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Complete Mitochondrial Genomes of Two Oriental Sweetlips, Plectorhinchus orientalis and Plectorhinchus vittatus (Perciformes: Haemulidae) with the Molecular Analysis on their Synonym Controversies

PJZ_51_3_871-885

 

 

Complete Mitochondrial Genomes of Two Oriental Sweetlips, Plectorhinchus orientalis and Plectorhinchus vittatus (Perciformes: Haemulidae) with the Molecular Analysis on their Synonym Controversies

Rishen Liang*, Meng Zhou, Zhenxiang Lin, Guozhang Li, Yuan Chen, Xuan Lin and Zaohe Wu

College of Animal Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China

ABSTRACT

Plectorhinchus orientalis and Plectorhinchus vittatus were two species of colorful coral reef sweetlips which distribute in the areas of Indo-Western Pacific. The two species have long been considered as a synonym (oriental sweetlips) in morphology. In order to investigate the validity of two species at the molecular level, complete mitochondrial genomes of the two species were first determined. The genomes were 16,546 bp (P. orientalis) and 16,545 bp (P. vittatus) in size, respectively, which both consisted of a typical structure of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one noncoding control region. Genomic composition, organization and gene order were similar to that obtained in most vertebrates. By comparative analysis of the two genomes, 941 variable sites (5.69%) were found. Sequence divergences of 13 protein-coding genes, 2 rRNA genes and one control region which are commonly used as molecular markers between the two species ranged from 2.4% (12S rRNA) to 11.2% (ND6), all divergence values were larger than 2%. Great variations of Cyt b and COI between P. orientalis and P. vittatus were revealed to be 6.0% and 7.4%, respectively, which were largely greater than the threshold of species diagnosis divergence value of 2%. Inner individual divergence values of each species were less than 0.5%. In the molecular phylogenetic trees, the longer branch length also clearly distinguished the independent placement of the two species. These results revealed great genetic differences between P. orientalis and P. vittatus, and strongly suggested that they might be two distinct species and should not be placed as synonym.


Article Information

Received 11 August 2017

Revised 10 October 2017

Accepted 13 November 2017

Available online 19 March 2019

Authors’ Contribution

RL and ZW designed the research and wrote the manuscript. RL and MZ collected the samples. RL, ZL and GL carried out experiments. YC and LX analyzed sequencing data and experimental results.

Key words

Complete mitochondrial genome, Plectorhinchus orientalis, Plectorhinchus vittatus, Molecular phylogeny, Mitogenome.

DOI: http://dx.doi.org/10.17582/journal.pjz/2019.51.3.871.885

* Corresponding author: cheetahliang@126.com

0030-9923/2019/0003-0871 $ 9.00/0

Copyright 2019 Zoological Society of Pakistan



Introduction

The vertebrate mitochondrial genome (mitogenome) is a small, double-stranded and circular DNA ranging in size from 15-20 kb. The structural gene organization is quite conserved within vertebrate mitogenome which contains 13 protein-coding genes, 2 ribosomal RNA genes (12S and 16S), 22 transfer RNA genes and one noncoding control region. In addition, mtDNA possesses two main non-coding regions involved in replication and transcription processes: the control region or D-loop and the light-strand replication origin or OL (Clayton, 1992; Shadel and Clayton, 1997; Boore, 1999). The mitochondrial DNA has been extensively used as a marker for molecular evolution, genetic diversity studies and phylogenetic analyses due to its compact size, maternal inheritance, rapid evolutionary rate and lack of recombination (Inoue et al., 2001; Miya et al., 2003; Saitoh et al., 2006; Kawahara et al., 2008). In fish, the mitogenome was first reported in freshwater loach (Crossostoma lacustre) by Tzeng et al. (1992). At the time of writing, complete mitogenomes from more than 472 species in Perciformes are available in NCBI database.

Family Haemulidae belongs to the suborder Percodei of order Perciformes, which comprised two subfamilies: Plectorhynchinae (sweetlips) and Haemulinae (grunts). Sweetlips are globally marine fish and mainly found in the oceanic waters of tropical, subtropical water along the Indo-Western Pacific. Most colorful sweetlips represent a drastic change in their external coloration appearance from juvenile to adult, which makes difficulties in species identification. Two oriental sweetlips Plectorhinchus orientalis (Bloch, 1793) and Plectorhinchus vittatus (Linnaeus, 1758) are common colorful sweetlips and mainly distributed in the areas of Indo-Western Pacific. P. vittatus has been widely known as P. orientalis (Satapoomin and Randall 2000), and most studies suggested P. orientalis and P. vittatus refer to the same species: Oriental sweetlips (McKay, 1984, 2001; Randall and Lim, 2000; Gillibrand et al., 2007; Unsworth, 2010) and considered P. orientalis as synonym of P. vittatus (Randall and Johnson, 2000; McKay, 2001; Randall, 2005; Froese and Pauly, 2014). Randall and Johnson (2000) has resurrected P. vittatus (Linnaeus) as an older name. Recently, some studies have separated oriental sweetlips from the Indian Ocean and Pacific Ocean populations and considered P. vittatus as the Indian Ocean populations (Indian Ocean oriental sweetlips) and P. orientalis (oriental sweetlips) as the Pacific Ocean populations. Despite a large number of morphology-based hypotheses, no molecular studies have been examined on the two debated species. As mention above, mitochondrial DNA has become a very useful marker for species identification and phylogenetic studies. Thus, further studies of genetic characteristics of P. orientalis and P. vittatus based on multiple mitochondrial gene markers appear necessary to recover conclusive phylogenetic relationships of the two species and resolve the classification and identification problem.

In the present study, we first reported the complete mitogenome sequences of P. orientalis and P. vittatus and further compared their genome structure and organization, nucleotide variation and codon usage. We also reported the phylogenetic analysis using protein sequences from P. orientalis, P. vittatus and other Haemulidae species to clarify the interrelationship of the two species and investigate their evolutionary position within Haemulidae.

 

Materials and Methods

Sweetlips samples collection and genomic DNA extraction

Sample of P. orientalis was collected in its natural habitats, the coral reef areas of Jiyin Island in Paracel Islands. Sample of P. vittatus was a vouchered specimens obtained from SAIAB (South African Institute for Aquatic Biodiversity). A small piece of fresh muscle was sampled and preserved in 95% ethanol and total genomic DNA was extracted using a Tissue Genomic DNA Extraction kit (Omega, USA) following the manufacturer’s protocol and stored at -20°C. All experimental procedures were conducted in conformity with institutional guidelines for the care and use of laboratory animals, and protocols were approved by the Institutional Animal Care and Use Committee in Zhongkai University of Agriculture and Engineering, Guangdong, China.

Primer design and long-PCR amplification

The complete mitochondrial genomes of P. orientalis and P. vittatus were both amplified using long PCR technique (Miya and Nishida, 1999). Three sets of primers were designed from conservative regions of the genes for 16SrRNA , CO II and tRNA(Leu) to efficiently amplify the complete mitochondrial genome in three long-PCRs using EX Taq DNA polymerase (TaKaRa, Japan). All PCR products were purified using QIAquick Gel Extraction Kit (Qiagen, German).

The purified PCR products were then cloned into the pUCm-T cloning vectors (Invitrogen, USA) and sequenced according to the manufacturer’s protocol by using T7 and M13R inner primers of pUCm-T vector. Primer walking method was applied for sequencing the DNA fragment. Each segment overlapped the next contig by 80–120 bp to ensure the accuracy of the sequence.

Sequence analysis

The primary DNA sequence data was characterized by BLAST tools at NCBI database (www.ncbi.nlm.nih.gov). Then the DNA sequences were edited and analyzed by the computer programs Vector NTI Suite 8 (Invitrogen, USA). The locations of the 13 protein-coding genes were determined by comparisons with nucleotide or amino acid sequences of other bony fish mitochondrial genomes. The 22 tRNA genes and their anticodon sequences were identified by their proposed cloverleaf secondary structures drawn by tRNAscan-SE software (Lowe and Eddy, 1997). The two ribosomal RNA (rRNA) genes and the control region were identified by sequence homology and proposed secondary structure (Gutell et al., 1993).

Phylogenetic analysis

To determine the phylogenetic position of P. orientalis and P. vittatus in the subfamily Plectorhynchinae, sequences of Cytb and COI genes of 21 ingroup species in Plectorhynchinae and 4 outgroup species in Haemulinae from GenBank were selected (Table I). individuals of certain species Besides, in order to examine the evolutionary status of Haemulidae of the phylogenetic relationships in Percoidei species, 12 protein-coding sequences of 42 species belonged to 25 families in the suborder Percoidei and one outgroup species Salarias fasciatus in suborder Blennioidei were also selected (Table II). Both datasets were aligned with Clustal X 1.85 (Thompson et al., 1994) with default gap penalties. The molecular phylogeny was analyzed by Maximum Likelihood (ML) and Bayesian Inference (BI) methods. The Modeltest 3.7 software (Posada and Crandall, 1998) was used as a guide to determine the best-fit evolutionary model under the Akaike information criterion (AIC) (Posada and Buckley, 2004) and the GTR (general time reversible) model was chosen in the data computing.

 

Table I.- Species used for Percoidei phylogenetic analysis, along with GenBank accession numbers and reference.

Families

Species

GenBank No.

References

Percoidei

Serranidae

Epinephelus coioides

EU043376

Zhuang et al., 2009

Anyperodon leucogrammicus

GQ131336

Unpublished

Carangidae

Carangoides armatus

AP004444

Miya et al., 2003

Caranx melampygus

AP004445

Miya et al., 2003

Seriola lalandi

AB517557

Iguchi et al., 2012

Latidae

Lates calcarifer

DQ010541

Lin et al., 2006

Toxotidae

Toxotes chatareus

AP006806

Yagishita et al., 2009

Haemulidae

Diagramma pictum

AP009167

Yamanoue et al., 2007

Parapristipoma trilineatum

AP009168

Yamanoue et al., 2007

Hapalogenys nigripinnis

HM754620

Liang et al., 2012

Plectorhinchus orientalis

This study

Plectorhinchus vittatus

This study

Centrarchidae

Micropterus salmoides

DQ536425

Broughton and Reneau, 2006

Micropterus dolomieu

AB378750

Mukai and Sato, 2009

Emmelichthyidae

Emmelichthys struhsakeri

AP004446

Miya et al., 2003

Monodactylidae

Monodactylus argenteus

AP009169

Yamanoue et al., 2007

Oplegnathidae

Oplegnathus fasciatus

DQ872160

Oh et al., 2007

Oplegnathus punctatus

AP011066

Yagishita et al., 2009

Kyphosidae

Labracoglossa argentiventris

AP011062

Yagishita et al., 2009

Scorpis lineolata

AP011063

Yagishita et al., 2009

Kyphosus cinerascens

AP011061

Yagishita et al., 2009

Acropomatidae

Doederleinia berycoides

AP009181

Yamanoue et al., 2007

Caesionidae

Pterocaesio tile

AP004447

Miya et al., 2003

Lutjanidae

Lutjanus malabaricus

FJ824741

Unpublished

Lutjanus sebae

FJ824742

Unpublished

Terapontidae

Rhynchopelates oxyrhynchus

AP011064

Yagishita et al., 2009

Chaetodontidae

Chaetodon auripes

AP006004

Yamanoue et al., 2007

Heniochus diphreutes

AP006005

Yamanoue et al., 2007

Sciaenidae

Larimichthys polyactis

GU586227

Cheng et al., 2012

Sciaenops ocellatus

JQ286004

Cheng et al., 2012

Lethrinidae

Lethrinus obsoletus

AP009165

Yamanoue et al., 2007

Monotaxis grandoculis

AP009166

Yamanoue et al., 2007

Kuhliidae

Kuhlia mugil

AP011065

Yagishita et al., 2009

Pomacanthidae

Chaetodontoplus septentrionalis

AP006007

Yamanoue et al., 2007

Centropyge loricula

AP006006

Yamanoue et al., 2007

Sparidae

Pagrus major

AP002949

Miya et al., 2001

Pagellus bogaraveo

AB305023

Ponce et al., 2008

Acanthopagrus latus

EF506764

Xia et al., 2008

Centracanthidae

Spicara maena

AP009164

Yamanoue et al., 2007

Pseudochromidae

Labracinus cyclophthalmus

AP009125

Mabuchi et al., 2007

Moronidae

Morone saxatilis

HM447585

Unpublished

Lateolabracidae

Lateolabrax japonicus

JQ860109

Unpublished

Sillaginidae

Sillago sihama

JQ048935

Unpublished

Blennioidei

Blenniidae

Salarias fasciatus

AP004451

Miya et al., 2003

 

Table II.- Species used for Haemulidae phylogenetic analysis, along with GenBank accession numbers of COI and Cyt b gene sequences.

Species

GenBank Accession No.

Cyt b

COI

Ingroup species

Plectorhinchus albovittatus

JX042230

JX042260

Plectorhinchus chaetodonoides

JX042231-JX042234

JX042261- JX042264

Plectorhinchus chubbi

JX042235

JX042293

Plectorhinchus cinctus

JX042236 -JX042238

JX042265- JX042267

Plectorhinchus diagrammus

JX042239- JX042241

JX042268- JX042270

Plectorhinchus flavomaculatus

JQ741559- JQ741561

JF494169- JF494171

Plectorhinchus gaterinus

JX042289- JX042290

JX042291- JX042292

Plectorhinchus gibbosus

JX042242- JX042243

JX042271- JX042272

Plectorhinchus lineatus

JX042244- JX042246

JX042273 -JX042275

Plectorhinchus macrolepis

HQ676733

HQ676788

Plectorhinchus orientalis

JX042247- JX042249

JX042276- JX042278

JX042256

JX042285

Plectorhinchus picus

JX042250- JX042251

JX042279- JX042280

Plectorhinchus plagiodesmus

JX042252

JX042281

Plectorhinchus playfairi

JX042253

JX042282

Plectorhinchus polytaenia

JQ741565

JQ741334

Plectorhinchus schotaf

JX042254

JX042283

Plectorhinchus sordidus

JX042255

JX042284

Plectorhinchus vittatus

JX042257- JX042259

JX042286 -JX042288

Diagramma pictum

JX042214 -JX042217

JX042226- JX042229

Diagramma centurio

JX042212- JX042213

JX042224-JX042225

Parapristipoma trilineatum

JX042210 -JX042211

JX042222- JX042223

Outgroup species

Pomadasys maculatus

JX042209

JX042221

Haemulon aurolineatum

JX042208

JX042220

Anisotremus virginicus

JX042206

JX042218

Conodon nobilis

JX042207

JX042219

 

BI analysis was implemented in Mrbayes version 3.1.2 (Ronquist and Huelsenbeck, 2003), The MCMC (Markov Chain Monte Carlo) simulation was run for 10 million generations, with trees sampled and saved every 1000 generations (10,000 trees saved per run), and the bootstrap value of internal branch of the phylogenetic tree was supported by the posterior probabilities.


 

Results

Genome information

The complete mitochondrial genomes of P. orientalis and P. vittatus were sequenced as 16,546 bp and 16,545 bp in length, which have been submitted to GenBank database (Accession no. KP966562, KP976103). The structural organization and arrangement of both genomes consisted of 13 typical vertebrate protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and one putative control region (Fig. 1A, B; Table III). Overall base compositions of L-strand nucleotide sequences in the two mitochondrial genome were as follows, P. orientalis: A, 27.9%; G, 16.4%; T, 24.7%; and C, 31.0%, A+T=52.6%C+G=47.4%; P. vittatus: A, 28.0%; G, 16.4%; T, 24.7%; and C, 30.9%, A+T=52.7%C+G=47.3% (Table IV).

 

Table III.- Main charateristic of mitochondrial genome of P. orientalis and P. vittatus.

Gene

Stra-nd

P. orientalis

P. vittatus

Codon

Position From -to

Nucle-otide Size /bp

Interg-enic nucle-otide

Position From-to

Nucle-otide Size/ bp

Interg-enic nucle-otide

Start

Stop

tRNAPhe

H

1-69

69

0

1-69

69

0

12S rRNA

H

70-1020

951

0

70-1021

952

0

tRNAval

H

1021-1091

71

0

1022-1092

71

0

16S rRNA

H

1092-2786

1695

0

1093-2783

1691

0

tRNALeu(UUR)

H

2787-2860

74

0

2784-2857

74

0

ND1

H

2861-3835

975

5

2858-3832

975

5

ATG/ ATG

TAA/ TAG

tRNAIle

H

3841-3910

70

-1

3838-3907

70

-1

tRNAGln

L

3910-3980

71

-1

3907-3977

71

-1

tRNAMet

H

3980-4049

70

0

3977-4046

70

0

ND2

H

4050-5096

1047

0

4047-5093

1047

0

ATG/ ATG

TAA/ TAA

tRNATrp

H

5097-5168

72

0

5094-5165

72

0

tRNAAla

L

5169-5237

69

1

5166-5234

69

1

tRNAAsn

L

5239-5311

73

40

5236-5308

73

39

tRNACys

L

5352-5418

67

-1

5348-5415

68

-1

tRNATyr

L

5418-5488

71

1

5415-5486

72

1

COI

H

5490-7049

1557

-13

5488-7050

1563

-13

GTG/ GTG

AGG/ AGG

tRNASer(UCN)

L

7037-7107

71

3

7038-7108

71

3

tRNAAsp

H

7111-7182

72

3

7112-7183

72

4

COII

H

7186-7876

691

0

7188-7878

691

0

ATG/ ATG

T--/ T--

tRNALys

H

7877-7951

75

1

7879-7953

75

1

ATPase8

H

7953-8120

168

-10

7955-8122

168

-10

ATG/ ATG

TAA/ TAA

ATPase6

H

8111-8793

683

0

8113-8795

683

0

ATG/ ATG

TA-/ TA-

COIII

H

8794-9578

785

0

8796-9580

785

0

ATG/ ATG

TA- /TA-

tRNAGly

H

9579-9650

72

0

9581-9652

72

0

ND3

H

9651-9999

349

0

9653-10001

349

0

ATG/ ATG

T--/ T--

tRNAArg

H

10000-10068

69

0

10002-10070

69

0

ND4L

H

10069-10365

297

-7

10071-10367

297

-7

ATG/ ATG

TAA/ TAA

ND4

H

10359-11739

1381

0

10361-11741

1381

0

ATG/ ATG

T--/ T--

tRNAHis

H

11740-11808

69

0

11742-11810

69

0

tRNASer(AGY)

H

11809-11875

67

4

11811-11877

67

4

tRNALeu(CUN)

H

11880-11952

73

0

11882-11954

73

0

ND5

H

11953-13791

1839

-4

11955-13793

1839

-4

ATG/ ATG

TAG/ TAA

ND6

L

13788-14309

522

0

13790-14311

522

0

ATG/ ATG

TAA/ TAA

tRNAGlu

L

14310-14378

69

4

14312-14380

69

4

Cytb

H

14383-15523

1141

0

14385-15525

1141

0

ATG/ ATG

T--/ T--

tRNAThr

H

15524-15595

72

33

15526-15597

72

29

tRNAPro

L

15629-15698

70

0

15627-15696

70

0

D-loop

H

15699-16546

848

0

15697-16545

849

0

 

Table IV.- Base composition of mtDNA in P. orientalis and P. vittatus.

P. orientalis

P. vittatus

T%

C%

A%

G%

A+T%

C+G%

T%

C%

A%

G%

A+T%

C+G%

Mitochondrial genome

24.7

31.0

27.9

16.4

52.6

47.4

24.7

30.9

28.0

16.4

52.7

47.3

13 protein-coding genes

26.5

32.4

25.2

15.9

51.7

48.3

26.5

32.3

25.4

15.8

51.9

48.1

1st

20.0

28.9

25.7

25.5

45.7

54.4

20.0

29.7

26.2

24.6

46.2

54.3

2nd

40.0

27.8

18.3

13.5

58.3

41.3

39.0

27.9

18.4

14.5

57.4

42.4

3rd

19.0

40.5

31.5

8.7

50.5

49.2

21.0

39.3

31.7

8.3

52.7

47.6

22 tRNAs

23.8

25.9

29.9

20.4

53.7

46.3

24.0

25.7

29.8

20.4

53.8

46.1

2 rRNAs

20.6

26.2

32.5

20.8

53.1

47.0

20.4

26.3

32.5

20.8

52.9

47.1

Control region

29.8

25.8

29.5

14.9

59.3

40.7

29.1

25.9

29.6

15.4

58.7

41.3

 

Protein-coding genes

The 13 protein-coding genes in the two sweetlips mtDNA were similar in length to their corresponding vertebrate counterparts. The total length of the protein-coding genes was 11,435 bp in P. orientalis and 11,441 bp in P. vittatus without introns, accounting for 69.12% and 69.15% of the complete genome. A6 bp differences of the protein-coding genes was found between the two species in gene COI, which was 1557 in P. orientalis and 1563 in P. vittatus (Table III). All protein-coding genes use ATG as a start codon except for COI, which started with GTG. A diverse pattern of codon usage was found within stop codons: six genes ended with TAA: ND1 (P. orientalis), ND2, ATPase8, ND4L, ND5 (P. vittatus) and ND6, two ended with TAG: ND1 (P. vittatus) and ND5 (P. orientalis), one ended with AGG: COI, the remaining genes had incomplete stop codons, TA (ATPase6, COIII) or T: COII, ND3, ND4 and Cyt b. Among the 13 protein-coding genes, three reading-frame overlaps were found: the pair of gene ATPase 8 and ATPase 6 overlapped by 10 nucleotides, ND4L and ND4 overlapped by 7 nucleotides, ND5 and ND6 overlapped by 4 nucleotides, no overlaps were between ATPase and COIII.

The base composition of the two sweetlips mitochondrial protein-coding genes is summarized in Table IV. The most frequent nucleotides at the first, second and third codon positions were C (28.9%, 29.7%), T (40.0%, 39.0%), C (40.5%, 39.3%) in P. orientalis and P. vittatus, respectively. The frequency of nucleotide G at the third codon position was relatively low (only 8.7%, 8.3%), showing a strong bias against G at this position. In addition, pyrimidines at the second codon position were over-represented (T+C=67.8%, 66.9%).

Codon usage in 13 protein-coding genes of the two sweetlips were analyzed and shown in Table V. The total number of codons for 20 amino acids were 3789 (P. orientalis) and 3791 (P. vittatus) excluding start and stop codons. The most frequent used amino acids are Leu (17.5%, 17.2%), followed by Ile (7.3%, 7.2%), Ser (6.4%, 6.5%), Gly (6.2%, 6.2%), and Val (5.7%, 5.5%). For amino acids with four-fold degenerate third positions, codon families ending in C were the most frequent, followed by codons ending in A. Among two-fold degenerate codons, C appeared to be used more than T in pyrimidine codon families, whereas purine codon families ended mostly with A.

Transfer RNA genes and ribosomal RNA genes

The two sweetlips mitochondrial genomes contain 22 tRNA genes, which are interspersed between rRNA and protein-coding genes, ranging from 67 (tRNACys, tRNASer(AGY)) to 76 (tRNALys(UUR)) nucleotides in length (Table III). Two forms of tRNA-Leu (UUR and CUN) and tRNA-Ser (UCN-AGY) in the two sweetlips were identified. The anticodons of 22 tRNA genes were shown in Table III. Two ribosomal RNA genes, the small subunit (12S) and the large subunit (16S) of rRNAs were 951bp and 1,695 bp in P. orientalis and 952bp and 1,691 bp in P. vittatus, respectively. The two ribosomal RNA genes were located between the genes of tRNA-Phe and tRNA-Leu, separated by the gene tRNA-Val.

Noncoding sequence

The light strand replication origin (OL) was comprised of 40 nucleotides in P. orientalis, and 39 nucleotides in P. vittatus, which could be folded into a stable stem-loop secondary structure containing 22 bp in the stem, 15 or 16 bp in the loop. The conserved motif of the two sweetlips were also 5’-GGCGG-3’ found at the base of the stem within the tRNA-Cys gene. The control region was located between the tRNAPro and tRNAPhe genes and determined to be 848 bp in P. orientalis and 849 bp in P. vittatus. The control regions of the two species were both heavily biased towards A+T nucleotides with A+T content 59.3% in P. orientalis and 58.7% in P. vittatus (Table III).

 

Table V.- Codon usage in P. orientalis and P. vittatus mitochondrial protein-coding genes.

Amino acid number

Codon

P. orientalis

P. vittatus

Amino acid

number

Codon

P. orientalis

P. vittatus

n

(%)

n

(%)

n

(%)

n

(%)

Phe

TTT

68

1.8

68

1.8

Tyr

TAT

33

0.9

41

1.1

TTC

164

4.3

145

3.8

TAC

85

2.2

80

2.1

Leu

TTA

52

1.4

47

1.2

Stop

TAA

0

0

7

0.2

TTG

21

0.6

26

0.7

TAG

1

0

0

0

CTT

133

3.5

136

3.6

His

CAT

27

0.7

25

0.7

CTC

194

5.1

194

5.1

CAC

79

2.1

84

2.2

CTA

194

5.1

190

5

Gln

CAA

87

2.3

86

2.3

CTG

69

1.8

59

1.6

CAG

13

0.3

14

0.4

Ile

ATT

123

3.2

120

3.2

Asn

AAT

24

0.6

40

1.1

ATC

157

4.1

153

4

AAC

97

2.6

80

2.1

ATA

91

2.4

95

2.5

Lys

AAA

67

1.8

69

1.8

Met

ATG

59

1.6

64

1.7

AAG

7

0.2

3

0.1

Val

GTT

46

1.2

51

1.3

Asp

GAT

20

0.5

19

0.5

GTC

79

2.1

67

1.8

GAC

56

1.5

55

1.5

GTA

64

1.7

63

1.7

Glu

GAA

79

2.1

78

2.1

GTG

27

0.7

25

0.7

CAG

19

0.5

16

0.4

Ser

TCT

46

1.2

46

1.2

Cys

TGT

4

0.1

7

0.2

TCC

72

1.9

70

1.8

TGC

19

0.5

22

0.6

TCA

62

1.6

61

1.6

Stop

TGA

97

2.6

96

2.5

TCG

6

0.2

6

0.2

Trp

TGG

23

0.6

18

0.5

Pro

CCT

58

1.5

74

2

Arg

CGT

8

0.2

15

0.4

CCC

110

2.9

112

3

CGC

19

0.5

23

0.6

CCA

49

1.3

52

1.4

CGA

43

1.1

42

1.1

CCG

8

0.2

10

0.3

CGG

5

0.1

11

0.3

Thr

ACT

44

1.2

46

1.2

Ser

AGT

12

0.3

10

0.3

ACC

123

3.2

124

3.3

AGC

45

1.2

53

1.4

ACA

125

3.3

118

3.1

Stop

AGA

0

0

5

0.1

ACG

13

0.3

14

0.4

AGG

0

0

11

0.3

Ala

GCT

65

1.7

57

1.5

Gly

GGT

22

0.6

30

0.8

GCC

147

3.9

148

3.9

GGC

89

2.3

80

2.1

GCA

102

2.7

103

2.7

GGA

80

2.1

88

2.3

GCG

25

0.7

15

0.4

GGG

46

1.2

37

1

The incomplete T/TA of the stop codon is not included.

 

Sequence comparison between P. orientalis and P. vittatus

The comparison analysis of 16 genes between P. orientalis and P. vittatus were showed in Table VI. The complete mitogenome of the two sweetlips were 16,546 bp (P. orientalis) and 16,545 bp (P. vittatus) in length, but there were 941 variable sites (5.69%) in the two mitogenomes, the sequence divergence value was revealed to be 6.5% based on the Kimura-2 Parameter model. The differences of 13 protein-coding genes, 2 ribosomal RNA genes and one control region which are commonly used as molecular markers between the two species were also analyzed. That showed great genetic differences between the two sweetlips existed in all 16 genes. The divergence values based on K-2-P model between P. orientalis and P. vittatus ranged from 2.4% (12S rRNA) to 11.2% (ND6) with nucleotide mutation ranged from 6 bp to 132 bp, all divergence values were larger than 2%, even in the two ribosomal RNA genes (12 and 16 rRNAs) which retained very low evolutionary rate, revealing a significant genetic differences between the two sweetlips at molecular level.

 

Table VI.- Comparison analysis of 16 gene sequences between P. orientalis and P. vittatus.

Length (P. orientalis)

Length(P. vittatus)

Number of variable sites (bp)

Bases variation

(%)

Sequence divergence

(%)

D-loop

848

849

83

9.78

10.6

12S rRNA

951

952

22

2.31

2.4

16S rRNA

1695

1691

45

2.66

2.7

COI

1557

1563

94

6.03

6.4

COII

691

691

23

3.33

3.4

COIII

785

785

41

5.22

5.5

ND1

975

975

76

7.79

8.4

ND2

1047

1047

91

8.69

9.4

ND3

349

349

26

7.49

8

ND4L

297

297

12

4.04

4.2

ND4

1381

1381

109

7.89

8.5

ND5

1839

1839

132

7.18

7.8

ND6

522

522

53

10.15

11.2

Cytb

1141

1141

82

5.69

7.7

ATPase6

683

683

40

5.86

6.2

ATPase8

168

168

6

3.57

3.7

Whole sequences

16546

16545

941

5.69

6.5

 

Phylogenetic analysis

Molecular phylogenetic trees of 21 sweetlips (Plectorhynchinae) were constructed using ML and BI methods based on combined Cyt b and COI sequences, the trees were well divided the sweetlilps into three groups with high bootstrap values and posterior probabilities (Fig. 2). Group one composed sweetlips with beautiful coloration pattern, group two and three composed sweetlips with simple patterns and dark appearances. Two sweetlips P. orientalis and P. vittatus were positioned in group one, clustering together as sister species and closely related to the cluster P. lineatus and P. diagrammus which also possessed black stripes along the body, indicating their closed relationships with each other. Another phylogenetic trees constructed from 42 Percoidei species of 25 families formed 5 large groups, Diagramma pictum, Parapristipoma trilineatum, P. orientalis and P. vittatus formed a monophyletic Haemulidae in group I, sister to the cluster Lethrinus obsoletus + Monotaxis grandoculis. The species Hapalogenys nigripinnis, which was a Haemulidae member morphologically, was separated from Haemulidae group. It was placed in group IV and clustered with Sillago sihama, revealing its distant relationship with Haemulidae species.

 

Discussion

Similar organization of two mitogenomes with other vertebrates

The two mitogenomes both consisted of 13 typical vertebrate protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and one putative control region, which were similar to other vertebrate mitogenomes. As in other vertebrate species (Miya et al., 2003; Oh et al., 2007; Ponce et al., 2008; Catanese et al., 2010), most genes were encoded on the H-strand except for one protein-coding gene ND6 and 8 tRNA genes (Gln, Ala, Asn, Cys, Tyr, SerUCN, Glu and Pro) which were encoded on the L-strand. As shown in Table IV, the contents of A+T of the two sweetlips were both higher than that of C+G, indicating a strong compositional base bias in the mitochondrial genome which was in accordance with the variation tendency of the A+T content in other vertebrates.

For 13 protein-coding genes (Table V), variances were observed in stop codons, which seemed to be a tendency in fish mitochondrial genomes (Miya and Nishida, 1999; Ponce et al., 2008; Catanese et al., 2010). The three reading-frame overlaps observed between protein coding genes showed different from the previously reported species that 1 nucleotide was overlapped between the two genes (Oh et al., 2007; Ponce et al., 2008; Catanese et al., 2010). As shown in Table IV, the base composition of the two sweetlips mitochondrial protein-coding genes showed a strong bias against G, which seemed due to the hydrophobic characteristic of the proteins (Naylor et al., 1995). These typical features of protein-coding genes were also found in most vertebrates (Oh et al., 2007; Catanese, 2010; Cheng et al., 2012a, b). These codon usage patterns in protein coding genes were in accordance with the overall bias against G, because G was the least common third position nucleotide in all codons except for glycine, in which G was more frequent than T. All these features were very similar to other bony fish (Miya et al., 2003; Ponce et al., 2008; Cheng et al., 2012a, b).


 

For tRNAs, They showed the typical arrangement in vertebrates. Most of them could be folded into the typical secondary structure-canonical cloverleaf, which were determined by the tRNAscan-SE software (Lowe and Eddy, 1997). The two ribosomal RNA genes were located between the genes of tRNA-Phe and tRNA-Leu, separated by the gene tRNA-Val, as in other vertebrates (Miya et al., 2001; Oh et al., 2007; Catanese et al., 2010). For noncoding sequences, the light strand replication origin (OL) in P.orientlais and P. vittatus was positioned in a cluster of five tRNA genes known as the WANCY region between the tRNAAsn and tRNACys genes as most of the vertebrates.

The differences of mitogenomes between P. orientalis and P. vittatus

Avise and Walker (1999) revealed divergence values between species of vertebrates in Cyt b were ordinarily greater than 2%. Hebert (2003a) and (2003b) studied the COI sequences of 13320 species from 11 phyla and suggested that the threshold of divergence values in COI for species diagnosis was 2%. Intraspecific divergences were rarely greater than 2% and most were less than 1% (Hebert, 2003b; Avise, 2000). In our study, sequence divergences were revealed in COI and Cyt b between the two sweetlips were 6.4% and 7.7%, respectively, largely greater than the 2% value suggested by Hebert. The other 14 genes in Table VI were also larger than the threshold 2% value, even in the two highly conserved ribosomal RNA genes. In our previous studies, we had investigated the phylogenetic relationship of 17 sweetlips involved 3 individuals of P. orientalis and 3 individuals of P. vittatus based on Cyt b and COI genes (Liang et al., 2016). The result revealed that sequence divergences in each individual sample of P. orientalis and P. vittatus were all less than 0.5% in the two genes. The study also discovered that the divergence value between P. orientalis and P. vittatus was larger than some inter-sweetlips species values like Plectorhinchus chubbi vs Plectorhinchus sordidus (COI: 3.6%; Cytb: 3.4%), Plectorhinchus chubby vs Plectorhinchus plafairi (COI: 4.8%; Cytb: 5.0%) and Plectorhinchus sordidus vs Plectorhinchus plafairi (COI: 5.7%; Cytb: 4.5%). All these pieces of evidences indicated that great sequence variation and molecular differentiation were existed in the two sweetlips, suggested that they might be considered as two separate species.

Phylogenetic analysis of P. orientalis and P. vittatus

Phylogenetic trees constructed from 21 Haemulidae species based on the the combined sequences of Cyt b, COI were well divided the sweetlilps into three groups (Fig. 2). Group one composed sweetlips with beautiful coloration pattern, group two and three composed sweetlips with simple patterns and dark appearances, which was in accordance with traditional morphological classifications (McKay, 1984, 2001). The two sweetlips P. orientalis and P. vittatus were positioned in group one, clustering together as sister species and closely related to the cluster P. lineatus and P. diagrammus, which was consistent with the molecular phylogeny of Haemulidae species based on 16S rRNA and TMO-4C4. By morphological diagnosis, they all had black stripes and bands on their bodies. In the phylogenetic trees, the long branch clearly distinguished the separated evolutionary positions of the two orientalis sweetlips. Along with the great genetic differences result of sequence comparison analysis on 16 molecular marker genes above, we suggested that P. orientalis and P. vittatus might be placed as two distinct species and were not synonym.

The phylogenetic position of Haemulidae among the Percoidei was also examined in this study (Fig. 3). The tree revealed 4 Haemulidae species Diagramma pictum, Parapristipoma trilineatum, P. orientalis and P. vittatus formed a monophyletic group except for Hapalogenys nigripinnis, which was placed in an independent position out of the Haemulidae clusters. Such finding was not congruent with the traditional morphological studies (Shen, 1993; McKay, 2001; Nelson, 2006) but agreed with some other morphology and molecule-based studies which suggested that the genus Hapalogenys were removed from Haemulidae (Springer and Raasch, 1995; Leis and Carson-Ewart, 2000; Froese and Pauly, 2014). Recent phylogenetic analysis on the relationships of Hapalogenys and Haemulidae also revealed a distant relationship between them (Ren and Zhang, 2007; Sanciangco et al., 2011). Our result was in agreement with those molecular reports, indicating the fundamental status of Hapalogenys in the Percoidei may need to be redefined. The family Haemulidae was grouped with family Lethrinidae as sister lineage and was closely related to families Lutjanidae, Caesionidae, Emmelichthyidae and Monodactylidae. Traditionally, potential sister groups to Haemulidae as well as its placement among Percoidei were uncertain either in morphological or in molecular studies (Johnson, 1981; Sanciangco et al., 2011; Tavera et al., 2012). Recent studies on higher-level relationships of percomorphs and acanthomorphs have shown potential outgroups for Haemulidae on the basis of molecular characters but the relationships and placement of Haemulidae varied through time according to different authors (Dettai and Lecointre, 2005; Chen et al., 2007; Craig and Hastings, 2007; Smith and Craig, 2007; Li et al., 2009). The current studies on Haemulidae relationships by Tavera et al. (2012) have revealed Sillaginidae sister clade to Haemulidae, but the support values were relatively low. Our molecular phylogenetic study on the placement of Haemulidae among Percoidei included the previously suggested potential Haemulidae-close families. The result recovered Haemulidae sister to Lethrinidae and was placed in a cluster comprised of families Lutjanidae, Caesionidae, Emmelichthyidae and Monodactylidae, which were consistent with the studies of Tavera et al. (2012). However, the Percoidei is the largest suborder of the Perciformes and the sequences of most Percoidei species are not available. A complete mitochondrial genomes are needed to be sequenced for further detailed analysis of the evolutionary relationships of Haemulidae within Percoidei species.


 

Conclusions

The mitochondrial genome of two synonyms debated species P. orientalis and P. vittatus were first determined in this study. The lengths of the two mitogenome are 16,546 bp and 16,545 bp, which both consist of 13 typical vertebrate protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and one putative control region. Genomic composition, organization, and gene order of the two genomes are similar to that obtained in most vertebrates. All sequence divergences of 13 protein-coding genes, 2 rRNA genes and one control region which are commonly used as molecular markers between the two species are larger than the species diagnosis divergence value 2%. And divergence values of Cyt b (6.0%) and COI (7.4%) are also largely greater than 2%. Furthermore, molecular phylogenetic trees also clearly distinguish the independent position of the two species. These results above reveal great genetic differences between P. orientalis and P. vittauts, and strongly suggest that they are two distinct species and should not be placed as synonyms.

 

Acknowledgments

The study was supported by the Natural Science Foundation of Guangdong Province, China (2016A030310236) and Foundation for Young Talents in Higher Education of Guangdong, China (2014KQNCX164). We wish to thank Bernard Mackenzie (SAIAB South African Institute for Aquatic Biodiversity, Grahamstown, South Africa) for his kind assistance in providing samples of P. vittatus. We would also like to thank the College of Animal Science in South China Agricultural University for their laboratory facilities and experimental support to this study.

 

Statement of conflict of interest

Authors declare that they have no competing interests.

 

References

Avise, J.C. and Walker, D., 1999. Species realities and numbers in sexual vertebrates: perspectives from an asexually transmitted genome. Proc. natl. Acad. Sci. USA, 96: 992-995. https://doi.org/10.1073/pnas.96.3.992

Avise, J.C., 2000. Phylogeography. The history and formation of species. Harvard University Press, Cambridge, MA.

Boore, J.L., 1999. Animal mitochondrial genomes. Nucl. Acids Res., 27: 1767-1780. https://doi.org/10.1093/nar/27.8.1767

Broughton, R.E. and Reneau, P.C., 2006. Spatial covariation of mutation and nonsynonymous substitution rates in vertebrate mitochondrial genomes. Mol. Biol. Evol., 23: 1516-1524. https://doi.org/10.1093/molbev/msl013

Catanese, G., Manchado, M. and Infante, C., 2010. Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: Strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species. Gene, 452: 35-43. https://doi.org/10.1016/j.gene.2009.12.004

Chen, W.J., Ruiz-Carus, R. and Ortí, G., 2007. Relationships among four genera of mojarras (Teleostei: Perciformes: Gerreidae) from the western Atlantic and their tentative placement among percomorph fishes. J. Fish Biol., 70: 202-218. https://doi.org/10.1111/j.1095-8649.2007.01395.x

Cheng, Y.Z., Shi, G., Xu, T.J., Li, H.Y., Sun, Y.Y. and Wang, R.X., 2012a. Complete mitochondrial genome of the red drum, Sciaenops ocellatus (Perciformes, Sciaenidae): Absence of the typical conserved motif in the origin of the light-strand replication. Mitochondrial DNA, 23: 126-128. https://doi.org/10.3109/19401736.2011.653807

Cheng, Y.Z., Wang, R.X., Xu, T.J. and Sun, Y.N., 2012b. The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny. Genet. Mol. Biol., 35: 191-199. https://doi.org/10.1590/S1415-47572012005000006

Clayton, D.A., 1992. Transcription and replication of animal mitochondrial DNAs. Int. Rev. Cytol., 141: 217-232. https://doi.org/10.1016/S0074-7696(08)62067-7

Craig, M.T. and Hastings, P.A., 2007. A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini. Ichthyol. Res., 54: 1-17. https://doi.org/10.1007/s10228-006-0367-x

Dettai, A. and Lecointre, G., 2005. Further support for the clades obtained by multiple molecular phylogenies in the acanthomorph bush. C. R. Biol., 328: 674-689. https://doi.org/10.1016/j.crvi.2005.08.001

Froese, R. and Pauly, D. (eds.), 2014. FishBase, version 03/2014. World Wide Web Electronic Publication. Available at: www.fishbase.org

Gillibrand, C.J., Harris, A.R. and Mara, E., 2007. Inventory and spatial assemblage study of reef fish in the area of Andavadoaka, South-West Madagascar (Western Indian Ocean). J. mar. Sci., 6: 183-197.

Gutell, R.R., Gray, M.W. and Schnare, M.N., 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucl. Acids Res., 21: 3055-3074. https://doi.org/10.1093/nar/21.13.3051

Hebert, P.D.N., Cywinska, A., Ball, S.L. and deWaard, J.R., 2003a. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B, 270: 313-322. https://doi.org/10.1098/rspb.2002.2218

Hebert, P.D.N., Ratnasingham, S. and de Waard, J.R., 2003b. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B, 270: 596-599. https://doi.org/10.1098/rsbl.2003.0025

Iguchi, J., Takashima, Y., Namikoshi, A. and Yamashita, M., 2012. Species identification method for marine products of seriola and related species. Fish Sci., 78: 179-206. https://doi.org/10.1007/s12562-011-0433-9

Inoue, J.G., Miya, M., Tsukamoto, K. and Nishida, M., 2001. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationship with longer DNA sequences. Mol. Phylogenet. Evol., 20: 275-285. https://doi.org/10.1006/mpev.2001.0970

Johnson, G.D., 1981. The limits and relationships of Lutjanidae and associated families. In: Bulletin of the Scripps Institution of Oceanography (eds. C.S. Cox, E.S. Vincent, A. Fleminger and R.H. Rosenblatt). University of California Press, Berkeley, pp. 1-112.

Kawahara, R., Miya, M., Mabuchi, K., Lavoué, S., Inoue J.G., Satoh, T.P., Kawaguchi, A. and Nishida, M. 2008. Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. Mol. Phylogenet. Evol., 46: 224-236. https://doi.org/10.1016/j.ympev.2007.07.009

Leis, J.M. and Carson-Ewart, B.M., 2000. The larvae of Indo-Pacific coastal fishes. An identification guide to marine fish larvae. Fauna Malesiana Handbooks 2. E.J. Brill., Leiden, pp. 870.

Li, B., Dettaï, A., Cruaud, C., Couloux, A., Desoutter-Meniger, M. and Lecointre, G., 2009. RNF213, a new nuclear marker for acanthomorph phylogeny. Mol. Phylogenet. Evol., 50: 345-363. https://doi.org/10.1016/j.ympev.2008.11.013

Liu, Z.S., Song, N., Yanagimoto, T., Han, Z.Q., Shui, B.N. and Gao, T.X., 2017 Complete mitochondrial genome of three fish species (Perciformes: Amblyopinae): Genome description and phylogenetic relationships. Pakistan J. Zool., 49: 111-120. http://dx.doi.org/10.17582/journal.pjz/2017.49.1.111.120

Liang, R.S., Zheng, W.J., Zou, Q., Zeng Y.D., Zhu, S.H. and Zou, J.X., 2012. The complete mitochondrial genome of black grunt Hapalogenys nigripinnis. Mitochondrial DNA, 23: 444-446. https://doi.org/10.3109/19401736.2012.710221

Liang, R.S., Wang, C., Zou, Q., Zhou, A.G. and Zhou, M., 2016. Molecular phylogenetic relationships of some common sweetlips Haemulidae Plectorhynchinae and the synonyms controversy of two Plectorhinchus species. Mitochondrial DNA, 27: 2209-2214.

Lin, G., Lo, L.C., Zhu, Z.Y., Feng, F., Chou, R. and Yue, G.H., 2006. The complete mitochondrial genome sequence and characterization of single-nucleotide polymorphisms in the control region of the Asian seabass (Lates calcarifer). Mar. Biotechnol., 8: 71-79. https://doi.org/10.1007/s10126-005-5051-z

Lowe, T.M. and Eddy, S.R., 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res., 25: 955-964. https://doi.org/10.1093/nar/25.5.0955

Mabuchi, K., Miya, M., Azuma, Y. and Nishida, M., 2007. Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes. BMC Evol. Biol., 7: 10. https://doi.org/10.1186/1471-2148-7-10

McKay, R.J., 1984. Haemulidae. In: FAO species identification sheets for fishery purposes (eds. W. Fischer and G Bianchi), Vol. 2. Western Indian Ocean (Fishing Area 51), FAO, Rome.

McKay, R.J., 2001. Haemulidae = Pomadasyidae. Grunts (also sweetlips, rubberlips, hotlips, and velvetchins). In: The living marine resources of the Western Central Pacific (eds. K.E. Carpenter and V.H. Niem), Volume 5. FAO, Rome, pp. 2961-2989.

Miya, M. and Nishida, M., 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Mar. Biotechnol., 1: 416-426. https://doi.org/10.1007/PL00011798

Miya, M., Kawaguchi, A. and Nishida, M., 2001. Mitogenomic exploration of higher teleostean phylogenies: A case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol., 18: 1993-2009. https://doi.org/10.1093/oxfordjournals.molbev.a003741

Miya, M., Takeshima, H., Endo, H., Ishiguro, N.B., Inoue, J.G., Mukai, T., Satoh, T.P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S.M. and Nishida, M., 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol., 26: 121-138. https://doi.org/10.1016/S1055-7903(02)00332-9

Mukai, T. and Sato, C., 2009. Complete mitochondrial DNA sequences of two haplotypes of the smallmouth bass, Micropterus dolomieu, collected from nonindigenous populations in Japan. Ichthyol. Res., 56: 204-207. https://doi.org/10.1007/s10228-008-0074-x

Naylor, G.J., Collins, T.M. and Brown, W.M., 1995. Hydrophobicity and phylogeny. Nature, 373: 565-566. https://doi.org/10.1038/373565b0

Nelson, J.S., 2006. Fishes of the world. John Wiley & Sons Inc., New York, pp. 368-369.

Oh, D.J., Kim, J.Y., Lee, J.A., Yoon, W.J., Park, S.Y. and Jung, Y.H., 2007. Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations. Gene, 392: 174-180. https://doi.org/10.1016/j.gene.2006.12.007

Ponce, M., Infante, C., Jiménez-Cantizano, R.M., Péreza, L. and Manchadoa, M., 2008. Complete mitochondrial genome of the blackspot seabream, Pagellus bogaraveo (Perciformes: Sparidae), with high levels of length heteroplasmy in the WANCY region. Gene, 409: 44-52. https://doi.org/10.1016/j.gene.2007.11.004

Posada, D. and Crandall, K., 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics, 14: 817-818. https://doi.org/10.1093/bioinformatics/14.9.817

Posada, D. and Buckley, T.R., 2004. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol., 53: 793-808. https://doi.org/10.1080/10635150490522304

Randall, J.E., 2005. Reef and shore fishes of the South Pacific. New Caledonia to Tahiti and the Pitcairn Islands. University of Hawaii Press, Honolulu, Hawaii, pp. 271.

Randall, J.E. and Johnson, J.W., 2000. Perca lineata and P. vittata established as valid species of Plectorhinchus (Perciformes: Haemulidae). Mem. Queensl. Mus., 45: 477-482.

Randall, J.E. and Lim, K.K.P., 2000. A checklist of the fishes of the South China Sea. Raffles Bull. Zool. Suppl., 8: 569-667.

Ren, G. and Zhang, Q., 2007. Phylogeny of haemulid with discussion on systematic position of the genus Hapalogenys. Acta Zootaxon. Sin., 32: 835-841.

Ronquist, F. and Huelsenbeck, J.P., 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574. https://doi.org/10.1093/bioinformatics/btg180

Saitoh, K., Sado, T., Mayden, R.L., Hanzawa, N., Nakamura, K., Nishida, M. and Miya, M., 2006. Mitogenomic evolution and interrelationships of the cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J. mol. Evol., 63: 826-841. https://doi.org/10.1007/s00239-005-0293-y

Sanciangco, M.D., Rocha, L.A. and Carpenter, K.E., 2011. A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes. Zootaxa, 2966: 37-50.

Satapoomin, U. and Randall, J.E., 2000. Plectorhinchus macrospilus, a new species of thicklip (Perciformes: Haemulidae) from the Andaman Sea off southestern Thailand. Phuket Mar. Biol. Cent. Res. Bull., 63: 9-16.

Shadel, G.S. and Clayton, D.A., 1997. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem., 66: 409-435. https://doi.org/10.1146/annurev.biochem.66.1.409

Shen, S.J., 1993. Fishes of Taiwan. National Taiwan University, Department of Zoology, Taipei, pp. 360-363.

Smith, W.L. and Craig, M.T., 2007. Casting the Percomorph Net Widely: The importance of broad taxonomic sampling in the search for the placement of Serranid and Percid fishes. Copeia, 1: 35-55. https://doi.org/10.1643/0045-8511(2007)7[35:CTPNWT]2.0.CO;2

Springer, V.G. and Raasch, M.S., 1995. Fishes, angling, and finfish fisheries on stamps of the World. American Topical Association. Fishes on Stamps Handbook, 129: 1-110.

Tavera, J., Acero, A., Balart, E.F. and Bernardi, G., 2012. Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World species. BMC Evol. Biol., 12: 57. https://doi.org/10.1186/1471-2148-12-57

Thompson, J.D., Higgins, D.G. and Gibson, T.J., 1994. CLUSIAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucl. Acids Res., 22: 4673-4680. https://doi.org/10.1093/nar/22.22.4673

Tzeng, C.S., Hui, C.F., Shen, S.C. and Huang, P.C., 1992. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: Conservation and variations among vertebrates. Nucl. Acids Res., 20: 4853-4858. https://doi.org/10.1093/nar/20.18.4853

Unsworth, R.K.F., 2010. Seagrass meadows of the Wakatobi National Park. In: Marine conservation and research in the coral triangle (eds. J. Clifton, R.K.F. Unsworth and D.J. Smith). The Wakatobi National Park. Nova Publishers, New York, pp. 101-126.

Xia, J.H., Xia, K.F. and Jiang, S.G., 2008. Complete mitochondrial DNA sequence of the yellowfin seabream Acanthopagrus latus and a genomic comparison among closely related sparid species. Mitochondria DNA, 19: 385-393.

Yagishita, N., Miya, M., Yamanoue, Y., Shirai, S.M., Nakayama, K., Suzuki, N., Satoh, T.P., Mabuchi, K., Nishida, M. and Nakabo, T., 2009. Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha). Mol. Phylogenet. Evol., 53: 258-266. https://doi.org/10.1016/j.ympev.2009.06.009

Yamanoue, Y., Miya, M., Matsuura, K., Yagishita, N., Mabuchi, K., Sakai, H., Katoh, M. and Nishida, M., 2007. Phylogenetic position of tetraodontiform fishes within the higherteleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences. Mol. Phylogenet. Evol., 45: 89-101. https://doi.org/10.1016/j.ympev.2007.03.008

Zhuang. X., Ding, S.X., Wang, J., Wang, Y. and Su, Y.Q., 2009. A set of 16 consensus primer pairs amplifying the complete mitochondrial genomes of orange-spotted grouper (Epinephelus coioides) and Hong Kong grouper (Epinephelus akaara). Mol. Ecol. Resour., 9: 1551-1553. https://doi.org/10.1111/j.1755-0998.2009.02716.x

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Pakistan Journal of Zoology

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Vol. 51, Iss. 6, Pages 1999-2399

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