Open Access

Characterization of the complete mitochondrial genomes of Nematodirus oiratianus and Nematodirus spathiger of small ruminants

Contributed equally
Parasites & Vectors20147:319

https://doi.org/10.1186/1756-3305-7-319

Received: 27 March 2014

Accepted: 29 June 2014

Published: 11 July 2014

Abstract

Background

Nematodirus spp. are among the most common nematodes of ruminants worldwide. N. oiratianus and N. spathiger are distributed worldwide as highly prevalent gastrointestinal nematodes, which cause emerging health problems and economic losses. Accurate identification of Nematodirus species is essential to develop effective control strategies for Nematodirus infection in ruminants. Mitochondrial DNA (mtDNA) could provide powerful genetic markers for identifying these closely related species and resolving phylogenetic relationships at different taxonomic levels.

Methods

In the present study, the complete mitochondrial (mt) genomes of N. oiratianus and N. spathiger from small ruminants in China were obtained using Long-range PCR and sequencing.

Results

The complete mt genomes of N. oiratianus and N. spathiger were 13,765 bp and 13,519 bp in length, respectively. Both mt genomes were circular and consisted of 36 genes, including 12 genes encoding proteins, 2 genes encoding rRNA, and 22 genes encoding tRNA. Phylogenetic analyses based on the concatenated amino acid sequence data of all 12 protein-coding genes by Bayesian inference (BI), Maximum likelihood (ML) and Maximum parsimony (MP) showed that the two Nematodirus species (Molineidae) were closely related to Dictyocaulidae.

Conclusions

The availability of the complete mtDNA sequences of N. oiratianus and N. spathiger not only provides new mtDNA sources for a better understanding of nematode mt genomics and phylogeny, but also provides novel and useful genetic markers for studying diagnosis, population genetics and molecular epidemiology of Nematodirus spp. in small ruminants.

Keywords

Nematodirus oiratianus Nematodirus spathiger Mitochondrial genome Phylogenetic analyses

Background

Nematodirus spp. are among the most common nematodes of ruminants and more than 45 species have been described in the genus Nematodirus Ransom, 1907 [1, 2]. Of these, Nematodirus oiratianus and N. spathiger are widely distributed as highly prevalent gastrointestinal nematodes, mainly inhabiting the small intestines of sheep and goats [35]. Although mild, or no symptoms are usually presented during Nematodirus infection in adult ruminants, growth retardation and emaciation of the growing host during infection may result in economic losses. During winter, Nematodirus eggs are able to develop to the gastrula stage within two weeks and then to infective larvae after another 4 weeks, and are strongly resistant to adverse environmental conditions [6]. These larvae therefore represent a potent source of infection during spring leading to high numbers of infected ruminants early in the growing season [6, 7].

Traditionally, Nematodirus species have been identified solely on morphological features of the adults, including characteristics of the spicule tips and copulatory bursae [8]. However, such criteria are often insufficient for specific identification and differentiation of Nematodirus species, especially for eggs, larvae and females [9, 10]. Due to the limitations of morphological approaches, various molecular methods have been used widely for the identification and differentiation of Nematodirus species. The internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) has previously been described as a useful marker for the identification and differentiation of Molineid nematodes [1113]. At least eight Nematodirus species, including N. battus, N. davtiani alpinus, N. europaeus, N. filicollis, N. helvetianus, N. oiratianus, N. spathiger and N. rupicaprae, could be identified by their ITS rDNA sequences [1113]. Compared to nuclear rDNA, mitochondrial (mt) DNA (mtDNA) is more reliable for identifying closely related species, particularly cryptic species, since the mtDNA sequences accumulate nucleotide substitutions much more quickly than ITS rDNA [14]. Indeed, various studies have indicated that mt genome sequences provide powerful genetic markers in resolving phylogenetic relationships at different taxonomic levels, particularly when concatenated protein-coding sequences are used for phylogenetic analysis [1522].

Based on recent progress in Long-range PCR-coupled sequencing and bioinformatic methods [23, 24], the objectives of the present study were to sequence and compare the complete mt genomes of N. oiratianus and N. spathiger. We also assessed phylogenetic relationships of the two Nematodirus species with a range of other Trichostrongyloid nematodes using complete, inferred mt protein sequence data sets.

Methods

Ethics statement

The performance of this study was strictly according to the recommendations of the Guide for the Care and Use of Laboratory Animals of the Ministry of Health, China, and our protocol was reviewed and approved by the Research Ethics Committee of Northwest A&F University.

Parasites

All the nematode samples were collected from animals with the permission of the Laboratory of Veterinary Parasitology of Northwest A&F University, with no specific permits being required by the authority for the sample collection.

Genomic DNA extraction

Female adults of N. oiratianus (Code: YLF2) and N. spathiger (JYF2) were obtained from the small intestines of naturally-infected goats and sheep, respectively, in Shaanxi Province, China. Adult worms from each host were washed separately in physiological saline, fixed in 70% (v/v) ethanol and stored at -20°C until further study. Nematodirus species were firstly identified morphologically according to characteristics of the spicule tips and copulatory bursae and distribution of bosses on the internal surfaces of the bursae [5, 8]. For each species, individual males were identified on the basis of bursal form, number of cuticular ridges and spicule morphology [25].

The Nematodirus species were further identified using a molecular method based on ITS rDNA. Total genomic DNA was isolated separately from individual worms of each species by proteinase K treatment, column-purification (TIANamp Genomic DNA Purification System, TIANGEN, China) and elution into 40 μl H2O according to the manufacturer’s recommendations. The region spanning ITS-1, 5.8S and ITS-2 rDNA was amplified from each individual using universal primers NC5 and NC2 [26] and sequenced directly. Phylogenetic analyses based on the ITS-2 rDNA sequences, using Maximum parsimony (MP) and Maximum likelihood (ML) methods, were used to further determine the Nematodirus species used in this study.

Long-range PCR-based sequencing of mtDNA

Using primers designed against relatively conserved regions within the cox 1, rrn L and nad 1 regions (Additional file 1) [27], the complete mt genome was amplified from total genomic DNA (from an individual worm) as four overlapping fragments between rrn L and nad 1, nad 1, nad 1 and cox 1, and cox 1 and rrn L (Additional file 1), respectively. Each fragment was amplified by long-range PCR using LA TAQ polymerase (TAKARA, China), following the manufacturer’s recommendations. The cycling conditions used were 92°C for 2 min (initial denaturation), then 92°C for 10 s (denaturation), 45°C for 30 s (annealing), and 60°C for 8 min (extension) for 9 cycles, followed by 92°C for 10 s, 45°C for 30 s, and 60°C for 9 min for 25 cycles, and a final extension at 60°C for 10 min. Each amplicon was represented by a single band in a 1.0% (w/v) agarose gel, following electrophoresis and ethidium-bromide staining. The amplicon was column-purified and then sequenced using a primer walking strategy [23].

Sequence annotation

Sequences were assembled manually and aligned against the complete mt genome sequences of other nematodes (available in GenBank) using the computer program MAFFT 7 [28] to infer gene boundaries. The open-reading frames (ORFs) were predicted by the Open Reading Frame Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) using the invertebrate mitochondrial code and subsequently compared with those of Trichostrongylus axei and Trichostrongylus vitrinus[29]. Each gene was translated into amino acid sequence using the invertebrate mitochondrial genetic code in MEGA 5 [30], and aligned based on its amino acid sequence using default settings. The alignment was back-translated into the corresponding nucleotide sequences. The translation initiation and termination codons were identified to avoid gene overlap and to optimize the similarity between the gene lengths of closely-related nematode mitochondrial genomes. Codon usages were examined based on the relationships between the nucleotide composition of codon families and amino acid occurrence, for which codons are partitioned into AT-rich codons, GC-rich codons and unbiased codons. The secondary structures of 22 tRNA genes were predicted using tRNAscan-SE [31] and/or manual adjustment [32], and the rRNA genes were predicted by comparison with those of closely-related nematodes (T. axei and T. vitrinus[29]) and their secondary structures.

Phylogenetic analyses

Amino acid sequences inferred from the 12 protein-coding genes were concatenated into a single alignment, and then aligned with those of eight other Trichostrongyloid nematodes (Cooperia oncophora, NC_004806 [33]; Haemonchus contortus, NC_010383 [24]; T. axei, NC_013824 [29]; T. vitrinus, NC_013807 [29]; Teladorsagia circumcincta, NC_013827 [29]; Mecistocirrus digitatus, NC_013848 [29]; Dictyocaulus viviparus, NC_019810 [34]; Dictyocaulus eckerti, NC_019809) [34]), using the Strongyloid nematode Oesophagostomum quadrispinulatum (NC_014181) as the outgroup [35]. Any regions of ambiguous alignment were excluded using Gblocks online server [36] (http://molevol.cmima.csic.es/castresana/Gblocks_server.html) using the options for less stringent selection. Phylogenetic analyses were conducted using three methods: Bayesian inference (BI), Maximum parsimony (MP) and Maximum likelihood (ML). The MtArt + G + F model of amino acid evolution was selected as the most suitable model of evolution by ProtTest 2.4 [37] based on the Akaike information criterion (AIC). As the MtArt model is not implemented in the current version of MrBayes, an alternative model, MtREV, was used in BI and four chains (three heated and one cold) were run simultaneously for the Monte Carlo Markov Chain. Two independent runs were performed for 1,000,000 metropolis-coupled MCMC generations, sampling a tree every 100 generation in MrBayes 3.1.1 [38]; the first 2,500 trees represented burn-in and the remaining trees were used to calculate Bayesian posterior probabilities (Bpp). MP analysis was conducted using PAUP 4.0 Beta 10 program [39], with indels treated as missing character states; 1,000 random additional searches were performed using TBR. Bootstrap frequency (Bf) was calculated using 1,000 bootstrap replicates, and 100 random taxon additions in PAUP. ML analysis was performed using PhyML 3.0 [40]. Bf was calculated using 100 bootstrap replicates. Phylograms were drawn using the program Tree View v.1.65 [41].

Results and discussion

Both nematode species have cephalic vesicles, two sets of reproductive organs, a single distribution of large black eggs, and a conical end with a transparent thin spine. Usually, species identification mostly depends on male morphological features, but in this study, identification of the parasites was mainly dependent on ITS rDNA sequences as all worms used herein were female [8, 42]. The region spanning ITS-1, 5.8S and ITS-2 rDNA was amplified from each individual worm using universal primers NC5 and NC2 [26] and sequenced directly. The ITS-1 rDNA sequences (GenBank accession nos. KC580735 and KC580745, respectively) of the N. oiratianus and N. spathiger samples had 96% and 99% identity to those of N. oiratianus and N. spathiger in public databases (HQ389233 and AF194144, respectively). The ITS-2 rDNA sequences (KC580735 and KC580745, respectively) of the N. oiratianus and N. spathiger samples had 94% and 100% identity to those of N. oiratianus and N. spathiger in public databases (HQ389233 and KC998746, respectively) [2]. Phylogenetic analysis based on the ITS-2 rDNA sequences, using Maximum parsimony (MP) and Maximum likelihood (ML), further showed that the Nematodirus isolates represented N. oiratianus and N. spathiger, respectively (Additional file 2).

The respective lengths of the four overlapping fragments amplified by long-PCR covering the entire mt genomes of N. oiratianus and N. spathiger were 4765 bp and 4741 bp for rrn L-nad 1, 511 bp and 510 bp for partial nad 1, 7084 bp and 7060 bp for nad 1-cox 1, and 2330 bp and 2320 bp for cox 1-rrn L, respectively. After sequence splicing, the complete mt genomes of N. oiratianus and N. spathiger (KF573750 and KF573749) were 13,765 bp and 13,519 bp in length, respectively (Figure 1). Both mt genomes contained 12 protein-coding genes (cox 1-3, nad 1-6, nad 4L, atp 6 and cyt b), 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions, but lacked an atp 8 gene (Table 1). These circular genomes are typical mt genomes of Chromadorea nematodes, such as Ascaris suum[15], Enterobius vermicularis[43], Oesophagostomum spp.[44] and Spirocerca lupi[45]. All mt genes were transcribed in the same direction, with same gene order as Gene arrangement 3 (GA3): nad 6 > nad 4L > tRNA-Trp (W) > tRNA-Glu (E) > rrn S > tRNA-SerUCN (S2) > tRNA-Asn (N) > tRNA-Tyr (Y) > nad 1 > atp 6 > tRNA-Lys (K) > tRNA-LeuUUR (L2) > tRNA-SerAGN (S1) > nad 2 > tRNA-Ile (I) > tRNA-Arg (R) > tRNA-Gln (Q) > tRNA-Phe (F) > cyt b > tRNA-LeuCUN (L1) > cox 3 > tRNA-Thr (T) > nad 4 > Non-coding region (NC1) > cox 1 > tRNA-Cys (C) > tRNA-Met (M) > tRNA-Asp (D) > tRNA-Gly (G) > cox 2 > tRNA-His (H) > rrn L > nad 3 > nad 5 > tRNA-Ala (A) > Non-coding region (NC2) > tRNA-Pro (P) > tRNA-Val (V) (Figure 1, Table 1).The nucleotide compositions of the completemt DNA sequences for N. oiratianus and N. spathiger are biased toward T and A, with T being the most favored nucleotide and C as the least favored. The contents of A + T were 76.14% (T = 47.69%; A = 28.46%; G = 16.8%; C = 7.06%) and 75.04% (T = 48.29%; A = 26.75%; G = 17.69%; C = 7.27%) for N. oiratianus and N. spathiger, respectively. The magnitude of sequence difference across the complete mt genome was 16.29% between N. oiratianus and N. spathiger.
Figure 1

Structure of the mitochondrial genomes of Nematodirus oiratianus and Nematodirus spathiger. Genes are designated according to standard nomenclature, except for the 22 tRNA genes, which are designated using one-letter amino acid codes, with numerals differentiating each of the two leucine- and serine-specifying tRNAs (L1 and L2 for codon families CUN and UUR, respectively; S1 and S2 for codon families AGN and UCN, respectively). “NC1” refers to a small non-coding region; “NC2” refers to a large non-coding region.

Table 1

The arrangements and contents of mitochondrial genomes for Nematodirus spathiger and N. oiratianus

Genes/regions

Positions

Length

Start/stop

Sequence difference (%)

NO

NS

NO

NS

NO

NS

nad 6

1-438

1-438

438

438

ATG /TAG

ATA /TAA

20.78

nad 4L

447-695

441-689

249

249

ATT/TAG

ATT/TAA

12.05

tRNA-Trp (W)

676-731

670-725

56

56

  

5.36

tRNA-Glu (E)

739-793

731-785

55

55

  

10.91

rrn S

794-1489

787-1481

696

695

  

9.05

tRNA-SerUCN (S2)

1490-1543

1482-1534

54

53

  

9.26

tRNA-Asn (N)

1544-1599

1536-1589

56

54

  

10.71

tRNA-Tyr (Y)

1606-1659

1596-1651

54

56

  

5.36

nad 1

1666-2532

1658-2524

867

867

ATG/TAA

ATA /TAA

12.34

atp 6

2533-3132

2524-3123

600

600

ATT/TAA

ATT /TAA

14.17

tRNA-Lys (K)

3131-3193

3127-3187

63

61

  

12.7

tRNA-LeuUUR (L2)

3195-3249

3189-3243

55

55

  

0

tRNA-SerAGN (S1)

3250-3300

3244-3295

51

52

  

19.23

nad 2

3307-4144

3302-4140

838

839

ATG/T

ATG/TA

8.34

tRNA-Ile (I)

4145-4200

4141-4196

56

56

  

19.64

tRNA-Arg (R)

4221-4274

4197-4251

54

55

  

3.64

tRNA-Gln (Q)

4328-4383

4254-4309

56

56

  

10.71

tRNA-Phe (F)

4396-4451

4316-4369

56

54

  

14.29

cyt b

4452-5564

4370-5481

1113

1112

ATT/TAA

ATT/TA

5.75

tRNA-LeuCUN (L1)

5565-5620

5482-5537

56

56

  

14.29

cox 3

5621-6386

5538-6303

766

766

ATT/T

ATA/T

10.18

tRNA-Thr (T)

6387-6441

6304-6357

55

54

  

27.27

nad 4

6442-7671

6358-7587

1230

1230

TTG/TAA

TTG/TAA

17.32

Non-coding region (NC1)

7672-7769

7588-7685

98

98

  

17.35

cox 1

7770-9345

7686-9261

1576

1576

ATA/T

ATA/T

11.55

tRNA-Cys (C)

9346-9399

9262-9316

54

55

  

16.36

tRNA-Met (M)

9401-9456

9319-9373

56

55

  

7.14

tRNA-Asp (D)

9457-9511

9373-9428

55

56

  

12.5

tRNA-Gly (G)

9513-9567

9430-9485

55

56

  

12.5

cox 2

9568-10261

9486-10181

694

696

ATT/T

ATT/TAG

12.79

tRNA-His (H)

10262-10315

10187-10240

54

54

  

20.37

rrn L

10316-11277

10241-11198

962

958

  

5.2

nad 3

11278-11604

11199-11525

327

327

ATA/TAG

ATG/TAA

12.54

nad 5

11608-13189

11525-13106

1582

1582

ATT/T

ATT/T

11.06

tRNA-Ala (A)

13190-13245

13107-13162

56

56

  

1.79

Non-coding region (NC2)

13246-13633

13163-13400

388

238

  

55.93

tRNA-Pro (P)

13634-13687

13401-13456

54

56

  

10.71

tRNA-Val (V)

13712-13765

13466-13519

54

54

  

5.56

NS: N. spathiger; NO: N. oiratiuns; Start/Stop: initiation and termination codons.

All protein-coding genes used ATA, ATT, ATG or TTG as their initiation codons, and TAA or TAG as their termination codons. Incomplete termination codons (TA and T) were also present (Table 1), which was consistent with studies of some other nematodes [15, 16, 44]. Excluding the termination codons, a total of 3419 and 3416 amino acids were encoded by the N. oiratianus and N. spathiger mt genomes, respectively. The codon usages for the two mt genomes are listed in Table 2. Codons composed of A and T were predominantly used, reflecting the high content of A + T in the complete mt genomes of the two Nematodirus species. The most frequent usage of codon was TTT (Phenylalanine) for both two species, with frequencies of 12.61% and 12.88% for N. oiratianus and N. spathiger, respectively, followed by TTA (Leucine) in the two species (10.95% and 9.17%, respectively). Codon CGC (Arginine) was not used in the mt genomes of either species, and codon TGC (Cysteine) was not used in the mt genome of N. spathiger.
Table 2

Codon usages of Nematodirus oiratianus and N. spathiger mitochondrial DNA encoded proteins

Amino acid

Codon

Number

Frequency (%)

Amino acid

Codon

Number

Frequency (%)

NO

NS

NO

NS

NO

NS

NO

NS

Phe

TTT

432

441

12.61

12.88

IIe

ATT

229

245

6.68

7.16

Phe

TTC

8

9

0.23

0.26

IIe

ATC

10

4

0.29

0.12

Leu

TTA

375

314

10.95

9.17

Met

ATA

150

125

4.38

3.65

Leu

TTG

160

194

4.67

5.67

Met

ATG

69

80

2.01

2.34

Ser

TCT

75

89

2.19

2.6

Thr

ACT

74

74

2.16

2.16

Ser

TCC

2

10

0.06

0.29

Thr

ACC

9

10

0.26

0.29

Ser

TCA

48

33

1.4

0.96

Thr

ACA

21

17

0.61

0.5

Ser

TCG

14

11

0.41

0.32

Thr

ACG

10

8

0.29

0.23

Tyr

TAT

182

190

5.31

5.55

Asn

AAT

135

130

3.94

3.8

Tyr

TAC

9

5

0.26

0.15

Asn

AAC

4

8

0.12

0.23

Term

TAA

5

6

0.15

0.18

Lys

AAA

49

41

1.43

1.2

Term

TAG

2

1

0.06

0.03

Lys

AAG

52

59

1.52

1.72

Cys

TGT

39

39

1.14

1.14

Ser

AGT

141

164

4.12

4.79

Cys

TGC

2

0

0.06

0

Ser

AGC

3

4

0.09

0.12

Trp

TGA

41

32

1.2

0.93

Ser

AGA

50

30

1.46

0.88

Trp

TGG

29

38

0.85

1.11

Ser

AGG

28

31

0.82

0.91

Leu

CTT

14

16

0.41

0.47

Val

GTT

141

146

4.12

4.27

Leu

CTC

4

3

0.12

0.09

Val

GTC

12

12

0.35

0.35

Leu

CTA

12

11

0.35

0.32

Val

GTA

94

76

2.74

2.22

Leu

CTG

5

11

0.15

0.32

Val

GTG

43

64

1.26

1.87

Pro

CCT

41

45

1.2

1.31

Ala

GCT

72

69

2.1

2.02

Pro

CCC

5

11

0.15

0.32

Ala

GCC

11

14

0.32

0.41

Pro

CCA

22

15

0.64

0.44

Ala

GCA

17

18

0.5

0.53

Pro

CCG

9

6

0.26

0.18

Ala

GCG

4

8

0.12

0.23

His

CAT

46

49

1.34

1.43

Asp

GAT

64

63

1.87

1.84

His

CAC

10

5

0.29

0.15

Asp

GAC

4

4

0.12

0.12

Gln

CAA

18

23

0.53

0.67

Glu

GAA

41

30

1.2

0.88

Gln

CAG

22

18

0.64

0.53

Glu

GAG

33

44

0.96

1.29

Arg

CGT

26

27

0.76

0.79

Gly

GGT

127

133

3.71

3.89

Arg

CGC

0

0

0

0

Gly

GGC

5

6

0.15

0.18

Arg

CGA

4

1

0.12

0.03

Gly

GGA

28

17

0.82

0.5

Arg

CGG

1

3

0.03

0.09

Gly

GGG

34

33

0.99

0.96

NO: N. oiratiuns; NS: N. spathiger; Total number of codon are 3426 for N. oiratiuns, and 3423 for N. spathiger, excluding the incomplete termination codons.

Twenty-two tRNA genes were predicted from the mt genomes of N. oiratianus and N. spathiger and varied from 51 to 63 bp in length. The secondary structures predicted for the genes were similar to those of T. axei and T. vitrinus[29]. Twenty tRNA genes (excluding two tRNA-Ser) had a predicted secondary structure with a 3-5 bp DHU arm and a DHU loop of 7-9 bases, in which the variable TψC arm and loop were replaced by a “TV-replacement loop” of 8-10 bases. As in almost all other nematode mtDNA sequences [29], the tRNA-Ser genes of both Nematodirus mt genomes are equipped with a TψC arm and loop but lacked the DHU arm and loop, consisting of a 6-8 bp TψC arm, TψC loop of 4-6 bases and a variable loop of 4 bases.

The rrn L and rrn S genes of N. oiratianus and N. spathiger were identified by comparison with those of T. axei and T. vitrinus[29]. The rrn L gene was located between tRNA-His and nad 3, and rrn S was located between tRNA-Glu and tRNA-SerUCN (Table 1). The length of rrn L was 962 bp for N. oiratianus and 958 bp for N. spathiger, with 5.2% of sequence difference. The length of rrn S was 696 bp for N. oiratianus and 695 bp for N. spathiger, with 9.05% of sequence difference. The A + T contents of rrn L for N. oiratianus and N. spathiger were 80.98% and 79.85%, respectively. The A + T contents of rrn S for N. oiratianus and N. spathiger were 76.29% and 77.70%, respectively.

Two non-coding regions (designated as NC1 and NC2) were inferred in the mt genomes of both N. oiratianus and N. spathiger. For both mt genomes, the AT-rich regions were located between nad 4 and cox 1, tRNA-Ala and tRNA-Pro (Figure 1; Table 1), with A + T contents of 81.25% for N. oiratianus and 81.07% for N. spathiger.

Phylogenetic analysis (Figure 2) based on concatenated amino acid sequence data of all 12 mt proteins showed that nematodes in families Molineidae and Dictyocaulidae grouped together, and parasites in families Trichostrongylidae (T. vitrinus, T. axei and T. circumcincta), Cooperiidae (Cooperia oncophora) and Haemonchidae (M. digitatus and H. contortus) clustered together. N. oiratianus and N. spathiger samples in the present study clustered together and were highly closely related to the family Dictyocaulidae with high clade support (Bpp = 1.00; Bf = 100), confirming the results of previous studies using the morphological features and ITS rDNA as the genetic marker [2, 9, 42]. However, amino acid sequence-based inferences of the relationship between the two Nematodirus species gave slightly different results to those using ITS rDNA data in which they clustered in sister clades with high support, possibly due to the different taxa inclusions and types of analysis performed [2, 1113, 46].
Figure 2

Genetic relationships of Nematodirus nematodes with other selected Trichostrongyloid nematodes inferred by Bayesian inference (BI) based on mitochondrial sequence data. Phylogenetic analyses based on the concatenated amino acid sequence data representing 12 protein-coding genes were conducted using Bayesian inference (BI), Maximum likelihood (ML) and Maximum parsimony (MP), with Oesophagostomum quadrispinulatum (NC_014181) as the outgroup. The scale bar indicated Posterior Probability.

Molecular analyses have provided new insights into population structure and species identification of parasites [15, 16, 34, 44]. In the present study, we utilized long-range PCR-coupled sequencing and bioinformatic methods [23] to characterize the complete mt genomes of two Nematodirus species from small ruminants and to assess the phylogenetic relationships of these Nematodirus species in relation to representative Trichostrongyloid nematodes. Given that there are no morphological characteristics to allow the explicit specific identification and differentiation of Nematodirus species (Nematoda: Molineidae) at some developmental stages, such as larvae and egg [9, 10], the use of mt DNA markers to investigate genetic composition in these species is a significant advance. To date, more than 45 Nematodirus species have been described based on their morphological features [1, 2], however, no information is yet available about their mt genomes. Although previous studies have indicated that ITS rDNA provides a useful marker for identification and differentiation of Nematodirus species [2, 11, 13], mtDNA in nematodes is usually more variable in sequences within a species than the nuclear ribosomal DNA [14].

The characterization of the mt genomes of N. oiratianus and N. spathiger also allows a reassessment of the systematic relationships of nematodes within the Trichostrongyloidea using mt proteomic datasets. For many years, there has been considerable debate surrounding the systematics of members within the Trichostrongyloidea (including Haemonchidae, Cooperiidae, Trichostrongylidae, Molineidae and Dictyocaulidae) [47]. Given the controversy, concatenated mt proteomic/genomic datasets might be applied effectively to genetically characterize and compare Trichostrongyloid nematodes. The current work has provided insight into the phylogenetic relationships among Trichostrongyloid nematodes, however, many species of Trichostrongyloid nematodes are not represented. Expanding taxon sampling is therefore necessary for future phylogenetic studies of a wide range of Trichostrongyloidea using mt proteomic/genomic datasets.

Conclusions

The present study determined the complete mt genome sequences of N. oiratianus and N. spathiger. The mtDNA data presented here not only provide new mtDNA resources for a better understanding of nematode mt genomics and phylogeny, but also provide novel and useful genetic markers for studying diagnosis, population genetics, and molecular epidemiology of Nematodirus spp. in small ruminants.

Notes

Declarations

Acknowledgements

This work was supported by grant from Fund of the “Special Fund for Agro-scientific Research in the Public Interest” (Grant No. 201303037). The authors thank Dr. Alasdair Nisbet of the Moredun Research Institute, UK, for help in editing the English in this manuscript.

Authors’ Affiliations

(1)
College of Veterinary Medicine, Northwest A&F University
(2)
Lanzhou Veterinary Research Institute, State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Chinese Academy of Agricultural Sciences

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© Zhao et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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