- Open Access
Chabertia erschowi (Nematoda) is a distinct species based on nuclear ribosomal DNA sequences and mitochondrial DNA sequences
- Guo-Hua Liu†1, 3,
- Lei Zhao†1, 2,
- Hui-Qun Song1,
- Guang-Hui Zhao4,
- Jin-Zhong Cai5,
- Quan Zhao2 and
- Xing-Quan Zhu1, 2, 3Email author
© Liu et al.; licensee BioMed Central Ltd. 2014
- Received: 14 December 2013
- Accepted: 18 January 2014
- Published: 22 January 2014
Gastrointestinal nematodes of livestock have major socio-economic importance worldwide. In small ruminants, Chabertia spp. are responsible for economic losses to the livestock industries globally. Although much attention has given us insights into epidemiology, diagnosis, treatment and control of this parasite, over the years, only one species (C. ovina) has been accepted to infect small ruminants, and it is not clear whether C. erschowi is valid as a separate species.
The first and second internal transcribed spacers (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) and the complete mitochondrial (mt) genomes of C. ovina and C. erschowi were amplified and then sequenced. Phylogenetic re-construction of 15 Strongylida species (including C. erschowi) was carried out using Bayesian inference (BI) based on concatenated amino acid sequence datasets.
The ITS rDNA sequences of C. ovina China isolates and C. erschowi samples were 852–854 bp and 862 -866 bp in length, respectively. The mt genome sequence of C. erschowi was 13,705 bp in length, which is 12 bp shorter than that of C. ovina China isolate. The sequence difference between the entire mt genome of C. ovina China isolate and that of C. erschowi was 15.33%. In addition, sequence comparison of the most conserved mt small subunit ribosomal (rrn S) and the least conserved nad 2 genes among multiple individual nematodes revealed substantial nucleotide differences between these two species but limited sequence variation within each species.
The mtDNA and rDNA datasets provide robust genetic evidence that C. erschowi is a valid strongylid nematode species. The mtDNA and rDNA datasets presented in the present study provide useful novel markers for further studies of the taxonomy and systematics of the Chabertia species from different hosts and geographical regions.
- Chabertia spp
- Nuclear ribosomal DNA
- Internal transcribed spacer (ITS)
- Mitochondrial DNA
- Phylogenetic analysis
The phylum Nematoda includes many parasites that threaten the health of plants, animals and humans on a global scale. The soil-transmitted helminthes (including roundworms, whipworms and hookworms) are estimated to infect almost one sixth of all humans, and more than a billion people are infected with at least one species. Chabertia spp. are common gastrointestinal nematodes, causing significant economic losses to the livestock industries worldwide, due to poor productivity, failure to thrive and control costs[2–6]. In spite of the high prevalence of Chabertia reported in small ruminants, it is not clear whether the small ruminants harbour one or more than one species. Based on morphological features (e.g., cervical groove and cephalic vesicle) of adult worms, various Chabertia species have been described in sheep and goats in China, including C. ovina, C. rishati, C. bovis, C. erschowi, C. gaohanensis sp. nov and C. shaanxiensis sp. nov[8–10]. However, to date, only Chabertia ovina is well recognized as taxonomically valid[11, 12]. Obviously, the identification and distinction of Chabertia to species using morphological criteria alone is not reliable. Therefore, there is an urgent need for suitable molecular approaches to accurately identify and distinguish closely-related Chabertia species from different hosts and regions.
Molecular tools, using genetic markers in mitochondrial (mt) genomes and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (rDNA), have been used effectively to identify and differentiate parasites of different groups[13–16]. For nematodes, recent studies showed that mt genomes are useful genetic markers for the identification and differentiation of closely-related species[17, 18]. In addition, employing ITS rDNA sequences, recent studies also demonstrated that Haemonchus placei and H. contortus are distinct species; Trichuris suis and T. trichiura are different nematode species[20, 21].
Using a long-range PCR-coupled sequencing approach, the objectives of the present study were (i) to characterize the ITS rDNA and mt genomes of C. ovina and C. erschowi from goat and yak in China, (ii) to compare these ITS sequences and mt genome sequences, and (iii) to test the hypothesis that C. erschowi is a valid species in phylogenetic analyses of these sequence data.
Parasites and isolation of total genomic DNA
Adult specimens of C. ovina (n = 6, coded CHO1-CHO6) and C. erschowi (n = 9, coded CHE1-CHE9) were collected, post-mortem, from the large intestine of a goat and a yak in Shaanxi and Qinghai Provinces, China, respectively, and were washed in physiological saline, identified morphologically[8, 10], fixed in 70% (v/v) ethanol and stored at -20°C until use. Total genomic DNA was isolated separately from 15 individual worms using an established method.
Long-range PCR-based sequencing of mt genome
Sequences of primers used to amplify mitochondrial DNA regions from Chabertia erschowi and Chabertia ovina from China
Sequence (5′ to 3′)
For rrn S
TCGTTTAGTGGGTATGTGTGGTTCT (for C. ovina)
GCCTACTCCCTAACAAATGACGCTC (for C. ovina)
GTGGTTTTTAGGTTAGGGTTGAGTG (for C. erschowi)
ACGCTCATACAAAGTAATAAACGCA (for C. erschowi)
For nad 2
TTTGTGG(C\T)TAAGAGTGTT(G\A)GCTATT (for C. ovina)
GAGCCGTAATCAAACATAGTAAATC (for C. ovina)
TTTGTGG(C\T)TAAGAGTGTT(G\A)GCTATT (for C. erschowi)
ACCGTAATCAAACATAGTAAAATCT (for C. erschowi)
For C. ovina
For C. erschowi
Sequencing of ITS rDNA and mt rrn S and nad 2
The full ITS rDNA region including primer flanking 18S and 28S rDNA sequences was PCR-amplified from individual DNA samples using universal primers NC5 (forward; 5′-GTAGGTGAACCTGCGGAAGGATCATT-3′) and NC2 (reverse; 5′-TTAGTTTCTTTTCCTCCGCT-3′) described previously. The primers rrn SF and rrn SR (Table1) designed to conserved mt genome sequences within the rrn S gene were employed for PCR amplification and subsequent sequencing of this complete gene (~ 700 bp) from multiple individuals of Chabertia spp. The primers nad 2F and nad 2R (Table1) designed to conserved mt genome sequences within the nad 2 gene were employed for PCR amplification and subsequent sequencing of this complete gene (~ 900 bp) from multiple individuals of Chabertia spp..
Sequences were assembled manually and aligned against the complete mt genome sequences of C. ovina Australia isolate using the computer program Clustal X 1.83 to infer gene boundaries. Translation initiation and termination codons were identified based on comparison with that of C. ovina Australia isolate. The secondary structures of 22 tRNA genes were predicted using tRNAscan-SE and/or manual adjustment, and rRNA genes were identified by comparison with that of C. ovina Australia isolate.
Amino acid sequences inferred from the 12 protein-coding genes of the two Chabertia spp. worms were concatenated into a single alignment, and then aligned with those of 14 other Strongylida nematodes (Angiostrongylus cantonensis, GenBank accession number NC_013065; Angiostrongylus costaricensis, NC_013067; Angiostrongylus vasorum, JX268542; Aelurostrongylus abstrusus, NC_019571; Chabertia ovina Australia isolate, NC_013831; Cylicocyclus insignis, NC_013808; Metastrongylus pudendotectus, NC_013813; Metastrongylus salmi, NC_013815; Oesophagostomum dentatum, FM161882; Oesophagostomum quadrispinulatum, NC_014181; Oesophagostomum asperum, KC715826; Oesophagostomum columbianum, KC715827; Strongylus vulgaris, NC_013818; Syngamus trachea, NC_013821, using the Ancylostomatoidea nematode, Necator americanus, NC_003416 as the outgroup. Any regions of ambiguous alignment were excluded using Gblocks (http://molevol.cmima.csic.es/castresana/Gblocks_server.html) with the default parameters (Gblocks removed 1.6% of the amino acid alignments) and then subjected to phylogenetic analysis using Bayesian Inference (BI) as described previously[35, 36]. Phylograms were drawn using the program Tree View v.1.65.
Nuclear ribosomal DNA regions of the two Chabertia species
The rDNA region including ITS-1, 5.8S rDNA and ITS-2 were amplified and sequenced from C. ovina China isolates, and they were 852-854 bp (GenBank accession nos. KF913466-KF913471) in length, which contained 367-369 bp (ITS-1), 153 bp (5.8S rDNA) and 231-239 bp (ITS-2). These sequences were 862-866 bp in length for C. erschowi samples (GenBank accession nos. KF913448-KF913456), containing 375-378 bp (ITS-1), 153 bp (5.8S rDNA) and 239-245 bp (ITS-2).
Features of the mt genomes of the two Chabertia species
Mitochondrial genome organization of Chabertia erschowi (CE) and Chabertia ovina China isolate (COC) and Australia isolate (COA)
Gene and region
Positions and nt sequence lengths (bp)
tRN A-Cys (C)
Non-coding region (NC1)
Non-coding region (NC2)
tRNA-Ser UCN (S2)
tRNA-Ser AGN (S1)
10404- 11516 (1113)
tRNA-Leu CUN (L1)
Non-coding region (NC3)
13628 – 1 (75)
Comparative analyses between C. ovina and C. erschowi
Nucleotide and/or predicted amino acid (aa) sequence differences for mt protein-coding and ribosomal RNA genes among Chabertia erschowi (CE) and Chabertia ovina China isolate (COC) and Australia isolate (COA)
Nucleotide length (bp)
Nucleotide difference (%)
Number of aa
aa difference (%)
Sequence variation in complete rrn S gene was assessed among 15 individuals of Chabertia from goat and yak. Sequences of the rrn S gene from the six C. ovina China isolate individuals were the same in length (696 bp) (GenBank accession nos. KF913478-KF913483). Nucleotide variation among the six C. ovina China isolate individuals was detected at seven sites (7/696; 1.0%). Sequences of the rrn S gene from the nine C. erschowi individuals were the same in length (696 bp) (GenBank accession nos. KF913457-KF913465). Nucleotide variation also occurred at 6 sites (6/696; 0.9%). All 15 alignments of the rrn S sequences revealed that all individuals of Chabertia differed at 56 nucleotide positions (56/696; 8.05%). Phylogenetic analysis of the rrn S sequence data revealed strong support for the separation of C. ovina and C. erschowi individuals into two distinct clades (Figure3B).
The ITS-1 and ITS-2 sequences from 10 individual adults of C. ovina China isolate were compared with that of 6 individual adults of C. erschowi. Sequence variations were 0–2.9% (ITS-1) and 0–2.7% (ITS-2) within the two Chabertia species, respectively. However, the sequence differences were 6.3-8.2% (ITS-1) and 10.4-13.6% (ITS-2) between the C. ovina China isolate and C. erschowi.
Chabertia spp. is responsible for economic losses to the livestock industries globally. Although several Chabertia species have been described from various hosts based on the microscopic features of the adult worms (e.g. cervical groove and cephalic vesicle), it is not clear whether C. erschowi is valid as a separate species due to unreliable morphological criteria. For this reason, we employed a molecular approach, so that comparative genetic analyses could be conducted.
In the present study, substantial levels of nucleotide differences (15.33%) were detected in the complete mt genome between C. ovina China isolate and C. erschowi, and 15.48% between C. ovina Australia isolate and C. erschowi. These mtDNA data provide strong support that C. erschowi represents a single species because a previous comparative study has clearly indicated that variation in mtDNA sequences between closely-related species were typically 10%-20%.
The difference in amino acid sequences of the concatenated 12 proteins encoded by the complete mt genome between C. ovina China isolate and C. erschowi is 9.36%, and 10% between the C. ovina Australia isolate and C. erschowi. This level of amino acid variation is higher than those of other nematodes. Previous studies of other congener nematodes have detected low level differences in 12 protein sequences. For example, differences in amino acid sequences between A. duodenale and A. caninum is 4.1%[29, 38], and between Toxocara malaysiensis and Toxocara cati is 5.6%, and between O. dentatum and O. quadrispinulatum is 3.22%. In addition, substantial levels of nucleotide differences (6.3%-8.2% in ITS-1 and 10.4-13.6% in ITS-2) were also detected between C. ovina China isolate and C. erschowi. These results also indicate that C. erschowi is a separate species from C. ovina. This proposal was further supported by phylogenetic analysis based on mtDNA sequences (Figure3), although, to date, only small numbers of adult worms have been studied molecularly. Clearly, larger population genetic and molecular epidemiological studies should be conducted using the mt and nuclear markers defined in this study to further test this proposal/hypothesis.
The findings of this study provide robust genetic evidence that C. erschowi is a separate and valid species from C. ovina. The mtDNA and rDNA datasets reported in the present study should provide useful novel markers for further studies of the taxonomy and systematics of Chabertia spp. from different hosts and geographical regions.
This work was supported in part by the International Science & Technology Cooperation Program of China (Grant No. 2013DFA31840), the “Special Fund for Agro-scientific Research in the Public Interest” (Grant No. 201303037) and the Science Fund for Creative Research Groups of Gansu Province (Grant No. 1210RJIA006).
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