Comparative analyses of the complete mitochondrial genomes of the two ruminant hookworms Bunostomum trigonocephalum and Bunostomum phlebotomum

Molecular characterization of a novel Spiruromorpha species in wild Chinese pangolin by mitogenome sequence analysis

Pangolins are susceptible to a variety of gastrointestinal nematodes due to their burrowing lifestyle and feeding habits, and few parasitic nematodes have been reported. Here, a Chinese pangolin with old wounds on its leg and tail was rescued from the Heyuan City, Guangdong Province. The cox1 and SSU rRNA of the worms from the intestine of the Chinese pangolin had the highest sequence identity of 89.58% and 97.95% to the species in the infraorder Spiruromorpha. The complete mitogenome of the worm was further assembled by next-generation sequencing, with a size of 13,708 bp and a GC content of 25.6%. The worm mitogenome had the highest sequence identity of 78.56% to that of Spirocerca lupi, sharing the same gene arrangement with S. lupi and some species in other families under Spiruromorpha. However, the mitogenome between the worm and S. lupi showed differences in codon usage of PCGs, sequences of NCR, and tRNA secondary structures. Phylogenetic analysis showed that the worm mitogenome was clustered with S. lupi in the family Thelaziidae to form a separate branch. However, it is still difficult to identify the worm in the family Thelaziidae because the species in the family Thelaziidae are confused, specifically S. lupi and Thelazia callipaeda in the family Thelaziidae were separated and grouped with species from other families. Thus, the parasitic nematode from the Chinese pangolin may be a novel species in Spiruromorpha and closely related to S. lupi. This study enriches the data on gastrointestinal nematodes in the Chinese pangolin.

The complete mitochondrial genome of Wellcomia compar (Spirurina: Oxyuridae) and its genome characterization and phylogenetic analysis

Wellcomia compar (Spirurina: Oxyuridae) is a pinworm that infects wild and captive porcupines. Despite clear records of its morphological structure, its genetics, systematics, and biology are poorly understood. This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. We sequenced the complete mt genome of W. comparand conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. The complete mt genome is 14,373 bp in size and comprises 36 genes, including 12 protein-coding, two rRNA and 22 tRNA genes. Apart from 28 intergenic regions, one non-coding region and one overlapping region also occur. A comparison of the gene arrangements of Oxyuridomorpha revealed relatively similar features in W. compar and Wellcomia siamensis. Phylogenetic analysis also showed that W. compar and W. siamensis formed a sister group. In Oxyuridomorpha the genetic distance between W. compar and W. siamensis was 0.0805. This study reports, for the first time, the complete W. compar mt genome sequence obtained from Chinese porcupines. It provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals.

The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications

Trematodes of the genus Ogmocotyle are intestinal flukes that can infect a variety of definitive hosts, resulting in significant economic losses worldwide. However, there are few studies on molecular data of these trematodes. In this study, the mitochondrial (mt) genome of Ogmocotyle ailuri isolated from red panda (Ailurus fulgens) was determined and compared with those from Pronocephalata to investigate the mt genome content, genetic distance, gene rearrangements and phylogeny. The complete mt genome of O. ailuri is a typical closed circular molecule of 14 642 base pairs, comprising 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. All genes are transcribed in the same direction. In addition, 23 intergenic spacers and 2 locations with gene overlaps were determined. Sequence identities and sliding window analysis indicated that cox1 is the most conserved gene among 12 PCGs in O. ailuri mt genome. The sequenced mt genomes of the 48 Plagiorchiida trematodes showed 5 types of gene arrangement based on all mt genome genes, with the gene arrangement of O. ailuri being type I. Phylogenetic analysis using concatenated amino acid sequences of 12 PCGs revealed that O. ailuri was closer to Ogmocotyle sikae than to Notocotylus intestinalis. These data enhance the Ogmocotyle mt genome database and provide molecular resources for further studies of Pronocephalata taxonomy, population genetics and systematics.

Gastrointestinal nematodes from buffalo in Minoufiya Governorate, Egypt with special reference to Bunostomum phlebotomum

Gastrointestinal nematodes cause massive economic losses as an important impediment to the development of animals around the world. This study aimed to investigate the microscopical diagnosis of nematode parasites of buffalo from Minoufiya, Egypt and molecular characterization of Bunostomum phlebotomum. We examined 390 fecal samples with floatation and fecal culture techniques to recognize different genera of nematodes. The results revealed B. phlebotomum (2.56%), Strongyloides papillosus (3.85%), Toxocara vitulorum (7.69%), Haemonchus sp. (1.28%), and Dictyocaulus viviparus (1.28%). The recovered eggs and larvae of nematodes were identified as well as the adults of B. phlebotomum. Age-wise, sex-wise, and seasonal prevalences of the recovered nematodes were recorded. Sequence analysis of the ITS-2 gene of B. phlebotomum was highly identical (99-100%) to sequences from Australia and China and occurred in the same clade with B. trigoncephalum. In conclusion, the study presented the coprological survey of gastrointestinal nematodes, and the genetic characterization of B. phlebotomum from Minoufiya Governorate, Egypt for the first time.

The complete mitochondrial genome of the beef cattle hookworm Bunostomum phlebotomum (Nematoda: Bunostominae)

The bovine hookworm Bunostomum phlebotomum (Nematoda: Bunostominae) is a blood-feeding nematode with important socioeconomic impact in the cattle breeding industry. In the present study, the complete mitochondrial genome sequence of a representative individual of B. phlebotomum from beef cattle in Southwest China was determined using the next generation sequencing technology. The genome was 13,799 bp in size and encoded 12 protein-coding genes, 22 tRNA genes and two rRNA genes. The phylogeny revealed that although B. phlebotomum from Chinese beef cattle and yaks were more closely related to each other than to that from Australian cows, these three bovine-originated B. phlebotomum grouped together and formed paraphyletic relationships with Bunostomum trigonocephalum (goat/sheep hookworm) and Necator americanus (human hookworm), supporting their sister-species relationships within Bunostominae. The cumulative mitochondrial DNA data provides a better understanding of phylogenetic relationships of this species in cattle.

Comparative analysis of mitochondrial DNA datasets indicates that Cylicostephanus minutus represents a species complex

Cyathostomins are one kind of the most important parasites in equids. Cylicostephanus minutus is a member of the subfamily Cyathostominae. In the present study, we determined the complete mitochondrial (mt) genomes from four Cs. minutus isolates and reconstructed the phylogenetic relationship of Strongylidae to test the hypothesis that Cs. minutus represents a species complex. The complete mt genome sequences of Cs. minutus were 13,772-13,822 bp in length, and contained 36 genes (12 protein coding genes, 22 tRNA genes, two rRNA genes), and two non-coding regions (NCRs). The intraspecific identity of nucleotide sequences and amino acid sequences in Cs. minutus (1-4) were 89.3-97.9% and 97.0-98.8%, respectively. Two operational taxonomic units (OTUs) were determined based on the mt genome sequences, OTU 2 (Csm 1 and Csm 2) and OTU 3 (Csm 3 and Csm 4). Sequence analysis showed the divergence between OTU 2 and OTU 3 was 8.9-10.7%. Pairwise comparisons of 12 protein coding genes between OTU 2 and OTU 3 showed a difference of 3.0-13.3% at the nucleotide level and 0-6.7% at the amino acid level. Phylogenetic analysis showed the separation of Cs. minutus isolates from the same host into different distinct clades based on mt genomes. Comparisons of partial mt cox1, nad5, and cytb and ITS2 sequences from 20 Cs. minutus isolates from the same host and the same geographical location with other Cs. minutus sequences available in GenBank revealed significant nucleotide differences. Phylogenetic analysis showed a separation of Cs. minutus into three distinct clades. Thus, the comparative and phylogenetic analyses of mtDNA datasets indicated that Cs. minutus represents a complex of at least three species. Our results have further confirmed the existence of a cryptic Cs. minutus species, and provides a reference for the taxonomical, population genetics, and systematics studies of other cyathostomin species.

Pinworms of the red howler monkey (Alouatta seniculus) in Colombia: Gathering the pieces of the pinworm-primate puzzle

Pinworms of primates are believed to be highly host specific parasites, forming co-evolutionary associations with their hosts. In order to assess the strength and reach of such evolutionary links, we need to have a broad understanding of the pinworm diversity associated with primates. Here, we employed an integrative taxonomic approach to assess pinworm diversity in red howler monkeys in Colombia. Molecular and morphological evidence validate the presence of at least four different species of Trypanoxyuris occurring in red howler monkeys: T. minutus, a widely distributed species, and three new species, T. seunimiii n. sp., T. kemuimae n. sp. and T. kotudoi n. sp. The mitochondrial COI gene and the 28S ribosomal gene were used for phylogenetic assessments through Bayesian inference. The three new species were morphologically distinct and formed reciprocally monophyletic lineages. Further molecular lineage subdivision in T. minutus and T. kotudoi n. sp. without morphological correspondence, suggests the potential scenario for the existence of cryptic species. Phylogenetic relationships imply that the different species of Trypanoxyuris occurring in each howler monkey species were acquired through independent colonization events. On-going efforts to uncover pinworm diversity will allow us to test the degree of host specificity and the co-phylogenetic hypothesis, as well as to further unravel the primate-pinworm evolutionary history puzzle.

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Three new species of pinworms from red howler monkeys are described.

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Phylogenetic analysis suggests the potential existence of cryptic species.

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Our results agree with pinworms of primates as highly host specific parasites.

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Trypanoxyuris species occurring in each howler species are not closely related.

Comparative analyses of the complete mitochondrial genomes of Cyathostomum pateratum and Cyathostomum catinatum provide new molecular data for the evolution of Cyathostominae nematodes

The parasite Cyathostomum pateratum, which occurs in the large intestine of equines, is a common species of the subfamily Cyathostominae. Cyathostominae nematodes are a complex nematode group for which only limited genetic information has been reported. To re-examine the phylogenetic relationships among Cyathostominae nematodes, we sequenced the complete mitochondrial (mt) genome of Cy. pateratum and compared it with the mt genome of the congeneric species Cyathostomum catinatum. The complete mtDNA sequence of Cy. pateratum was 13,822 bp in length, 16 bp shorter than that of Cy. catinatum. The mtDNA sequences of both species contained 12 protein-coding genes, two rRNA genes and 22 tRNA genes, and all 36 genes were transcribed in the same direction and in the same strand. Pairwise comparisons of the 12 predicted amino acid sequences between Cy. catinatum and Cy. pateratum revealed differences of 0.4-3.1%; the least conserved sequence was that of cytochrome c oxidase subunit 3 (cox3). Phylogenetic analysis of the concatenated amino acid sequences using Bayesian inference and maximum likelihood methods showed that Cy. catinatum and Cy. pateratum clustered together with very high nodal support, and Cylicostephanus goldi was closer to the Cyathostomum nematodes than to other Cyathostominae nematodes. The mtDNA sequence of Cy. pateratum is reported here for the first time. The study will shed some light on the genetic evolution among parasitic nematodes in Cyathostomum.

Characterization of the complete mitochondrial genome of Setaria digitata (Nematoda: Setariidae) from China

Setaria digitata is a filarial parasite that causes fatal cerebrospinal nematodiasis in goats, horses and sheep, resulting in substantial economic losses to livestock farmers. In the present study, the complete mitochondrial (mt) genome of S. digitata from China was determined, characterized and compared with that of S. digitata from Sri Lanka. The identity of the mt genomes was 98.3% between S. digitata from China and Sri Lanka, and the complete mt genome sequence of S. digitata from China was slightly shorter (25 bp) than that from Sri Lanka. For the 12 protein genes, this comparison revealed sequence differences at both the nucleotide (1.4%) and amino acid (2.2%) levels. The present study determined the complete mt genome sequence of S. digitata from China, providing novel genetic markers for the study of the population genetics and molecular epidemiology of S. digitata in animals.

Comparative analysis of Ancylostoma ceylanicum mitochondrial genome with other Ancylostoma species

Ancylostoma ceylanicum may inhabit the small intestine of canids, felids and humans, can pose a potential risk to public health. This study is the first time to amplify complete mitochondrial genome sequence of A. ceylanicum from dog and to compare it with Ancylostoma tubaeforme, Ancylostoma duodenale and Ancylostoma caninum. The results showed that the complete mitochondrial genome of A. ceylanicum was 13,660 bp in length, including 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes and 3 non-coding regions (AT-rich region, SNCR and LNCR). Its mtDNA was the shortest, biased toward A and T at base composition, and higher than other three Ancylostoma species at total AT content. Its nad5 and nad6 genes used TTG and ATT as initiation codons, while other three Ancylostoma species used ATT and GTG or ATG. The 22 tRNA genes were different in length among four Ancylostoma species, but their anticodons were the same. Among 12 protein-coding genes, the cox1 gene was the lowest at AT content and minimum at Ka/Ks while the nad2 gene was the opposite. The phylogenetic tree showed that in the lineage of Ancylostoma, A. ceylanicum occurred on a branch external to other three Ancylostoma species, and A. caninum and A. tubaeforme had closer phylogenetic relationship than A. duodenale. This study not only enhances the mitochondrial genome database of Ancylostomatidae nematodes, but also provides new data for further phylogenetic studies among Ancylostomatidae nematodes.

The mitochondrial genome of Ancylostoma tubaeforme from cats in China

Ancylostoma tubaeforme may infect canids, felids and humans, and pose a potential risk to public health. Polymerase chain reaction (PCR) techniques were used to amplify the complete mitochondrial (mt) genome sequence of A. tubaeforme from cats and to analyse its sequence characteristics after molecular identification based on the internal transcribed spacer ITS1+ sequence. The results show that the complete mt genome sequence (GenBank accession number KY070315) of A. tubaeforme from cats was 13,730 bp in length, including 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, two non-coding regions and an AT-rich region. The nucleotide content of A and T was 77.93%, biased toward A and T. Twelve protein-coding genes used ATT, TTG and GTG as initiation codons, and TAA, TAG, TA and T as termination codons. The length of the 22 tRNA genes ranged from 52 to 62 bp, their predicted secondary structures were D loops and V loops. The lengths of the two rRNAs were 958 and 697 bp. Phylogenetic analyses showed that A. tubaeforme from cats was in the lineage of Ancylostoma, having a close phylogenetic relationship with A. caninum. This study reports for the first time the mt genome of A. tubaeforme from cats in China, which could enhance the mt genome database of Ancylostomatidae nematodes, and it offers the scientific basis for further studies in the genetic diversity of hookworms among different hosts.

Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae) and Its Phylogenetic Analysis

The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, Cetonurus globiceps. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70 bp tRNA(Thr)-tRNA(Pro) intergenic spacer is present. The C. globiceps mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of C. globiceps were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA(Ser(AGY)) lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E), was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

Mitochondrial genomes of Heterakis gallinae and Heterakis beramporia support that they belong to the infraorder Ascaridomorpha

Heterakis gallinae and Heterakis beramporia are the most prevalent nematode infecting native chicken breed, causing major economic losses. In the present study, the complete mitochondrial genomes (mt) of H. gallinae and H. beramporia were amplified by long-PCR and then sequenced. The complete mt genomes of H. gallinae and H. beramporia were 13,973bp and 14,012bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. All genes are transcribed in the same direction and the gene arrangement is identical to Ascaridia spp. Phylogenetic analysis based on the 12 protein-coding genes revealed that the family Heterakidae (represented by H. gallinae and H. beramporia) was more closely related to the infraorder Ascaridomorpha than it was to the infraorder Oxyuridomorpha. The present study determined the complete mt genome sequences for two Heterakis species, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these Heterakis parasites.

The mitochondrial genome of Angiostrongylus mackerrasae as a basis for molecular, epidemiological and population genetic studies

Background

Angiostrongylus mackerrasae is a metastrongyloid nematode endemic to Australia, where it infects the native bush rat, Rattus fuscipes. This lungworm has an identical life cycle to that of Angiostrongylus cantonensis, a leading cause of eosinophilic meningitis in humans. The ability of A. mackerrasae to infect non-rodent hosts, specifically the black flying fox, raises concerns as to its zoonotic potential. To date, data on the taxonomy, epidemiology and population genetics of A. mackerrasae are unknown. Here, we describe the mitochondrial (mt) genome of A. mackerrasae with the aim of starting to address these knowledge gaps.

Methods

The complete mitochondrial (mt) genome of A. mackerrasae was amplified from a single morphologically identified adult worm, by long-PCR in two overlapping amplicons (8 kb and 10 kb). The amplicons were sequenced using the MiSeq Illumina platform and annotated using an in-house pipeline. Amino acid sequences inferred from individual protein coding genes of the mt genomes were concatenated and then subjected to phylogenetic analysis using Bayesian inference.

Results

The mt genome of A. mackerrasae is 13,640 bp in size and contains 12 protein coding genes (cox1-3, nad1-6, nad4L, atp6 and cob), and two ribosomal RNA (rRNA) and 22 transfer RNA (tRNA) genes.

Conclusions

The mt genome of A. mackerrasae has similar characteristics to those of other Angiostrongylus species. Sequence comparisons reveal that A. mackerrasae is closely related to A. cantonensis and the two sibling species may have recently diverged compared with all other species in the genus with a highly specific host selection. This mt genome will provide a source of genetic markers for explorations of the epidemiology, biology and population genetics of A. mackerrasae.

The complete mitochondrial genome of Strongylus equinus (Chromadorea: Strongylidae): Comparison with other closely related species and phylogenetic analyses

The roundworms of genus Strongylus are the common parasitic nematodes in the large intestine of equine, causing significant economic losses to the livestock industries. In spite of its importance, the genetic data and epidemiology of this parasite are not entirely understood. In the present study, the complete S. equinus mitochondrial (mt) genome was determined. The length of S. equinus mt genome DNA sequence is 14,545 bp, containing 36 genes, of which 12 code for protein, 22 for transfer RNA, and two for ribosomal RNA, but lacks atp8 gene. All 36 genes are encoded in the same direction which is consistent with all other Chromadorea nematode mtDNAs published to date. Phylogenetic analysis based on concatenated amino acid sequence data of all 12 protein-coding genes showed that there were two large branches in the Strongyloidea nematodes, and S. equinus is genetically closer to S. vulgaris than to Cylicocyclus insignis in Strongylidae. This new mt genome provides a source of genetic markers for the molecular phylogeny and population genetics of equine strongyles.

Gnathostoma spinigerum Mitochondrial Genome Sequence: a Novel Gene Arrangement and its Phylogenetic Position within the Class Chromadorea

Human gnathostomiasis is an emerging food-borne parasitic disease caused by nematodes in the genus Gnathostoma. In spite of their significance as pathogens, these parasites remain poorly understood at the molecular level. In the present study, we sequenced the mitochondrial (mt) genome of G. spinigerum, which infects a range of definitive hosts including dogs, cats, tigers, leopards and humans. The mt genome of G. spinigerum is 14,079 bp in size and shows substantial changes in gene order compared to other nematodes studied to date. Phylogenetic analyses of mt genome sequences by Bayesian inference (BI) revealed that the infraorder Gnathostomatomorpha (represented by G. spinigerum) is closely related to the infraorder Ascaridomorpha. G. spinigerum is the first species from the infraorder Gnathostomatomorpha for which a complete mt genome has been sequenced. The new data will help understand the evolution, population genetics and systematics of this medically important group of parasites.

Complete mitochondrial genome of Sinergasilus polycolpus (Copepoda:Poecilostomatoida)

The full mitochondrial (mt) genome of Sinergasilus polycolpus is 14 000 bp in length, and it contains 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and 1 non-coding region. The genome organization, nucleotide composition and codon usage are different compared to other Copepodas, such as Lernaea cyprinacea. The full mt genome of S. polycolpus provides useful information for further studies on epidemiology and phylogenetics.

Complete Mitochondrial genome of an equine intestinal parasite, Triodontophorus brevicauda (Chromadorea: Strongylidae): the first characterization within the genus

The complete mitochondrial (mt) genome sequence of Triodontophorus brevicauda, an intestinal equine nematode parasite was determined for the first time. The circular T. brevicauda mt genome is 14,305 bp in length and contains 36 genes, of which 12 code for protein, 22 for transfer RNA, and two for ribosomal RNA, and lacks atp8 mtDNA gene. Phylogenetic analysis based on the concatenated amino acid sequence of the 12 protein-coding genes was performed using three different tree-building methods. The Strongyloidea cluster divides into two large branches, and each nematode family included in our study forms an independent clade, though paraphyly confounds the issue at some nodes. T. brevicauda clusters together with Cylicocyclus insignis with high statistical support. The mtDNA data in this study not only provide a new mtDNA resource for phylogeny, but also become a novel and useful genetic marker for further studies on the identification, population genetics, and molecular epidemiology of the genus Triodontophorus in equine.

The complete mitochondrial genome of the gullet worm Gongylonema pulchrum: gene content, arrangement, composition and phylogenetic implications

Background

Gongylonema pulchrum (Nematoda: Gongylonematidae), a thread-like spirurid gullet worm, infects a range of mammalian definitive hosts, including cattle, pigs, equines, goats, primates and humans, and can cause gongylonemiasis.

Methods

In the present study, the complete mitochondrial (mt) genome of G. pulchrum was obtained using Long-range PCR and subsequent primer walking. The phylogenetic position of G. pulchrum within the Spiruromorpha was established using Bayesian analyses of the protein-coding genes at the amino acid level.

Results

The length of this AT-rich (75.94%) mt genome is 13,798 bp. It contains 12 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one non-coding region. The gene arrangement is the same as those of Thelazia callipaeda (Thelaziidae) and Setaria digitata (Onchocercidae), but distinct from that of Heliconema longissimum (Physalopteridae). Phylogenetic analyses, based on the concatenated amino acid sequence data for all 12 protein-coding genes using Bayesian inference (BI) method, showed that G. pulchrum (Gongylonematidae) was more closely related to Spirocerca lupi (Spiruroidea) than other members of the infraorder Spiruromorpha.

Conclusions

The present study represents the first mt genome sequence for the family Gongylonematidae, which provides the opportunity to develop novel genetic markers for studies of epidemiology, population genetics and systematics of this nematode of human and animal health significance.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-0697-5) contains supplementary material, which is available to authorized users.

Mitochondrial genome plasticity among species of the nematode genus Meloidogyne (Nematoda: Tylenchina)

The mitochondrial (mt) genomes of the plant-parasitic root-knot nematodes Meloidogyne arenaria, Meloidogyne enterolobii and Meloidogyne javanica were sequenced and compared with those of three other root-knot nematode species in order to explore the mt genome plasticity within Meloidogyne. The mt genomes of M. arenaria, M. enterolobii and M. javanica are circular, with an estimated size of 18.8, 18.9 and 19.6 kb, respectively. Compared to other nematodes these mt genomes are larger, due to the presence of large non-coding regions. The mt genome architecture within the genus Meloidogyne varied in the position of trn genes and in the position, length and nucleotide composition of non-coding regions. These variations were observed independent of the species' natural environments or reproductive modes. M. enterolobii showed three main non-coding regions whereas Meloidogyne chitwoodi, Meloidogyne incognita, M. javanica and M. arenaria had two non-coding regions, and Meloidogyne graminicola had a unique large non-coding region interrupted by two trn genes. trn genes were positioned in different regions of the mt genomes in M. chitwoodi, M. enterolobii and M. graminicola, whereas the trn gene order was identical between M. arenaria, M. incognita and M. javanica. Importantly, M. graminicola had extra copies of trnV and trnS2. High divergence levels between the two copies of each trn might indicate duplication events followed by random loss and mutations in the anticodon. Tree-based methods based on amino acid sequences of 12 mt protein-coding genes support the monophyly for the tropical and mitotic parthenogenetic species, M. arenaria, M. enterolobii, M. incognita and M. javanica and for a clade that includes the meiotic parthenogenetic species, M. chitwoodi and M. graminicola. A comparison of the mt genome architecture in plant-parasitic nematodes and phylogenetic analyses support that Pratylenchus is the most recent ancestor of root-knot nematodes.

Complete mitochondrial genome of Lernaea cyprinacea (Copepoda: Cyclopoida)

The complete mitochondrial genome of Lernaea cyprinacea is 14,656 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two rRNA genes (12S and 16S), as well as two non-coding regions (NCRs, the control regions). The genome organization, nucleotide composition and codon usage do not differ significantly from other Copepodas. The complete mitogenome sequence information of L. cyprinacea provides useful data for further studies on phylogenetics, stock evaluation and conservation genetics.

Complete mitochondrial genome of Philometra carassii (Nematoda: Philometridae)

The complete mitochondrial genome of Philometra carassii is 14,378 bp in size, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 rRNA genes (12S and 16S), as well as one non-coding region (NCR, the control region), but lacks an atp8 gene. The genome organization, nucleotide composition and codon usage do not differ significantly from other nematodes. The complete mitogenome sequence information of P. carassii can provides useful data for further studies on phylogenetics, stock evaluation and conservation genetics.