Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae

First Molecular Identification and Prevalence of Sarcocystis spp. in Sheep Intended for Human Consumption in Shanxi Province, China

Sarcocystis species are intracellular coccidian protozoans that can infect a range of animals and humans and cause public health problems and economically significant losses. Sarcocystosis in sheep (Ovis aries) can cause abortion, neurological symptoms, and even death and results in significant economic losses to the livestock industry. To date, however, it is yet unknown whether sheep in Shanxi Province, north China, are infected with Sarcocystis spp. The purpose of this study was to investigate the prevalence of Sarcocystis spp. in sheep in Shanxi Province. Thus, 582 muscle samples of sheep were purchased from farmers' markets from ten representative counties in Shanxi Province, north China, and examined for the presence and prevalence of Sarcocystis spp. by PCR amplification of the mitochondrial cytochrome c oxidase subunit I (cox1) gene. Of the examined 582 mutton samples, 197 samples (33.85%) were Sarcocystis-positive and were sequenced. Of the obtained 197 cox1 sequences, 196 sequences showed nucleotide similarity of 98.56-99.81% with those of S. tenella, and the remaining one cox1 sequence showed nucleotide similarity of 99.71% with that of S. arieticanis. Two representative cox1 sequences of S. tenella (accession nos. PQ189447 and PQ189448) have 99.52% and 99.61% identity with S. tenalla (KC209725) and S. tenalla (MK419984), respectively. The sequence of S. arieticanis (accession no. PQ165949) obtained in this study has 99.71% identity with S. arieticanis (MK419975). This present study documents the occurrence and prevalence of Sarcocystis spp. in sheep in Shanxi Province for the first time, which enriches the data on the distribution of Sarcocystis spp. in sheep in China and has implications for the control of sheep sarcocystosis.

Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications

Insertions and deletions constitute the second most important source of natural genomic variation. Insertions and deletions make up to 25% of genomic variants in humans and are involved in complex evolutionary processes including genomic rearrangements, adaptation, and speciation. Recent advances in long-read sequencing technologies allow detailed inference of insertions and deletion variation in species and populations. Yet, despite their importance, evolutionary studies have traditionally ignored or mishandled insertions and deletions due to a lack of comprehensive methodologies and statistical models of insertions and deletion dynamics. Here, we discuss methods for describing insertions and deletion variation and modeling insertions and deletions over evolutionary time. We provide practical advice for tackling insertions and deletions in genomic sequences and illustrate our discussion with examples of insertions and deletion-induced effects in human and other natural populations and their contribution to evolutionary processes. We outline promising directions for future developments in statistical methodologies that would allow researchers to analyze insertions and deletion variation and their effects in large genomic data sets and to incorporate insertions and deletions in evolutionary inference.

The Genetic Identification of Numerous Apicomplexan Sarcocystis Species in Intestines of Common Buzzard (Buteo buteo)

The common Buzzard (Buteo buteo) was previously shown to transmit two Sarcocystis species (S. glareoli and S. microti) forming cysts in the brains of rodents. Due to a lack of research, the richness of Sarcocystis species spread by these birds of prey is expected to be much higher. A total of 30 samples of the small intestine of the Common Buzzard were collected in Lithuania and subjected to Sarcocystis species identification based on nested PCR of 28S rRNA and ITS1, following the sequencing of amplified DNA fragments. Six known Sarcocystis spp., S. cornixi, S. glareoli, S. halieti, S. kutkienae, S. turdusi, and S. wobeseri, along with three genetically distinct species (Sarcocystis sp. Rod3, Sarcocystis sp. Rod4, and Sarcocystis sp. Rod5), were identified. Phylogenetically, these three potentially new species clustered with Sarcocystis spp. characterised by a rodents-birds life cycle. Sarcocystis spp. employing rodents and birds as their intermediate hosts were detected in 66.7% and 50.0% of samples, respectively. These findings are consistent with the diet preferences of Common Buzzards. Notably, co-infections with two or more species were observed in a half of the samples. Altogether, the obtained results indicate that the Common Buzzard could serve as definitive host of various Sarcocystis species.

Study of specific immunodominant antigens in different stages of Neospora caninum, Toxoplasma gondii, Sarcocystis spp. and Hammondia spp

The family Sarcocystidae includes several intracellular coccidial parasites such as Toxoplasma gondii, Neospora caninum, Sarcocystis spp. and Hammondia spp. with heteroxenous life cycles involving different parasitic stages (oocysts/sporocysts, tachyzoites and bradyzoites in tissue cysts). The aim of this work was to evaluate monoclonal antibodies (MAb) (anti NcSAG1, anti NcSAG4 and anti TgCC2) and/or polyclonal antibodies (PAb) (anti NcSAG4 and anti TgBAG1) to label specific immunodominant antigens in different parasitic stages of N. caninum (oocyst, bradyzoite and tachyzoite), T. gondii (oocyst, cyst and tachyzoite), H. heydorni (oocyst), S. cruzi (cyst and bradyzoite) and S. falcatula (sporocyst). It was observed that the MAb directed against NcSAG1 reacted exclusively with N. caninum tachyzoites. In contrast, the MAb directed against NcSAG4 did not react with any of the parasites tested at any stage. The MAb directed against NcSAG4 reacted with both N. caninum and T. gondii tachyzoites, T. gondii tissue cysts and S. cruzi tissue cysts and bradyzoites. As expected, the MAb directed against the T. gondii tissue cyst wall antigen TgCC2 reacted with T. gondii tissue cysts, N. caninum bradyzoites, but also with T. gondii and H. heydorni oocysts and S. falcatula sporocysts. Finally, the PAb directed against the T. gondii bradyzoite proteinTgBAG1 reacted with T. gondii tissue cysts, N. caninum bradyzoites, and also with S. cruzi tissue cysts and bradyzoites. These data reveal a wide range of cross-reactions between different species of protozoa and between different developmental stages, which should be taken into account in the design and evaluation of diagnostic tests, as well as in the assessment of vaccination and challenge studies.

First Observations of Buzzards (Buteo) as Definitive Hosts of Sarcocystis Parasites Forming Cysts in the Brain Tissues of Rodents in Lithuania

Representatives of the genus Sarcocystis are worldwide distributed apicomplexan parasites characterised by two-host prey-predator relationships. Sarcocystis spp. produce sarcocysts in the muscles and brains of intermediate hosts and develop sporocysts in the intestines of definitive hosts. Two species, Sarcocystis glareoli and Sarcocystis microti, previously assigned to the genus Frenkelia, form cysts in the brains of rodents and are transmitted through the common buzzard (Buteo buteo). In our study, brain samples of 694 small mammals caught in different regions of Lithuania were examined for Sarcocystis spp. Additionally, 10 B. buteo and two rough-legged buzzards (Buteo lagopus) were tested for sporocysts of the analysed parasites. Sarcocystis species were identified based on 28S rRNA sequence comparison. Of the eleven species of small mammals tested, Sarcocystis parasites were observed only in the bank vole (Clethrionomys glareolus). Cysts of S. glareoli were detected in 34 out of 374 C. glareolus (9.1%, 95% CI = 6.4-12.5%). Molecular investigation showed the presence of only S. glareoli in the intestines of 50% of B. buteo. Furthermore, two species, Sarcocystis sp. Rod3 and Sarcocystis sp. Rod4, were confirmed in B. lagopus. Our results demonstrate the need for further studies on Sarcocystis cycling between rodents and birds.

A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov

BACKGROUND

The geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known.

METHODS

Experimental infections, morphological and molecular characterizations were used for discrimination of a new Sarcocystis species isolated from colubrid snakes and small mammals collected in Thailand, Borneo and China.

RESULTS

We identified a new species, Sarcocystis muricoelognathis sp. nov., that features a relatively wide geographic distribution and infects both commensal and forest-inhabiting intermediate hosts. Sarcocystis sporocysts collected from rat snakes (Coelognathus radiatus, C. flavolineatus) in Thailand induced development of sarcocysts in experimental SD rats showing a type 10a cyst wall ultrastructure that was identical with those found in Rattus norvegicus from China and the forest rat Maxomys whiteheadi in Borneo. Its cystozoites had equal sizes in all intermediate hosts and locations, while sporocysts and cystozoites were distinct from other Sarcocystis species. Partial 28S rRNA sequences of S. muricoelognathis from M. whiteheadi were largely identical to those from R. norvegicus in China but distinct from newly sequenced Sarcocystis zuoi. The phylogeny of the nuclear 18S rRNA gene placed S. muricoelognathis within the so-called S. zuoi complex, including Sarcocystis attenuati, S. kani, S. scandentiborneensis and S. zuoi, while the latter clustered with the new species. However, the phylogeny of the ITS1-region confirmed the distinction between S. muricoelognathis and S. zuoi. Moreover, all three gene trees suggested that an isolate previously addressed as S. zuoi from Thailand (KU341120) is conspecific with S. muricoelognathis. Partial mitochondrial cox1 sequences of S. muricoelognathis were almost identical with those from other members of the group suggesting a shared, recent ancestry. Additionally, we isolated two partial 28S rRNA Sarcocystis sequences from Low's squirrel Sundasciurus lowii that clustered with those of S. scandentiborneensis from treeshews.

CONCLUSIONS

Our results provide strong evidence of broad geographic distributions of rodent-associated Sarcocystis and host shifts between commensal and forest small mammal species, even if the known host associations remain likely only snapshots of the true associations.

Recent insights into the morphology, molecular characterization and tissue localization of the caprine Sarcocystis species infecting domestic goats (Capra hiricus): Sarcocystis moulei, Sarcocystis capracanis, and Sarcocystis hircicanis

Ninety-seven (64.67%) out of 150 domestic goats (Capra hiricus) carcasses were found to be infected by Sarcocystis moulei, Sarcocystis capracanis, and Sarcocystis hircicanis sarcocysts. Sarcocystis moulei macrosarcocysts were detected in the cardiac, esophageal, skeletal, lingual, and diaphragmatic muscles of seven goats (4.67%) out of the 150 examined animals, whereas the microscopic Sarcocystis species were found in (90/150 = 60%). Two morphotypes of S. moulei were observed. Morphotype (I) macrosarcocysts were large-sized oval, ovoid, spherical, and measured 2-7 mm in length x 2-6 mm in width. Sarcocystis moulei morphotype (II) macrosarcocysts were spindle-shaped, spheroid, sometimes elongated, and measured 1.8-6 x 0.5-2 mm. By TEM, all S. moulei morphotypes were ultrastructurally the same and had a sarcocyst wall that was characterized by highly branched or cauliflower-like villar protrusions (VP) with dumbbell-like structures. The VP interior was packed with well-developed microtubules in longitudinal and cross arrangements. Sarcocystis moulei cyst wall was 3-6 μm thick. Sarcocystis capracanis microsarcocysts detected herein had a cyst wall that ranged from 4-8 μm in thickness. The VP was upright finger-like or cylindrical. The PVM had electron-dense corrugations in the region of the VP. Few amounts of microfilaments were detected inside the cores of VP. Sarcocystis hircicanis had a thinner cyst wall (~1-3 μm) with hairy long VP that ranged from 1 to 7.5 μm in length. Microtubules were missing inside the cores of the VP. The three caprine Sarcocystis species were molecularly characterized on the level of the 18S rRNA, 28S rRNA, and Cox1 genes.

Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

We investigated the morphology and phylogenetic relationships of novel and previously recognized Sarcocystis spp. infecting small mammals and colubrid snakes in Asia. The nuclear 18S rRNA and mitochondrial cox1 of Sarcocystis sp.1 from mangrove snakes (Boiga dendrophila) in Thailand and Sarcocystis sp.2 from a ricefield rat (Rattus argentiventer) in Sumatra were partially sequenced. Sporocysts of Sarcocystis sp.1 induced development of sarcocysts in experimentally infected rats, which showed a unique ultrastructure that was observed previously by S.P. Kan in rats from Malaysia; therefore, we describe this species as Sarcocystis kani sp. nov. Its integration into the 18S rRNA phylogeny of Sarcocystis spp. cycling between small mammals and colubrid snakes helped clarify relationships among the so-called S. zuoi-complex of molecularly cryptic species: Sarcocystis kani sp. nov., S. sp.2, S. attenuati, S. scandentiborneensis, and S. zuoi were all included in this clade. Tree topology was resolved into dichotomies congruent with the morphological disparities between the taxa. However, cox1 gene sequencing (including newly sequenced S. singaporensis and S. zamani) revealed that Sarcocystis kani, S. attenuati, and S. scandentiborneensis were identical suggesting a recent, common ancestry. To identify other distinctive features, lineage-specific molecular patterns within both genes were examined revealing that all 18S rRNA sequences of the S. zuoi - complex possess a unique, 7-nt long motif in helix 38 of domain V7 that was different in S. clethrionomyelaphis which branched off basally from the complex. Three-dimensional homology modelling of COX1 protein structure identified amino acid substitutions within the barcode area specific for the S. zuoi-complex and substantial divergence in structurally important amino acids between Sarcocystis species of snakes as definitive hosts and other lineages of the Sarcocystidae. We discuss the utility of selected genes for species delimitation of the Sarcocystis spp. under investigation, which probably evolved during recent radiations of their intermediate and definitive hosts.

Sarcocystis sp. shed by the common boa snake (Boa constrictor) in Brazil

The genus Sarcocystis contains around 200 species and 25 of these infect snakes. Two Sarcocystis spp. shed by snakes have called special attention of the scientific community. S. nesbitti, which is shed by scrub pythons (Simalia amethistina), causes myopathy in humans that consume water or food contaminated with the parasite. Sporocysts of S. singaporensis, excreted by reticulated pythons (Malayopython reticulatus), is letal for rats and was successfully tested in the biological control of these rodents. A high biodiversity of snakes is found in Brazil, however, scarce information is available about Sarcocystis spp. in Brazilian snakes. Herein, we investigated Sarcocystis sp. in feces of the common boa (Boa constrictor) from Salvador, as it is widely distributed in Brazil and it is also bred in other countries. Feces of 65 boas were examined, and Sarcocystis sp. was found in 1/65 (1.53%) snakes. All snakes were alive, and for this reason, intestinal scrapping, which is the most sensitive method to detect the parasite, was not performed. Morphometric evaluation of sporocysts showed significant differences in their sizes. PCR and multilocus sequencing of four genetic markers (cox1, 18S, ITS1, and 28S) revealed that sporocysts corresponded to a new Sarcocystis species. Sequences of cox1 and 18S had identities of 100% and higher than 98%, respectively, with sequences obtained from the rodent Lagostomus maximus in Argentina. ITS1 and 28S sequences did not match with any known Sarcocystis sp. No ITS1 and 28S sequences were available for the Sarcocystis sp. found in the Argentinian L.maximus. Bioassay using the boa sporocysts was conducted in three mouse lineages and in Rattus norvegicus, but no parasitic stages were detected in these rodents. We concluded that the common boa is probably the definitive host of a new species of Sarcocystis sp. that has L. maximus or related rodents as intermediate hosts.

Protozoan Parasites of Sarcocystis spp. in Rodents from Commercial Orchards

Small mammals are an important group of wildlife that can transmit pathogens to humans and animals. There is a lack of comprehensive studies on the protozoan parasites of the genus Sarcocystis in agricultural areas. The aim of the current research was to evaluate the prevalence of Sarcocystis spp., and to identify the parasite species found in the skeletal muscles of rodents and insectivores from commercial orchards. A total of 679 muscle samples from small mammals, mainly rodents (n = 674), belonging to eight species were examined. Muscle samples were pooled into groups, then digested, and the presence of the Sarcocystis species was confirmed by molecular methods. The examined parasites were determined in five rodent species, Apodemus agrarius, A. flavicollis, Clethrionomys glareolus, Microtus arvalis, and M. oeconomus. The prevalence of Sarcocystis spp. was low: 2.23% in voles and 0.79% in mice. Based on a sequence comparison of cox1 and 28S rDNA, four species were identified: S. myodes, Sarcocystis cf. strixi, Sarcocystis sp. Rod1, and Sarcocystis sp. Rod2. This is the first report of S. myodes in A. agrarius, A. flavicollis, and M. arvalis. The identified species were most closely related to Sarcocystis spp., and were transmitted by predatory mammals and birds. Future studies are needed to describe the species morphologically, as well as to define the host spectrum and to evaluate their possible pathogenicity.

Integrative taxonomy for the traditional coccidians (Chromista: Miozoa: Eimeriidae) from island canaries (Aves: Passeriformes: Fringillidae): Worldwide distribution, morphological and molecular characterization, revaluations and establishment of junior synonyms

Island canaries Serinus canaria (Linnaeus) are finches native to the North Atlantic Islands, however, they have a worldwide distribution in captivity due to their relevance as a pet bird. Coccidians are the most reported parasites of passerines worldwide, both in the wild and in captivity, being frequently associated with disease in passerines kept in rehabilitation centers and commercial breeders. This study aimed to identify coccidians from island canaries kept in captivity in Brazil. Three hundred and fifteen genomic DNA extracted from fecal samples of island canaries from different breeders from Southern and Southeastern Brazil were used to perform a nested PCR assay to amplify a partial fragment of the 28S small subunit ribosomal RNA gene (28S) of Isospora spp. Microscopic screening and morphological identification of Isospora oocysts was performed in fecal samples corresponding to PCR positive DNA samples. Fecal samples have been formalin-stored for approximately four years. Positivity rate for both microscopy and PCR was 10.5% (33/315). Posteriorly, Isospora serini (Aragão, 1933) Box, 1975 and Isospora canaria Box, 1975 were morphologically identified from fresh fecal samples of island canaries maintained by a breeder in the State of São Paulo, Southeastern Brazil, providing a genotypic characterization via sequencing of the mitochondrial cytochrome c oxidase subunit 1 (COI) and 28S genes. The 28S and COI sequences referring to the morphological identification of I. canaria was, respectively, 100% and 99% similar to sequences deposited as Isospora serinuse Yang, Brice, Elliot & Ryan, 2015 from island canaries kept in a rehabilitation center in Australia. The COI sequence referring to the morphological identification of I. serini was 100% similar to a sequence of an extraintestinal Isospora, corroborating this identification/sequencing since I. serini is the first isosporan with an extra-intestinal cycle demonstrated. The comparison of morphological and molecular data from I. canaria and I. serini from this study with published data of Isospora spp. from canaries worldwide, allowed the specific identification from preliminary generic identifications, correction of misidentifications, as well as the establishment of junior synonyms. Finally, this study provides morphological and molecular data that ensure the correct identification of the two Isospora spp. from island canaries in future studies worldwide.

Phylogenies from unaligned proteomes using sequence environments of amino acid residues

Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Several algorithms have been implemented in diverse software packages. Despite the great number of existing methods, most of them are based on word statistics. Although they propose different filtering and weighting strategies and explore different metrics, their performance may be limited by the phylogenetic signal preserved in these words. Herein, we present a different approach based on the species-specific amino acid neighborhood preferences. These differential preferences can be assessed in the context of vector spaces. In this way, a distance-based method to build phylogenies has been developed and implemented into an easy-to-use R package. Tests run on real-world datasets show that this method can reconstruct phylogenetic relationships with high accuracy, and often outperforms other alignment-free approaches. Furthermore, we present evidence that the new method can perform reliably on datasets formed by non-orthologous protein sequences, that is, the method not only does not require the identification of orthologous proteins, but also does not require their presence in the analyzed dataset. These results suggest that the neighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility in phylogenomics.

Morphological and Molecular Description of Sarcocystis myodes n. sp. from the Bank Vole (Clethrionomys glareolus) in Lithuania

Numerous rodent species have been broadly examined for Sarcocystis parasites. Nevertheless, recent investigations on Sarcocystis spp. in voles are lacking. As many as 45 bank voles (Clethrionomys glareolus) captured in several locations in Lithuania were examined in the present study. Based on morphological, genetic, and phylogenetic results, sarcocysts detected in one bank vole were described as Sarcocystis myodes n. sp. Using light microscopy analysis, the observed sarcocysts were ribbon-shaped, 6000−3000 × 70−220 µm in size. Sarcocysts were characterized by a relatively thin (about 1 μm) and apparently smooth cyst wall. The lancet-shaped bradyzoites were 9.6−12.0 × 3.1−4.6 μm in size. By transmission electron microscopy, the sarcocyst wall was up to 1 μm thick, parasitophorous vacuolar membrane had small knob-like blebs. Based on 18S rDNA, 28S rDNA, cox1, rpoB, and ITS1 loci, S. myodes showed highest similarity with S. ratti from the black rat (Rattus rattus). According to phylogenetic placement, S. myodes was most closely related to Sarcocystis spp. that employ predatory mammals as their definitive hosts. Morphologically, sarcocysts of S. myodes have similar features to those of S. cernae, S. dirumpens, and S. montanaensis described in voles, however, they use birds of prey or snakes as their definitive hosts.

Bovine besnoitiosis in a cattle herd in Sicily: an isolated outbreak or the acknowledgment of an endemicity?

Bovine besnoitiosis is a debilitating infectious disease caused by Besnoitia besnoiti (Apicomplexa; Sarcocystidae). The disease is mainly characterized by cutaneous and systemic signs, infertility in bulls, and abortion in cows. The current study describes an autochthonous outbreak of bovine besnoitiosis in Sicily, Southern Italy, being the first report of B. besnoiti infection in the island so far. In a cattle farm located in Syracuse province, a 4-year-old Belgian blue bull born in Sicily displayed typical clinical signs of the sub-acute/chronic disease phase with thickening of the skin of the scrotum and testicular degeneration. Histological examination of scrotal biopsies revealed the presence of several tissue cysts of B. besnoiti. The serological analysis of the herd using a commercial ELISA revealed a high seroprevalence (45 out of 55; 82%) of antibodies against B. besnoiti. Few seropositive animals (5 out of 45; 11%) showed clinical signs, cysts in vestibulum vaginae (1 out of 31; 3.2%), and testicular degeneration (4 out of 14; 28.6%) assessed by ultrasonographic investigations. The paucity of clinical signs associated with the high seroprevalence in the farm led to hypothesize that bovine besnoitiosis is endemic in the area though further studies are needed. Local practitioners should be more aware of the disease to facilitate the early detection of cases, prevent the spread of infection, and avoid economic losses and animal health problem.

Sarcocystis neurona and related Sarcocystis spp. shed by opossums (Didelphis spp.) in South America

Protozoan parasites of the genus Sarcocystis are obligatory heteroxenous cyst-forming coccidia that infect a wide variety of animals and encompass approximately 200 described species. At least four Sarcocystis spp. (S. falcatula, S. neurona, S. lindsayi and S. speeri) use opossums (Didelphis spp.) as definitive hosts, and two of them, S. neurona and S. falcatula, are known to cause disease in horses and birds, respectively. Opossums are restricted to the Americas, but their distribution in the Americas is heterogeneous. Five Didelphis spp. are distributed in South America (D. aurita, D. albiventris, D. marsupialis, D. imperfecta and D. pernigra) whereas just one opossum species (D. virginiana) is found in North America. Studies conducted in the last decades show that Sarcocystis spp., derived from South American Didelphis spp., have biological and genetic differences in relation to Sarcocystis spp. shed by the North American opossum D. virginiana. The aim of this review was to address the peculiar scenario of Sarcocystis species shed by South American opossums, with a special focus on diagnosis, epidemiology, and animal infections, as well as the genetic characteristics of these parasites.

Cytochrome c oxydase I phylogenetic analysis of Haemogregarina parasites (Apicomplexa, Coccidia, Eucoccidiorida, Haemogregarinidae) confirms the presence of three distinct species within the freshwater turtles of Tunisia

Species of Haemogregarina are apicomplexan blood parasites that use vertebrates as intermediate hosts. Due to limited interspecific morphological characters within the genus during the last decade, 18S rRNA gene sequences were widely used for species identification. As coinfection patterns were recently reported from nuclear molecular data for two sympatric freshwater turtles Mauremys leprosa and Emys orbicularis from Tunisia, our objectives were to design COI specific primers to confirm the presence of three distinct species in both host species. Blood samples were collected from 22 turtles, from which DNAs were extracted and used as templates for amplification. Following different rounds of PCR and nested PCR, we designed specific Haemogregarina COI primers that allowed the sequencing of nine distinct haplotypes. Phylogenetic Bayesian analysis revealed the occurrence of three well-differentiated sublineages that clustered together into a single clade. Based on pairwise genetic distances (p-distance), we confirmed the occurrence of three distinct but phylogenetically closely related species coinfecting M. leprosa and E. orbicularis in the same aquatic environments. Our results demonstrate that the use of fast evolving genes within Haemogregarina will help to investigate the parasite diversity within both intermediate vertebrate and definitive invertebrate hosts, and to assess the evolution, historical biogeography and specificity of haemogregarines.

Detection of Eumonospora henryae (Apicomplexa: Sarcocystidae) from Falco columbarius (Falconiformes: Aves): Comparison of host-parasite phylogram and comments on the family Sarcocystidae Poche, 1913

The genus Eumonospora Allen, 1933 (Apicomplexa: Sarcocystidae), an avian coccidia, is characterized by monosporocystic and octasporozoic oocysts without Stieda and substieda bodies. Some members of Eumonospora, which infect several raptor species, exhibit high levels of pathogenicity, making eumonosporiosis the leading cause of death in captive-bred raptors. The host specificity of these species appears to be mesostenoxenous, as evidenced by unsuccessful transmission between different orders of avian hosts. However, several studies have detected Eumonospora spp. in taxonomically distant avian hosts, indicating that some of these species may be euryxenous. In the current study, diarrheic fecal examination of a captive-bred juvenile merlin (Falconiformes: Aves) in Tokyo, Japan, was conducted, and a large number of oocysts were morphologically and molecularly identified as E. henryae (Yakimoff and Matschulsky, 1932), a coccidia species reported only in Strigiformes. This is a new recorded host for this coccidia. Phylogenetic analyses via Bayesian inference and maximum likelihood methods using concatenated genomic datasets consisting of nuclear 18S rDNA, nuclear 28S rDNA and mitochondrial cytochrome C oxidase subunit 1 gene, revealed a well-supported monophyletic clade of Eumonospora spp. belonging to the family Sarcocystidae Poche 1913, which largely corresponded to the avian host phylogram. Therefore, based on distinguishable oocyst morphology, a new subfamily, Eumonosporinae, within the family Sarcocystidae, is proposed, and a reconsideration of the definition of Sarcocystidae is suggested. Further molecular characterization of this emerging pathogen, as well as clarification of its complete life cycle, including cyst-forming ability, is required for more appropriate generic assessment.

Disseminated protozoal infection in a wild feathertail glider (Acrobates pygmaeus) in Australia

This is the first report of a disseminated protozoal infection in a wild feathertail glider (Acrobates pygmaeus) from south-eastern Australia. The glider was found dead in poor body condition. Histologically, large numbers of zoites were seen predominantly in macrophages in the liver, spleen and lung, with protozoal cysts present in the liver. Molecular and phylogenetic analyses inferred that the protozoan parasite belongs to the family Sarcocystidae and is closely related to previously identified apicomplexans found in yellow-bellied gliders (Petaurus australis) in Australia and southern mouse opossums (Thylamys elegans) in Chile.

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A novel apicomplexan parasite caused a disseminated fatal disease in a wild feathertail glider.

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The apicomplexan parasite is a member of the family Sarcocystidae.

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It is most closely related to parasites previously identified in yellow-bellied gliders in Australia and southern mouseopossums in Chile.

Molecular phylogeny of Sarcocystis fayeri (Apicomplexa: Sarcocystidae) from the domestic horse Equus caballus based on 18S rRNA gene sequences and its prevalence

Sarcocystosis is a parasitic disease caused by an intracellular protozoan parasite Sarcocystis belonging to the phylum Apicomplexa. These parasites have a requisite two-host life cycle. Recently, there are many Sarcocystis species that identified morphologically. In the present study, diaphragmatic muscle samples from the domestic horse (Equus caballus) were examined for Sarcocystis infection. The natural infection with sarcocysts was recorded to be 62·5% for only microcysts in the infected muscles. Molecular analysis using the 18S rRNA gene was conducted to swiftly and accurately identify the recovered species. Studies on the expression of the 18S rRNA gene have confirmed that the present parasite isolates belong to the Sarcocystis genus. The sequence data showed significant identities (>80%) with archived gene sequences from species within the Sarcocystidae family, and a dendrogram showing the phylogenetic relationship was constructed. The most closely related species were the previously described Sarcocystis fayeri and Sarcocystis bertrami. The current data showed that the present species was identified as S. fayeri and deposited in GenBank (accession number MF614956.1). This study highlights the importance of the genetic data in the exact taxonomy within sarcocystid species.

The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life

BACKGROUND

The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that automated alignment protocols can yield inaccuracies, but the relative impact of various sources error on phylogenomic analysis is not yet known. This study employs an updated mammal data set of 5162 coding loci sampled from 90 species to evaluate the effects of alignment uncertainty, substitution models, and fossil priors on gene tree, species tree, and divergence time estimation. Additionally, a novel coalescent likelihood ratio test is introduced for comparing competing species trees against a given set of gene trees.

RESULTS

The aligned DNA sequences of 5162 loci from 90 species were trimmed and filtered using trimAL and two filtering protocols. The final dataset contains 4 sets of alignments - before trimming, after trimming, filtered by a recently proposed pipeline, and further filtered by comparing ML gene trees for each locus with the concatenation tree. Our analyses suggest that the average discordance among the coalescent trees is significantly smaller than that among the concatenation trees estimated from the 4 sets of alignments or with different substitution models. There is no significant difference among the divergence times estimated with different substitution models. However, the divergence dates estimated from the alignments after trimming are more recent than those estimated from the alignments before trimming.

CONCLUSIONS

Our results highlight that alignment uncertainty of the updated mammal data set and the choice of substitution models have little impact on tree topologies yielded by coalescent methods for species tree estimation, whereas they are more influential on the trees made by concatenation. Given the choice of calibration scheme and clock models, divergence time estimates are robust to the choice of substitution models, but removing alignments deemed problematic by trimming algorithms can lead to more recent dates. Although the fossil prior is important in divergence time estimation, Bayesian estimates of divergence times in this data set are driven primarily by the sequence data.

ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models

Evolutionary reconstruction algorithms produce models of the evolutionary history of proteins or species. Such algorithms are highly sensitive to their inputs: the sequences used and their alignments. Here, we asked whether the variance introduced by selecting different input sequences could be used to better identify accurate evolutionary models. We subsampled from available ortholog sequences and measured the distribution of observed relationships between paralogs produced across hundreds of models inferred from the subsamples. We observed two important phenomena. First, the reproducibility of an all-sequence, single-alignment reconstruction, measured by comparing topologies inferred from 90% subsamples, directly correlates with the accuracy of that single-alignment reconstruction, producing a measurable value for something that has been traditionally unknowable. Second, topologies that are most consistent with the observations made in the ensemble are more accurate and we present a meta algorithm that exploits this property to improve model accuracy.

Morphological and molecular description of Sarcocystis ratti n. sp. from the black rat (Rattus rattus) in Latvia

Rodents have been widely studied as intermediate hosts of Sarcocystis; however, only a few reports on these parasites in the black rat (Rattus rattus) are known. Having examined 13 black rats captured in Latvia, sarcocysts were found in skeletal muscles of two mammals and were described as Sarcocystis ratti n. sp. Under a light microscope, sarcocysts were ribbon-shaped, 0.9-1.3 × 0.09-0.14 mm in size and had a thin (0.8-1.3 μm) and smooth cyst wall. The lancet-shaped bradyzoites were 8.3 × 4.3 (7.5-9.3 × 3.9-4.8) μm. Under a transmission electron microscope, the cyst wall was up to 1.3 μm thick, wavy, the ground substance appeared smooth, type 1a-like. Morphologically, sarcocysts of S. ratti were somewhat similar to those of S. cymruensis, S. rodentifelis, and S. dispersa-like previously identified in the brown rat (Rattus norvegicus). On the basis of 18S rDNA, 28S rDNA, and cox1, significant genetic differences (at least 2.3, 4.5, and 5.8%, respectively) were observed when comparing S. ratti with other Sarcocystis species using rodents as intermediate hosts. While ITS1 sequences of S. ratti were highly distinct from other Sarcocystis species available in GenBank. Phylogenetic and ecological data suggest that predatory mammals living near households are definitive hosts of S. ratti.

Prevalence and molecular characterisation of Sarcocystis miescheriana and Sarcocystis suihominis in wild boars (Sus scrofa) in Italy

A sample of the diaphragm was collected from each of 100 wild boars legally hunted in the Val Grande National Park in north-western Italy and examined for the presence of Sarcocystis infection by histological and molecular methods. In histological sections, thick-walled sarcocysts consistent with those of Sarcocystis miescheriana were detected in 32 wild boars. Genomic DNA extracted from diaphragm samples was initially subjected to PCR amplification of the internal transcribed spacer 1 (ITS1) region, and 97 wild boars were found to harbour a Sarcocystis infection at this screening. Selected DNA samples were then subjected to PCR amplification and sequencing of the ITS1 region and the 18S and 28S ribosomal RNA (rRNA) genes of the nuclear ribosomal DNA unit, while all positive samples were subjected to PCR amplification of the mitochondrial cytochrome c oxidase subunit I (cox1) gene. S. miescheriana was identified in 97 wild boars (97%), while the zoonotic Sarcocystis suihominis was identified in one wild boar (1%), which also harboured S. miescheriana. Intra-specific sequence variation was found in all four DNA regions of S. miescheriana examined and in the 18S rRNA gene and ITS1 region of S. suihominis. The partial cox1 gene was amplified and sequenced from 72 isolates of S. miescheriana, yielding 43 haplotypes with pairwise sequence identities of 97.6-99.9%. These haplotypes were 79.1-79.8% identical with the cox1 sequence of S. suihominis. Phylogeny based on cox1 sequences placed S. miescheriana and S. suihominis as sister species within a clade comprising mainly Sarcocystis spp. of ruminants with felids as known or presumed definitive hosts. The same was true for the phylogeny based on 18S rRNA gene sequences.

Pathological and molecular characterization of systemic isosporosis (atoxoplasmosis) in captive green-winged saltator (Saltator similis)

Systemic isosporosis, also called atoxoplasmosis or visceral coccidiosis, is a disease that affects birds in general. Pathogenesis of systemic isosporosis and its etiologic agent have not been well characterized, but taxonomically Atoxoplasma is currently considered a junior objective synonym of Isospora. The present report aimed to describe pathological and molecular findings of systemic isosporosis in captive green-winged saltators (Saltator similis) from the State of Espírito Santo, Brazil. In a commercial breeding facility eleven birds with two to nine months of age died from 2015 to 2016. These birds developed nonspecific clinical signs, including bristly feathers, hyporexia, loss of weight, and apathy. Two birds were necropsied, and grossly there were hepatomegaly, splenomegaly, necrosis of lymphoid follicles, hepatic necrosis, and severe enteritis. Merozoites were observed in the heart, small intestine, proventriculus, brain, liver, spleen, and kidneys. 23 S RNA PCR amplicons from DNA extracted from the liver and the intestinal contents had 99% identity with Atoxoplasma sp., whereas amplicons of mitochondrial cytochrome c oxidase subunit 1 ha d 97% identity with Isospora greineri. In conclusion, this report indicates that systemic isosporosis in green-winged saltator is a disease that affects the spleen, liver, and small intestine, with high mortality for young birds, resulting in significant loses to commercial breeding facilities.

Molecular evidence for host-parasite co-speciation between lizards and Schellackia parasites

Current and past parasite transmission may depend on the overlap of host distributions, potentially affecting parasite specificity and co-evolutionary processes. Nonetheless, parasite diversification may take place in sympatry when parasites are transmitted by vectors with low mobility. Here, we test the co-speciation hypothesis between lizard final hosts of the Family Lacertidae, and blood parasites of the genus Schellackia, which are potentially transmitted by haematophagous mites. The effects of current distributional overlap of host species on parasite specificity are also investigated. We sampled 27 localities on the Iberian Peninsula and three in northern Africa, and collected blood samples from 981 individual lizards of seven genera and 18 species. The overall prevalence of infection by parasites of the genus Schellackia was ∼35%. We detected 16 Schellackia haplotypes of the 18S rRNA gene, revealing that the genus Schellackia is more diverse than previously thought. Phylogenetic analyses showed that Schellackia haplotypes grouped into two main monophyletic clades, the first including those detected in host species endemic to the Mediterranean region and the second those detected in host genera Acanthodactylus, Zootoca and Takydromus. All but one of the Schellackia haplotypes exhibited a high degree of host specificity at the generic level and 78.5% of them exclusively infected single host species. Some host species within the genera Podarcis (six species) and Iberolacerta (two species) were infected by three non-specific haplotypes of Schellackia, suggesting that host switching might have positively influenced past diversification of the genus. However, the results supported the idea that current host switching is rare because there existed a significant positive correlation between the number of exclusive parasite haplotypes and the number of host species with current sympatric distribution. This result, together with significant support for host-parasite molecular co-speciation, suggests that parasites of the genus Schellackia co-evolved with their lizard hosts.

Molecular characterization of the ribosomal DNA unit of Sarcocystis singaporensis, Sarcocystis zamani and Sarcocystis zuoi from rodents in Thailand

Sarcocystis species are heteroxenous cyst-forming coccidian protozoan parasites with a wide host range, including rodents. In this study, Sarcocystis spp. samples were isolated from Bandicota indica, Rattus argentiventer, R. tiomanicus and R. norvegicus across five provinces of Thailand. Two major groups of Sarcocystis cysts were determined in this study: large and small cysts. By sequence comparisons and phylogenetic analyses based on the partial sequences of 28S ribosomal DNA, the large cysts showed the highest identity value (99%) with the S. zamani in GenBank database. While the small cysts could be divided into 2 groups of Sarcocystis: S. singaporensis and presupposed S. zuoi. The further analysis on 18S rDNA supported that the 2 isolates (S2 and B6 no.2) were as identified as S. singaporensis shared a high sequence identity with the S. singaporensis in GenBank database and the unidentified Sarcocystis (4 isolates, i.e., B6 no.10, B6 no.12, B10 no.4 and B10 no.7) showed 96.3–99.5% identity to S. zuoi as well as high distinct identity from others Sarcocystis spp. (≤93%). The result indicated that these four samples should be S. zuoi. In this study, we provided complete sequence of internal transcribed spacer 1 (ITS1), 5.8S rDNA and internal transcribed spacer 2 (ITS2) of these three Sarcocystis species and our new primer set could be useful to study the evolution of Sarcocystis.

Importance of serological cross-reactivity among Toxoplasma gondii, Hammondia spp., Neospora spp., Sarcocystis spp. and Besnoitia besnoiti

Toxoplasma gondii, Neospora spp., Sarcocystis spp., Hammondia spp. and Besnoitia besnoiti are genetically related cyst-forming coccidia. Serology is frequently used for the identification of T. gondii, Neospora spp. and B. besnoiti-exposed individuals. Serologic cross-reactions occur in different tests among animals infected with T. gondii and H. hammondi, as well as among animals infected by T. gondii and N. caninum. Infections caused by N. caninum and N. hughesi are almost indistinguishable by serology. Neospora caninum, B. besnoiti and Sarcocystis spp. infections in cattle show some degree of serologic cross-reactivity. Antibody cross-reactivity between Neospora spp. and H. heydorni-infected animals is suspected, but not proven to occur. We review serologic cross-reactivity among animals and/or humans infected with T. gondii, Neospora spp., Sarcocystis spp., Hammondia spp. and B. besnoiti. Emphasis is laid upon antigens and serological methods for N. caninum diagnosis which were tested for cross-reactivity with related protozoa. Species-specific antigens, as well as stage-specific proteins have been identified in some of these parasites and have promising use for diagnosis and epidemiological surveys.

Toxoplasmatinae Parasites in Bats from Bahia State, Brazil

Toxoplasma gondii and Neospora caninum are widespread cyst-forming coccidian parasites of the subfamily Toxoplasmatinae that infect a wide range of wild and domestic animals. Whereas T. gondii is a zoonotic disease, N. caninum is restricted to nonhuman animals. Some chiropteran species can be infected by T. gondii and present fatal toxoplasmosis. In most cases, T. gondii -infected bats are believed to remain asymptomatic and to act as an infection source to other animals. It is not known whether N. caninum can infect bats. We determined infection rates of T. gondii and N. caninum in free-living bats in the state of Bahia, Brazil. Brain samples from 97 bats of seven species, captured in 2008-15, were analyzed by PCRs for T. gondii and N. caninum . Two of the 97 samples were positive for T. gondii DNA. None of the samples were positive for N. caninum DNA, suggesting that the bats were not susceptible to N. caninum infection or that its prevalence was very low.

High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments

Since the advent of large-scale genomic sequencing, and the consequent availability of large numbers of homologous protein sequences, there has been burgeoning development of methods for extracting functional information from multiple sequence alignments (MSAs). One type of analysis seeks to identify specificity determining positions (SDPs) based on the assumption that such positions are highly conserved within groups of sequences sharing functional specificity, but conserved to different amino acids in different specificity groups. This unsupervised approach to utilizing evolutionary information may elucidate mechanisms of specificity in protein-protein interactions, catalytic activity of enzymes, sensitivity to allosteric regulation, and other types of protein functionality. We present an analysis of SDPs in the LacI family of transcriptional regulators in which we 1) relax the constraint that all specificity groups must contribute to SDP signal, and 2) use a novel approach to robust treatment of sequence alignment uncertainty based on sub-sampling. We find that the vast majority of SDP signal occurs at positions with a conservation pattern that significantly complicates detection by previously described methods. This pattern, which we term “partial SDP”, consists of the commonly accepted SDP conservation pattern among a subset of specificity groups and strong degeneracy among the rest. An upshot of this fact is that the SDP complement of every specificity group appears to be unique. Additionally, sub-sampling gives us the ability to assign a confidence interval to the SDP score, as well as increase fidelity, as compared to analysis of a single, comprehensive alignment—the current standard in multiple sequence alignment methodologies.

Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genus Hammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

Molecular phylogenetic analyses of tissue coccidia (sarcocystidae; apicomplexa) based on nuclear 18s RDNA and mitochondrial COI sequences confirms the paraphyly of the genus Hammondia

Partial mitochondrial cytochromecoxidase subunit I (mt COI) sequences were generated from:Toxoplasma gondii(strains CTG, GTI, MAS, ME49, PTG, TgCatBr5, TgCat, Br64, TgCgCal, TgToucan);Neospora caninum(Strain NC1);Hammondia hammondi(Strain H.H–20);H. heydorni; H. cf.triffittae; Cystoisospora felis; C. suis; C. canis; C. rivolta; C. cf.ohioensis; Caryospora bigenetica; Sarcocystis rileyi; andS. neurona. Nuclear 18S rDNA sequences were generated forH. heydorni, H. hammondi, C. suis, C. canis, C. felis, C. rivolta, C. cf.ohioensis, S. neurona, andS. rileyi. Aligned, concatenated 18S rDNA and COI sequences were Bayesian analysed using partitioned nucleotide substitution models [HKY + I + G for 18S; GTR + I + G codon (code = metmt) for COI]. Phylogenetic hypotheses supported a monophyletic Sarcocystidae and its subfamilie with two major clades within the Toxoplasmatinae: (1) a monophyletic clade ofCystoisosporaspp. withNephroisospora eptesici; and (2) a clade ofToxoplasma, NeosporaandHammondia. Within the latter,Hammondiawas shown to be paraphyletic;H. heydorniandH. triffittaewere monophyletic withN. caninum[canine definitive hosts (DHs)], whereasH. hammondiwas monophyletic withT. gondii(feline DHs). A new genus is erected to resolve the paraphyly of the genusHammondiaconfirmed using mt COI and combined 18S/COI sequence datasets.

Genetic diversity within ITS-1 region of Eimeria species infecting chickens of north India

Coccidiosis, caused by apicomplexan parasites of the genus Eimeria, inflicts severe economic losses to the poultry industry around the globe. In the present study, ITS-1 based species specific nested PCR revealed prevalence of E. acervulina, E. brunetti, E. maxima, E. mitis, E. praecox, E. necatrix and E. tenella in 79.2%, 12.5%, 64.6%, 89.6%, 60.4%, 64.6% and 97.9% poultry farms of north India, respectively. The ITS-1 sequences of different Eimeria spp. from north India were generated and analyzed to establish their phylogenetic relationship. The sequence identity with available sequences ranged from 80 to 100% in E. tenella, 95 to 100% in E. acervulina, 64 to 97% in E. necatrix, 96 to 99% in E. brunetti and 97 to 98% in E. mitis. Only long ITS-1 sequences of E. maxima could be generated in the present study and it had 80-100% identity with published sequences. Two out of the four ITS-1 sequences of E. maxima had mismatches in the published nested primer sequences from Australia, while one sequence of E. necatrix had a mismatch near 3' end of both forward and reverse published nested primer sequences, warranting for the need of designing new set of degenerate primers for these two species of Eimeria. In the phylogenetic tree, all isolates of E. acervulina, E. brunetti, E. mitis, E. tenella and E. necatrix clustered in separate clades with high bootstrap value. E. maxima sequences of north Indian isolates grouped in a long form of E. maxima clade. Complete ITS-1 sequences of E. necatrix and E. mitis are reported for the first time from India. Further studies are required with more number of isolates to verify whether these differences are unique to geographical locations.

ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding

DNA barcoding is a promising species identification method, but it has proved difficult to find a standardized DNA marker in plant. Although the ITS/ITS2 RNA transcript has been proposed as the core barcode for seed plants, it has been criticized for being too conserved in some species to provide enough information or too variable in some species to align it within the different taxa ranks. We selected 30 individuals, representing 16 species and four families, to explore whether ITS2 can successfully resolve species in terms of secondary structure. Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs. This conserved structure facilitated the alignment of ambiguous sequences from divergent families. The structure alignment yielded a MP tree, in which most topological relationships were congruent with the tree constructed using nucleotide sequence data. When the data was combined, we obtained a well-resolved and highly supported phylogeny, in which individuals of a same species were clustered together into a monophyletic group. As a result, the different species that are often referred to as the herb “Mu tong” were successfully identified using short fragments of 250 bp ITS2 sequences, together with their secondary structure. Thus our analysis strengthens the potential of ITS2 as a promising DNA barcode because it incorporates valuable secondary structure information that will help improve discrimination between species.

Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii

Toxoplasma gondii is a human obligate intracellular parasite that has infected over 20% of the world population and has a vast intermediate host range compared to those of its nearest relatives Neospora caninum and Hammondia hammondi. While these 3 species have highly syntenic genomes (80 to 99%), in this study we examined and compared species-specific structural variations, specifically at loci that have undergone local (i.e., tandem) duplication and expansion. To do so, we used genomic sequence coverage analysis to identify and curate T. gondii and N. caninum loci that have undergone duplication and expansion (expanded loci [ELs]). The 53 T. gondii ELs are significantly enriched for genes with predicted signal sequences and single-exon genes and genes that are developmentally regulated at the transcriptional level. We validated 24 T. gondii ELs using comparative genomic hybridization; these data suggested significant copy number variation at these loci. High-molecular-weight Southern blotting for 3 T. gondii ELs revealed that copy number varies across T. gondii lineages and also between members of the same clonal lineage. Using similar methods, we identified 64 N. caninum ELs which were significantly enriched genes belonging to the SAG-related surface (SRS) antigen family. Moreover, there is significantly less overlap (30%) between the expanded gene sets in T. gondii and N. caninum than would be predicted by overall genomic synteny (81%). Consistent with this finding, only 59% of queried T. gondii ELs are similarly duplicated/expanded in H. hammondi despite over 99% genomic synteny between these species.

Gene duplication, expansion, and diversification are a basis for phenotypic differences both within and between species. This study represents the first characterization of both the extent and degree of overlap in gene duplication and locus expansion across multiple apicomplexan parasite species. The most important finding of this study is that the locus duplications/expansions are quantitatively and qualitatively distinct, despite the high degree of genetic relatedness between the species. Given that these differential expansions are prominent species-specific genetic differences, they may also contribute to some of the more striking phenotypic differences between these species. More broadly, this work is important in providing further support for the idea that postspeciation selection events may have a dramatic impact on locus structure and copy number that overshadows selection on single-copy genes.

Molecular identification of Sarcocystis spp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Sarcocystis spp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containing Sarcocystis spp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two different Sarcocystis spp. sequences were identified and registered as Sarcocystis sp. from M. viridis in GenBank. Both showed a 95-97% sequence identity with the 18S rRNA gene of Sarcocystis singaporensis. Phylogenetic analysis positioned these sequences together with other Sarcocystis spp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts for Sarcocystis spp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes with Sarcocystis spp. may be used to assess compliance with regulations on the trade with wildlife species.

What an rRNA secondary structure tells about phylogeny of fungi in Ascomycota with emphasis on evolution of major types of ascus

Background

RNA secondary structure is highly conserved throughout evolution. The higher order structure is fundamental in establishing important structure-function relationships. Nucleotide sequences from ribosomal RNA (rRNA) genes have made a great contribution to our understanding of Ascomycota phylogeny. However, filling the gaps between molecular phylogeny and morphological assumptions based on ascus dehiscence modes and type of fruitbodies at the higher level classification of the phylum remains an unfulfilled task faced by mycologists.

Methodology/Principal Findings

We selected some major groups of Ascomycota to view their phylogenetic relationships based on analyses of rRNA secondary structure. Using rRNA secondary structural information, here, we converted nucleotide sequences into the structure ones over a 20-symbol code. Our structural analyses together with ancestral character state reconstruction produced reasonable phylogenetic position for the class Geoglossomycetes as opposed to the classic nucleotide analyses. Judging from the secondary structure analyses with consideration of mode of ascus dehiscence and the ability of forming fruitbodies, we draw a clear picture of a possible evolutionary route for fungal asci and some major groups of fungi in Ascomycota. The secondary structure trees show a more reasonable phylogenetic position for the class Geoglossomycetes.

Conclusions

Our results illustrate that asci lacking of any dehiscence mechanism represent the most primitive type. Passing through the operculate and Orbilia-type asci, bitunicate asci occurred. The evolution came to the most advanced inoperculate type. The ascus-producing fungi might be derived from groups lacking of the capacity to form fruitbodies, and then evolved multiple times. The apothecial type of fruitbodies represents the ancestral state, and the ostiolar type is advanced. The class Geoglossomycetes is closely related to Leotiomycetes and Sordariomycetes having a similar ascus type other than it was originally placed based on nucleotide sequence analyses.

Molecular diagnostics of Sarcocystis spp. infections

Protozoa of the genus Sarcocystis (phylum Apicomplexa, family Sarcocystidae) is one of the most common parasites affecting animals. Interspecies diagnostic of Sarcocystis genus was based on electron microscopy for many years. Because of absence of visible differences between species with reachable magnifications, light microscopy is useless. In many cases serological diagnostic method have lack of sensitivity. A variety of molecular methods have been developed and used to detect and identify Sarcocystis spp. and to assess the genetic diversity among this protozoan from different population/hosts. Nowadays, molecular diagnostic is the common, time/cost effective method used all over the world to interspecies differentiation.

Evaluation of the protective efficacy of the anticoccidial vaccine Coccivac-B in broilers, when challenged with Egyptian field isolates of E. tenella

The present study was performed to explore the efficacy of the commercial anticoccidial vaccine (Coccivac B®) in broiler chickens using five field strains of Eimeria tenella that were isolated from five provinces in Egypt. This study also analyzed the ITS-1-rDNA sequence of these five strains and its corresponding sequence in the vaccine. In a floor pen experiment, 216 one-day-old commercial broiler chicks were classified into vaccinated and non-vaccinated groups. Each main group was classified into six subgroups. The chicks were challenged on the 28th day of age with 10(4) sporulated oocysts of one of the five field strains of E. tenella. Our results indicated that Coccivac B® produced variable degrees of protection in the birds infected with the five different strains of E. tenella. Aligning the ITS-1 sequences from the five strains with the ITS-1 sequence of E. tenella from the vaccine revealed 96 % sequence similarity with the Kafer El-Sheikh strain, 94 % with the Gharbia strain, 90 % with the Alexandria strain, and 78 % with the Matrouh and Behera strains. While interesting, these similarity values were not useful for predicting the protection conferred by the vaccine against the five field isolates. However, based on the data reported here, we can conclude that Coccivac B® produced variable degrees of protection in the birds infected with the five different strains of E. tenella.

Ultrastructural and molecular characterization of Sarcocystis isolated from camel (Camelus dromedarius) in Iran

Sarcocystis cameli was first described in one-humped camels (Camelus dromedarius), and it is the only species which have so far reported in camels. Although more than 150 species of Sarcocystis were described in various animals, only a few data on camel Sarcocystis ultrastructure were published, and this report is the first for molecular information (DNA sequence and RLFP digestion pattern). The main objective of the present work is to characterize Sarcocystis isolated from camels by electron microscopy and PCR-RFLP methods. Muscle samples were taken from the fresh esophagus, diaphragm, skeletal muscles, and heart of one-humped camels (C. dromedarius) slaughtered in abattoirs of Tehran and Ghazvin provinces, Iran. The dissection and trypsin digestion techniques were applied for the detection of the cysts. The infected samples were fixed in glutaraldehyde and/or frozen at -20°C until use for ultrastructural and molecular studies, respectively. The ultrastructural and molecular studies were carried out contemporaneously. The 18S rRNA gene of the parasites was amplified by PCR. The PCR products were cloned into a pTZ57R/T and sequenced. In addition, the PCR products were digested separately with each of the four restriction enzymes for RFLP. Our results indicated that only microcysts were observed in muscle samples. The microcysts were white, elongated, spindled, and a few spiral-shaped, with mean size 260 × 75 μm which are identical with S. cameli. The ultrastructure of microcyst wall had many non-branched finger-like protrusions irregularly folded. There was a 600-bp specific band amplified after PCR with specific primers. The molecular data for camel Sarcocystis is reported for the first time in Iran and the world.

Monophyly of marsupial intraerythrocytic apicomplexan parasites from South America and Australia

Intraerythrocytic parasites (Apicomplexa: Sarcocystidae) of the South American mouse opossum (Thylamys elegans) from Chile, South America, and of the yellow-bellied glider (Petaurus australis) from Australia were found to be monophyletic using SSU rDNA and partial LSU rDNA sequences. Phylogenetic reconstruction placed both species within the family Sarcocystidae. These intraerythrocytic parasites of marsupials represent an as yet unnamed genus predicted to have bisporocystic oocysts and tetrazoic sporocysts, which is a characteristic feature of all members of the family Sarcocystidae. These results show that erythrocytic parasites share a common ancestor and suggest co-evolution with their vertebrate host.

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

Background

Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare.

Results

Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites.

Conclusion

By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations underscore the importance of using large phylogenies to uncover important evolutionary patterns and we present a fast and simple method for constructing these phylogenies.