ND4L and Cytb/ND6, tRNAs are interspersed between protein and rRNA encoding sequences (Table I). It has been suggested that short sequences at 5’ end of some proteins genes with secondary structure potential may serve as signals for transcript processing in the absence of tRNA (Bibb et al., 1981). In cases where tRNAs are the intervening sequences they may serve as signals for processing larger transcripts from which proteins are translated (Battey and Clayton, 1981; Ojala et al., 1981).

Long-noncoding regions (LNCRs)

In cephalopod, species in Decapodiformes carry two or three near identical LNCRs, while species in Octopodiformes and Nautiloida carry only one LNCR in the mitochondrial genomes (Yokobori et al., 2004, 2007; Akasaki et al., 2006; Boore, 2006; Cheng et al., 2011). In LNCRs, the control region (CR) or displacement loop region (D-loop) plays the very essential role in controlling elements and/or start points of replication and transcription (Wolstenholme, 1992). The control region is also called A+T-rich region because of its high content of adenine and thymine. The length of CR in O. dollfusi was 926 nucleotides, which was not an unusually large number (Supplementary Table IV). The previous study found that three of the five species with only one CR carry repeated sequences and these repeats were the major cause for the elongation of CR (Yokobori et al., 2004; Akasaki et al., 2006; Boore, 2006). Such nucleotide repeats were not found in the CR of O. dollfusi as well as A. aegina, O. minor and V. infernalis (Yokobori et al., 2007; Cheng et al., 2011; Zhang et al., 2015).

Phylogenetic analysis

Phylogenetic tree was produced by the MEGA 6.0 using ClustalW alignment with 24 complete mitochondrial genome sequences of cephalopods (Fig. 2). Phylogenetic analysis indicated that O. dollfusi is most closely related to A. aegina. The group including O. dollfusi and A. aegina is sister to A. fangsiao and O. ocellatus. In Octopoda, O. conispadiceus was farthest to O. dollfusi and O. minor came second. The morphological and ecological data also supported the phylogenic result. Both O. dollfusi and O. ocellatus belong to the short wrist type octopus and the hectocotylized arms are similar with each other while the hectocotylized arms of O. minor differs obviously with that of the other two octopus species. It also suggested a monophyletic status for the Octopoda with strong support.

Vampyroteuthis infernalis is the sister group of Octopoda, which is consistent with Cheng’s result used LNCRs and PCGs (Cheng et al., 2011). Since the phylogenetic researches based on morphological data have largely avoid the genus Octopus, the molecular phylogenetic analyses of octopus would play more important roles. The mt gene organization of V. infernalis and Octopoda have more similar to the proposed ancestral cephalopod mt gene organization than the Decapoda (Cheng et al., 2011). Combined phylogenetic analysis of both molecular and morphological data, Vampyromorpha has been inferred to be the sister group to Octopoda (Lindgren et al., 2004).

Phylogenetic results seemed to support Norman’s notion that O. dollfusi should be considered as synonym of A. aegina. To further confirm this notion, we compared the mt genome sequence of O. dollfusi with all the available partial sequence either under the name O. dollfusi, O. aegina, or under the name A. aegina submitted by authors from around the world. The results showed that all these partial sequence has quite high homology with the mt genome sequence of O. dollfusi. All the sequences seemed to form a monophyly, suggesting likely belonging to a single species. Otherwise, at least two lineages should be recognized if O. dollfusi and A. aegina are valid different species. However, we still argue that it is far from jumping a conclusion that O. dollfusi should be regarded as synonym of A. aegina. In our another attempt to study the genetic variation of different population of O. dollfusi along the coast of China, we found that there likely existed cryptic or subspecies in O. dollfusi (data unpublished). What the possible cryptic or subspecies means to O. dollfusi, and A. aegina still awaiting further study and more solid evidences.

 

Conclusion

 

In conclusion, this study determined the complete mtDNA sequence for O. dollfusi. The availability of the complete mitochondrial genome sequence of the O. dollfusi provides useful information for further investigations of phylogenetic relationship, taxonomic resolution and phylogeography of the cephalopod and other cephalopods. Either phylogenetic analysis using whole mt genome sequence or nucleotide BLAST analysis using partial mt genes disclosed high sequence homology between O. dollfusi and A. aegina, supports the notion that O. dollfusi is the synonym of A. aegina. More efforts should be made to resolve the taxonomic status of O. dollfusi in the future.

 

Acknowledgements

 

The authors alone are responsible for the content and writing of the paper. This study was supported by National Natural Science Foundation of China (41576131), National Natural Science Foundation of Zhejiang (LY13C190001) and the Open Foundation from Marine Sciences in the Most Important Subjects of Zhejiang (No.20160110).

 

Supplementary material

There is supplementary material associated with this article. Access the material online at: http://dx.doi.org/10.17582/journal.pjz/2018.50.2.463.472

 

Statement of conflict of interest

The authors report no conflicts of interest.

 

References

 

Akasaki, T., Nikaido, M., Tsuchiya, K., Segawa, S., Hasegawa, M. and Okada, N., 2006. Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol. Phylogen. Evolut., 38: 648-658. https://doi.org/10.1016/j.ympev.2005.10.018

Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A. and Sanger, F., 1981. Sequence and organization of the human mitochondrial genome. Nature, 290: 457-465. https://doi.org/10.1038/290457a0

Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., And, C.A.R. and Saunders, N.C., 2003. Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. System., 18: 489-522. https://doi.org/10.1146/annurev.es.18.110187.002421

Battey, J. and Clayton, D.A., 1981. The transcription map of human mitochondrial DNA implicates transfer rna excision as a major processing event. J. biol. Chem., 255: 11599-11606.

Beagley, C.T., Okimoto, R. and Wolstenholme, D.R., 1998. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): Introns, a paucity of trna genes, and a near-standard genetic code. Genetics, 148: 1091-1108.

Bibb, M.J., Etten, R.A.V., Wright, C.T., Walberg, M.W. and Clayton, D.A., 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell, 26: 167-180. https://doi.org/10.1016/0092-8674(81)90300-7

Boore, J.L. and Brown, W.M., 1998. Big trees from little genomes: Mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Develop., 8: 668-674. https://doi.org/10.1016/S0959-437X(98)80035-X

Boore, J.L., 1999. Animal mitochondrial genomes. Nucleic Acids Res., 27: 1767-1780.

Boore, J.L. and Staton, J.L., 2002. The mitochondrial genome of the sipunculid Phascolopsis gouldii supports its association with annelida rather than mollusca. Mol. Biol. Evol., 19: 127-137. https://doi.org/10.1093/oxfordjournals.molbev.a004065

Boore, J.L., 2006. The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics, 7: 1-13. https://doi.org/10.1186/1471-2164-7-182

Boyle, P. and Rodhouse, P., 2007. Cephalopods: Ecology and fisheries (eds. P. Boyle and P. Rodhouse). Blackwell Science Ltd., NJ, USA. https://doi.org/10.1002/9780470995310

Caballero, S., Trujillo, F., Vianna, J. A., Barrios-Garrido, H., Montiel, M. G., Beltrán-Pedreros, S. and Marmontel, M., 2007. Taxonomic status of the genus sotalia: species level ranking for “tucuxi” (Sotalia fluviatilis) and “costero” (Sotalia guianensis) dolphins. Mar. Mammal Sci., 23: 358-386. https://doi.org/10.1111/j.1748-7692.2007.00110.x

Chen, X.J., Liu, B.L. and Wang, Y.G., 2009. Cephalopod of the World. Ocean Press, Beijing.

Cheng, R., Zheng, X., Lin, X., Yang, J., and Li, Q., 2012. Determination of the complete mitochondrial DNA sequence of Octopus minor. Mol. Biol. Rep., 39: 3461-3470. https://doi.org/10.1007/s11033-011-1118-2

Clary, D.O. and Wolstenholme, D.R., 1985. The ribosomal RNA genes of drosophila mitochondrial DNA. Nucl. Acids Res., 13: 4029-4045. https://doi.org/10.1093/nar/13.11.4029

Crozier, R.H. and Crozier, Y.C., 1993. The mitochondrial genome of the honeybee Apis mellifera: Complete sequence and genome organization. Genetics, 133: 97-117.

Domínguez-Contreras, J.F., Munguia-Vega, A., Ceballos-Vázquez, B.P. and Arellano-Martinez, M., 2015. The complete mitochondrial genome of Octopus bimaculatus Verrill, 1883 from the Gulf of California. Mitochondrial DNA Part A, 27: 4584-4585. https://doi.org/10.3109/19401736.2015.1101575

Dong, Z., 1979. A preliminary report of the cephalopods from the Xisha waters, Guangdong Province, China. Stud. Mar. Sin., 15: 71-74.

Dong, Z., 1988. Chinese fauna, mollusca, cephalopods. Science Press, Beijing.

Gestal, C. and Castellanos-Martínez, S., 2015. Understanding the cephalopod immune system based on functional and molecular evidence. Fish Shellf. Immunol., 46: 120-130.

Grande, C., Templado, J., Cervera, J.L. and Zardoya, R., 2002. The complete mitochondrial genome of the nudibranch Roboastra europaea (Mollusca: Gastropoda) supports the monophyly of opisthobranchs. Mol. Biol. Evolut., 19: 1672-1685. https://doi.org/10.1093/oxfordjournals.molbev.a003990

Gray, J.E., 1849. Catalogue of the mollusca in the collection of the British museum. Cephalopoda Antepedia, London, pp. 164.

Groth, J.G., Arbisser, I., Landman, N.H. and Barrowclough, G.F., 2015. The mitochondrial genome of Allonautilus (Mollusca: Cephalopoda): Base composition, noncoding-region variation, and phylogenetic divergence. Am. Mus. Novitates, 3834: 1-13. https://doi.org/10.1206/3834.1

Guzik, M.T., Norman, M.D. and Crozier, R.H., 2005. Molecular phylogeny of the benthic shallow-water Octopuses (Cephalopoda: Octopodinae). Mol. Phylogen. Evolut., 37: 235-248. https://doi.org/10.1016/j.ympev.2005.05.009

Helfenbein, K.G. and Boore, J.L., 2004. The mitochondrial genome of Phoronis architecta--comparisons demonstrate that phoronids are lophotrochozoan protostomes. Mol. Biol. Evolut., 21: 153-157. https://doi.org/10.1093/molbev/msh011

Herke, S. and Foltz, D., 2001. Phylogeography of two squid (Loligopealei and L. Plei) in the gulf of mexico and northwestern atlantic ocean. Mar. Biol., 140: 103-115.

Herrero, B., Lago, F.C., Vieites, J.M. and Espiñeira, M., 2012. Rapid method for controlling the correct labeling of products containing European squid (Loligo vulgaris) by fast real-time PCR. Europ. Fd. Res. Technol., 234: 77-85. https://doi.org/10.1007/s00217-011-1617-3

Huang, Z., Tu, F. and Ke, D., 2017. Complete mitochondrial genome of blue-throated bee-eater merops viridis (coraciiformes: meropidae) with its taxonomic consideration. Pakistan J. Zool., 49: 79-84. https://doi.org/10.17582/journal.pjz/2017.49.1.79.84

Huffard, C.L. and Hochberg, F.G., 2005. Description of a new species of the genus Amphioctopus (Mollusca: Octopodidae) from the hawai’ian islands. Molluscan Res., 25: 113-128.

Jiang, L., Liu, W., Zhang, J., Zhu, A. and Wu, C., 2015. Complete mitochondrial genome of argentine shortfin squid (Illex Argentines). Mitochondrial DNA, 27: 3335-3336. https://doi.org/10.3109/19401736.2015.1018210

Kimura, M., 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. mol. Evolut., 16: 111-120. https://doi.org/10.1007/BF01731581

Kurabayashi, A. and Ueshima, R., 2000. Complete sequence of the mitochondrial DNA of the primitive opisthobranch gastropod Pupa strigosa: Systematic implication of the genome organization. Mol. Biol. Evol., 17: 266-277. https://doi.org/10.1093/oxfordjournals.molbev.a026306

Lei, X., Zhao, S., Yang, Z., Fan, X. and Wu, H., 2006. The nutrient analysis and evaluation of octopus dollfusi in south china sea. Acta Nutrim. Sin., 2006: 58-61

Jiang, L.H., Ge, C.K., Liu, W., Wu, C.W. and Zhu, A.Y., 2016. Complete mitochondrial genome of the Loligo duvaucelii. Mitochondrial DNA Part A: DNA Mapp. Seq. Anal., 27: 2723-2724. https://doi.org/10.3109/19401736.2014.987249

Lindgren, A.R., Giribet, G. and Nishiguchi, M.K., 2004. A combined approach to the phylogeny of Cephalopoda (mollusca). Cladistics, 20: 454-486. https://doi.org/10.1111/j.1096-0031.2004.00032.x

Liu, Y. and Cui, Z., 2010. Complete mitochondrial genome of the asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): Gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods. Mol. Biol. Rep., 37: 2559-2569. https://doi.org/10.1007/s11033-009-9773-2

Liu, Y. and Cui, Z., 2011. Complete mitochondrial genome of the chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): Genome characterization and phylogenetic considerations. Mol. Biol. Rep., 38: 403-410. https://doi.org/10.1007/s11033-010-0122-2

Ma, Y., Zheng, X., Cheng, R. and Li, Q., 2016. The complete mitochondrial genome of Octopus conispadiceus (Sasaki, 1917) (Cephalopoda: Octopodidae). Mitochondrial DNA Part A: DNA Mapp. Seq. Anal., 27: 1058-1059. https://doi.org/10.3109/19401736.2014.928866

Nakao, M., Mcmanus, D.P., Schantz, P.M., Craig, P.S. and Ito, A., 2007. A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrialgenomes. Parasitology, 134: 713-722. https://doi.org/10.1017/S0031182006001934

Norman, M.D. and Hochberg, F.G., 2005. The current state of octopus taxonomy. pp. 127-154.

Norman, M.D. and Sweeney, M.J., 1997. The shallow-water Octopuses (Cephalopoda: Octopodidae) of the philippines. Inverteb. System., 11: 89-140. https://doi.org/10.1071/IT95026

Obuchi, N., Takahashi, M., Nouchi, T., Satoh, M., Arimura, T., Ueda, K., Akai, J., Ota, M., Naruse, T. and Inoko, H., 2001. Identification of MICA alleles with a long Leu-repeat in the transmembrane region and no cytoplasmic tail due to a frameshift-deletion in exon 4. Tissue Antigens, 56: 520-535. https://doi.org/10.1034/j.1399-0039.2001.057006520.x

Ojala, D., Montoya, J. and Attardi, G., 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature, 290: 470-474. https://doi.org/10.1038/290470a0

Pont-Kingdon, G.A., Beagley, C.T., Okimoto, R. and Wolstenholme, D.R., 1994. Mitochondrial DNA of the sea anemone, Metridium senile (cnidaria): Prokaryote-like genes for tRNAf-met and small-subunit ribosomal RNA, and standard genetic code specificities for AGR and ATA codons. J. mol. Evolut., 39: 387-399. https://doi.org/10.1007/BF00160271

Robson, G.C., 1932. A monograph of the recent Cephalopoda based on the collections in the British Museum (Natural History). Nature, 129: 636-636. https://doi.org/10.1038/129636b0

Roper, C.F.E. and Hochberg, F.G., 1988. Behavior and systematics of cephalopods from lizard island, australia, based on color and body patterns. Malacologia, 29: 153-193.

Saccone, C., Giorgi, C.D., Gissi, C., Pesole, G. and Reyes, A., 1999. Evolutionary genomics in metazoa: The mitochondrial DNA as a model system. Gene, 238: 195-209. https://doi.org/10.1016/S0378-1119(99)00270-X

Sambrook, J., Fritsch, F.E., Maniatis, T., 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, pp. 463-471.

Sarvesan, R., 1969. Some observations on parental care in Octopus dollfusi robson (cephalopoda : Octopodidae). J. Mar. Assoc. India, 11: 203-205.

Shen, X., Wang, H., Ren, J., Tian, M. and Wang, M., 2010. The mitochondrial genome of Euphausia superba (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers. Mol. Biol. Rep., 37: 771-784. https://doi.org/10.1007/s11033-009-9602-7

Sundaram, S. and Sawant, A.D., 2010. Occurrence of Octopus dollfusi robson 1928 in maharashtra waters. Mar. Fish. Inform. Serv.; Tech. Extension Ser., http://eprints.cmfri.org.in/id/eprint/8451

Tomita, K., Yokobori, S.I., Oshima, T., Ueda, T. and Watanabe, K., 2002. The cephalopod Loligo bleekeri mitochondrial genome: Multiplied noncoding regions and transposition of tRNA genes. J. mol. Evolut., 54: 486-500. https://doi.org/10.1007/s00239-001-0039-4

Voight, J.R., 1994. Morphological variation in shallow-water Octopuses (Mollusca: Cephalopoda). J. Zool., 232: 491-504. https://doi.org/10.1111/j.1469-7998.1994.tb01590.x

Voss, G.L. and Williamson, G.R., 1972. Cephalopods of Hong Kong. Hong Kong Government Press, Hong Kong, pp. 138.

Wolstenholme, D.R., 1992. Animal mitochondrial DNA: Structure and evolution. Int. Rev. Cytol., 141: 173-216. https://doi.org/10.1016/S0074-7696(08)62066-5

Xu, K., Kanno, M., Yu, H., Li, Q. and Kijima, A., 2011. Complete mitochondrial DNA sequence and phylogenetic analysis of zhikong scallop Chlamys farreri (Bivalvia: Pectinidae). Mol. Biol. Rep., 38: 3067-3074. https://doi.org/10.1007/s11033-010-9974-8

Yokobori, S., Fukuda, N., Nakamura, M., Aoyama, T. and Oshima, T., 2004. Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes. Mol. Biol. Evolut., 21: 2034-2046. https://doi.org/10.1093/molbev/msh227

Yokobori, S. and Pääbo, S., 1995. Transfer rna editing in land snail mitochondria. Proc. natl. Acad. Sci. U.S.A., 92: 10432-10435. https://doi.org/10.1073/pnas.92.22.10432

Yokobori, S.I., Lindsay, D.J., Yoshida, M., Tsuchiya, K., Yamagishi, A., Maruyama, T. and Oshima, T., 2007. Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis , and extant cephalopods. Mol. Phylogen. Evolut., 44: 898-910. https://doi.org/10.1016/j.ympev.2007.05.009

Zhang, X., Zheng, X., Ma, Y. and Li, Q., 2015. Complete mitochondrial genome and phylogenetic relationship analyses of Amphioctopus aegina (Gray, 1849) (Cephalopoda: Octopodidae). Mitochondrial DNA, 6: 1-2. https://doi.org/10.3109/19401736.2015.1060425

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