Nuclear 18S rDNA Sequences Research Articles

A new species of the Trichia botrytis complex from the cloud forest in Ecuador

The paper describes a new myxomycete species, Trichia tuberculata, from the Ecuadorian cloud forest. The phylogeny constructed with nuclear 18S rDNA and mitochondrial 17S rDNA sequences indicates that the taxon is closely related to the recently described species T. acetocorticola, T. nubila, and T. pinicola, all within the T. botrytis complex. The morphology of the inner peridium surface and capillitium also aligns T. tuberculata with these species. However, the distinctive tuberculate peridium, short elater tips, and perhaps the distribution range (so far found in the equatorial zone only) distinguish T. tuberculata from related taxa.

Freshwater ‘microcroissants’ shed light on a novel higher-level clade within the Trebouxiophyceae and reveal the genus Chlorolobion to be a trebouxiophyte

ABSTRACT The Trebouxiophyceae is a widespread and species-rich green algal class encompassing mostly coccoid algae with a simple spherical, ovoid or ellipsoidal outline. However, some poorly sampled lineages have evolved more elaborate shapes or even complex thalli, adding to the morphological diversity of the class. By investigating new and previously established strains, this study expands the range of morphologies exhibited by the class members by uncovering a clade of croissant-like trebouxiophytes. Phylogenetic analyses inferred from nuclear 18S rDNA and chloroplast rbcL sequences confirmed the monophyly of the ‘microcroissant’ clade, which we propose to be classified as a new family, Ragelichloridaceae. This family includes two novel genera, Ragelichloris and Navichloris, and the previously described Thorsmoerkia. The position of Ragelichloridaceae within Trebouxiophyceae stayed unresolved but chloroplast phylogenomics showed that the family belongs to the broader incertae sedis group that also includes Xylochloris and Leptosira. In addition, our study showed that the similar morphotype-bearing genus Chlorolobion, previously classified within Chlorophyceae, is a genuine trebouxiophyte, potentially related to Ragelichloridaceae.

Morphological and phylogenetic analyses reveal four species of myxomycetes new to China.

Four species of myxomycetes (Arcyria pseudodenudata, Diderma europaeum, Lycogala irregulare, and Trichia armillata) new to China were observed via light microscope and scanning electron microscope, and detailed descriptions and illustrations are provided, along with comparisons with related species. Among them, A. pseudodenudata was discovered for the first time outside of the type locality, D. europaeum was discovered for the first time outside of Europe, and L. irregulare and T. armillata were reported again after being named. Phylogenetic analyses based on nuclear 18S rDNA and elongation factor-1 alpha sequences or nuclear 18S rDNA and cytochrome oxidase subunit I sequences was performed to provide a molecular basis for morphological identification. These specimens were deposited in the Herbarium of Fungi of Nanjing Normal University.

DNA Barcoding of Nematode Parasites Infecting Ompok bimaculatus and Nemacheilus anguilla From Barvi Reservoir, Maharashtra

In the present study, the DNA barcoding of the nematode parasite infecting Ompok bimaculatus and Nemacheilus anguilla fish species was carried out in Barvi Reservoir, Maharashtra. To ascertain the taxonomic status of these nematode parasites, an 18S gene marker was used. Accurate identification of fish parasites is essential to formulate preventive strategies and to study host–environment relations. The present study did barcoding of the nematode parasites of the fishes caught from the Barvi Reservoir using the nuclear 18S rDNA (SSU) sequence. The nuclear 18S rDNA (SSU) was amplified into two overlapping amplicons and sequenced to identify the species based on the sequence similarity with the NCBI GenBank database. The present study sequences (both fragments) showed 98% similarity with the species of Eustrongylides. The average genetic distance value between the present study sample and species of Eustrongylides was 0.003. In the phylogenetic tree also, the sequence was clustered with the species of Eustrongylides with significant bootstrap values. The present study identified the nematode parasite of the fish caught from the Barvi Reservoir, as species of Eustrongylides. The species‐level identification could not be possible due to the insufficient/lack of reference sequences in the database. It indicates the knowledge gap concerning the species‐specific molecular markers for nematode parasites of the fish.

The First Isospora Species (Apicomplexa: Eimeriidae) Described from the Northern Yellow-Shafted Flicker (Colaptes auratus luteus) in Ontario, Canada.

Members of the genus Isospora commonly infect a wide variety of wild birds. By combining morphometric and genetic data, we are able to differentiate and describe a new apicomplexan parasite, Isospora picoflavae n. sp., from the Northern Yellow-shafted Flicker (Colaptes auratus luteus) in Ontario, Canada. Unsporulated oocysts were observed in intestinal contents obtained during necropsy; these oocysts completed exogenous sporulation within 7days at room temperature. Complete nuclear 18S rDNA and complete mitochondrial genome sequences were obtained from this previously undescribed Isospora sp. to compare with related coccidia. Sporulated oocysts were subspherical in shape measuring an average of 22.7 × 21.7μm (n = 53; mean shape index 1.05) containing a near-spherical polar granule. Sporocysts were ovoidal to ellipsoidal in shape, measuring an average size of 17.0 × 10.5μm (n = 9; mean shape index 1.62). Sporocyst residuum was concentrated in an irregular, spherical mass in the middle of each sporocyst. The isolated oocysts differed morphologically from other Isospora species reported to infect members of the family Picidae. Based on phylogenetic analyses using either combined nuclear 18S rDNA and mitochondrial cytochrome c oxidase I (COI) sequences or complete mitochondrial genome sequences, this Isospora sp. n. isolated from the Northern Flicker grouped within a clade containing Isospora species described from various passeriform hosts. Based on combined morphological and molecular data, the oocysts found in the gastrointestinal contents of Colaptes auratus luteus represent a new species of Isospora named herein as Isospora picoflavae n. sp.

New species of the genus Spio (Annelida, Spionidae) from the southern and western coasts of Korea.

A new spionid polychaete, Spiopigmentatasp. nov., is described from the southern and western coasts of Korea. This new species differs from its congeners by the combination of the following morphological characteristics: the presence of orange-brown pigmentation on the anterior part of the prostomium, black pigmentation on the peristomium and along the body, U-shaped nuchal organs, a comparatively long extension of metameric dorsal ciliated organs, three pairs of white dots per chaetiger, two to three posterior abranchiate chaetigers, and the presence of tridentate neuropodial hooded hooks. The partial 16S ribosomal DNA (rDNA) and nuclear 18S rDNA sequences of the new species and Spio sp. 2 reported by Abe and Sato-Okoshi (2021) from Japan showed high similarity, indicating that these two specimens belong to the same species. A detailed description and illustrations of the new species, together with molecular information, are provided.

First report on Mermithidae (Mermithida) infection in Ligidium sp. (Isopoda, Ligiidae).

Specimens of Ligidium sp. (Crustacea, Isopoda, Oniscidea) collected from Kanagawa Prefecture in Japan were found to be infected with parasitic nematodes. We have obtained two Mermithidae (Nematoda) by dissecting the fresh specimen and from the dead specimen of Ligidium, which marks the second known discovery of a mermithid infection in the order Isopoda. Herein, a report on the nuclear 28S rDNA and 18S rDNA sequence of the isolated Mermithidae nematodes and on the morphology of the juveniles is provided.

Full Mitochondrial Genome and Nuclear 18S rDNA Sequences Refine the Taxonomic Placement of Choleoeimeria taggarti n. comb. from the Prostate of Antechinus flavipes (Yellow-Footed Antechinus)

An unusual coccidian parasite was described previously from the prostate of a male Antechinus flavipes (family: Dasyuridae; common name: yellow-footed antechinus). Morphometrics and a partial nuclear 18S small subunit rDNA (18S rDNA) sequence were used to assign this parasite to the genus Eimeria; it was named Eimeria taggarti. We generated full nuclear 18S rDNA and mitochondrial genome sequences from this parasite and used the newly completed 18S rDNA and mitochondrial cytochrome c oxidase subunit I (COI) sequences to perform a more in-depth phylogenetic analysis. The parasite clustered closely with Choleoeimeria spp. and Acroeimeria spp. infecting herptiles in a well-supported clade that was the sister lineage to the Eimeriidae sensu stricto. The mitochondrial genome of this parasite contained 2 inverted segments compared to mitochondrial genomes from parasites in the Eimeriidae sensu stricto (i.e., Stieda body-possessing coccidia with 4 dizoic sporocysts); this mitochondrial genome arrangement was shared with the only Choleoeimeria species for which sequence data were available publicly. Examination of histological preparations and TEM images uncovered bivalvate sporocysts and otherwise confirmed previously described morphological features of the parasite. Based on our phylogenetic analyses and histological observations, we propose the generic reclassification of E. taggarti to Choleoeimeria taggarti n. comb.

Redescription of Gyrinicola japonica, a Tadpole-Endoparasitic Nematode from Japan, with Resurrection of the Family Gyrinicolidae (Nematoda: Oxyurina).

The taxonomic account of the tadpole-parasitic nematode Gyrinicola japonica Yamaguti, 1938, which is the type species of the genus, was reassessed based on syntypes and newly-collected specimens from the type locality. Our redescription of G. japonica addresses the erroneous original description of a spicule in this nematode, and emends the diagnosis of the species. Additionally, molecular phylogenetic trees based on nuclear 18S and 28S rDNA sequences revealed that G. japonica forms a distinctive lineage within the suborder Oxyurina, and this tadpole-specialist is phylogenetically close to the lizard-parasitic nematodes that belong to the family Pharyngodonidae. The results of morphological examination with the aid of molecular phylogenetic trees highlight the systematic uniqueness of this tadpole-parasitic group within Oxyurina, and Gyrinicolidae is accordingly resurrected as a distinctive oxyurinan family, with redefinition of the family and the genus Gyrinicola.

Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa)

Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences. Although alignment of the mt COI sequences was unambiguous, substitution saturation was evident for comparisons of COI sequences between ingroup (eimeriid) and outgroup (sarcocystid) taxa. Consequently, a combined dataset applying partition-specific analytical and alignment improvements was used to generate a robust molecular phylogeny. Most eimeriid parasites that infect closely related definitive hosts were found in close proximity on the resulting tree, frequently in a single clade. Whether this represents coevolution or co-accommodation or a combination remains an open point. Unlike host associations, basic oocyst configuration (number of sporocysts per oocyst and sporozoites per sporocyst) was not correlated with phylogeny. Neither ‘Eimeria-type’ nor ‘Isospora-type’ oocyst morphotypes formed monophyletic groups. In the combined dataset tree (representing only a tiny fraction of described eimeriid coccidia), at least 10 clades of Eimeria spp. would need to be re-assigned to nine distinct genera to resolve their paraphyly. The apparent lack of congruence between morphotype and genotype will require taxonomists to balance nomenclatural stability and diagnostic ease against the ideal of monophyletic genera. For now, recognition of paraphyletic eimeriid genera defined by basic oocyst configuration may be necessary for reasons of taxonomic stability and diagnostic utility. Future taxonomic revisions to produce monophyletic eimeriid genera will ultimately require the identification of reliable phenotypic characters that agree with the molecular phylogeny of these parasites or, less optimally, acceptance that genotyping may be needed to support monophyletic supraspecific taxonomic groups.

Identification of a new characteristic species of Nitella (Charophyceae) from southwestern China based on morphology and molecular phylogeny

Nitella fuiana Lan & Qing sp. nov., a special kind of charophyte from Mingshan, Sichuan, China, was described in this study. The systematic position of the new species was assessed based on morphological and molecular analysis. The results of morphology comparison showed that the charophyte possessed stipulodes and 10-cell coronula. Nuclear 18S rDNA and plastid rbcL sequences analysis revealed that N. fuiana was a single clade as clustered with other species of Nitella. Combined with the morphological and molecular analysis data, our study strongly supported that N. fuiana was a new species of Nitella. This is the first report of Nitelleae species with stipulodes, which increased the morphological diversity of charophytes. This study also reminds us to pay close attention to the characteristics of stipulodes for further research on charophytes.

Isolation and identification of Acanthamoeba strains from soil and tap water in Yanji, China

BackgroundMembers of the genus Acanthamoeba are widely distributed throughout the world, and some of them are considered pathogenic, as they are capable of causing corneal and central nervous system diseases. In this study, we isolated Acanthamoeba strains from soil and tap water in Yanji, China.MethodsWe identified four strains of Acanthamoeba (CJY/S1, CJY/S2, CJY/S3, and CJY/W1) using mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) analysis. Nuclear 18S rDNA sequences were used for phylogenetic analysis and species identification.ResultsGenotypic characterization of the isolates showed that they belonged to genotypes T4 (CJY/S1 and CJY/S2), T5 (CJY/S3), and T16 (CJY/W1). Sequence differences between CJY/S1 and Acanthamoeba castellanii Neff, CJY/S2 and Acanthamoeba KA/E7, and CJY/S3 and Acanthamoeba lenticulata 68–2 were 0.31, 0.2, and 0.26%, respectively. 18S ribosomal deoxyribonucleic acid (rDNA) of CJY/W1 had 99% sequence identity to that of Acanthamoeba sp. U/H-C1. Strains CJY/S1 and CJY/S2, isolated from soil, had similar mtDNA RFLP patterns, whereas strain CJY/W1, isolated from tap water, displayed a different pattern.ConclusionsTo the best of our knowledge, this is the first report on the identification of genotypes T4, T5, and T16 from environmental sources in Yanji, China.

Rediscovery of Tetraëdriella subglobosa Pascher, a member of the Eustigmatophyceae

An algal strain from an acidic pool near the shore of Lake Macha, Czech Republic, was identified as Tetraedriella subglobosa Pascher by light microscopy. Phylogenetic analysis of nuclear 18S rDNA and plastid rbcL sequence data indicated that this alga is a member of the Eustigmatophyceae, rather than the Xanthophyceae as presently classified. This is the first report of T. subglobosa since Pascher's description of the species in 1930.

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

SUMMARYPartial 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.

Molecular phylogenetics of eimeriid coccidia (Eimeriidae, Eimeriorina, Apicomplexa, Alveolata): A preliminary multi-gene and multi-genome approach.

Coccidia possess three distinct genomes: nuclear, mitochondrial, and plastid. Sequences from five genes located on these three genomes were used to reconstruct the phylogenetic relationships of members of the phylum Apicomplexa: 18S rDNA sequences from the nuclear (nu) genome, partial cytochrome c oxidase subunit I sequences from the mitochondrial (mt) genome, and partial 16S and 23S rDNA sequences and RNA polymerase B sequences from plastid (pl) genomes. Maximum parsimony, maximum likelihood, and Bayesian inference were used in conjunction with nuclear substitution models generated from data subsets in the analyses. Major groups within the Apicomplexa were well supported with the mitochondrial, nuclear, and a combination of mitochondrial, nuclear and concatenated plastid gene sequences. However, the genus Eimeria was paraphyletic in phylogenetic trees based on the nuclear gene. Analyses using the individual genes (18S rDNA and cytochrome c oxidase subunit I) resolved the various apicomplexan groups with high Bayesian posterior probabilities. The multi-gene, multi-genome analyses based on concatenated nu 18S rDNA, pl 16S, pl 23S, pl rPoB, pl rPoB1, and mt COI sequences appeared useful in resolving phylogenetic relationships within the phylum Apicomplexa. Genus-level relationships, or higher, appear best supported by 18S rDNA analyses, and species-level analyses are best investigated using mt COI sequences; for parasites for which both loci are available, nuclear 18S rDNA sequences combined with mitochondrial COI sequences provide a compact and informative molecular dataset for inferring the evolutionary relationships taxa in the Apicomplexa.

Ulvella tongshanensis (Ulvellaceae, Chlorophyta), a new freshwater species from China, and an emended morphological circumscription of the genus Ulvella

A new freshwater species of Ulvella, U. tongshanensis H. Zhu et G. Liu, is described from material collected from rocks under small waterfalls in Hubei Province, China. This unusual species differs from other species in the genus by the macroscopic and upright parenchymatous thalli, and by the particular habitat (most Ulvella species occur in marine environments). Phylogenetic analyses of plastid encoded rbcL and tufA, and nuclear 18S rDNA sequences, pointed towards the generic placement of U. tongshanensis and also showed a close relationship with two other freshwater species, Ulvella bullata (Jao) H. Zhu et G. Liu, comb. nov. and Ulvella prasina (Jao) H. Zhu et G. Liu, comb. nov. The latter two were previously placed in the genus Jaoa and are characterized by disc-shaped to vesicular morphology. Our study once again shows that traditionally used morphological characters are poor indicators for phylogenetic relatedness in morphologically simple algae like the Ulvellaceae. Thus, the morphological circumscription of the genus Ulvella is here expanded to include: (1) thalli that are uniseriate in basal and apical parts, and parenchymatous in the middle portion with distinct differentiation of an unbranched dorsal side and a ventral side developing many short branches, and (2) epibiotic or epilithic, disc-shaped to vesicular thalli with a di- or tristromatic structure.

Phylogenetics and systematics of Angiostrongylus lungworms and related taxa (Nematoda: Metastrongyloidea) inferred from the nuclear small subunit (SSU) ribosomal DNA sequences

The Angiostrongylus lungworms are of public health and veterinary concern in many countries. At the family level, the Angiostrongylus lungworms have been included in the family Angiostrongylidae or the family Metastrongylidae. The present study was undertaken to determine the usefulness and suitability of the nuclear 18S (small subunit, SSU) rDNA sequences for differentiating various taxa of the genus Angiostrongylus, as well as to determine the systematics and phylogenetic relationship of Angiostrongylus species and other metastrongyloid taxa. This study revealed six 18S (SSU) haplotypes in A. cantonensis, indicating considerable genetic diversity. The uncorrected pairwise 'p' distances among A. cantonensis ranged from 0 to 0.86%. The 18S (SSU) rDNA sequences unequivocally distinguished the five Angiostrongylus species, confirmed the close relationship of A. cantonensis and A. malaysiensis and that of A. costaricensis and A. dujardini, and were consistent with the family status of Angiostrongylidae and Metastrongylidae. In all cases, the congeneric metastrongyloid species clustered together. There was no supporting evidence to include the genus Skrjabingylus as a member of Metastrongylidae. The genera Aelurostrongylus and Didelphostrongylus were not recovered with Angiostrongylus, indicating polyphyly of the Angiostrongylidae. Of the currently recognized families of Metastrongyloidea, only Crenosomatidae appeared to be monophyletic. In view of the unsettled questions regarding the phylogenetic relationships of various taxa of the metastrongyloid worms, further analyses using more markers and more taxa are warranted.

The diversity and phylogeny of the commercially important algal class Eustigmatophyceae, including the new clade Goniochloridales

The Eustigmatophyceae is a class of yellow-green algae allied with the Chrysophyceae and other chlorophyll c possessing stramenopile (heterokont) algae. Some members of the class, especially the marine species of the genus Nannochloropsis, are under intense investigation for their potential for production of biofuels and beneficial fatty acids. The class has generally been thought to comprise a small number of genera and species, and these organisms were considered rare or infrequently encountered. In this study, we examined the phylogeny and diversity of this class by analysis of nuclear 18S rDNA sequence data. Our analysis included sequences from all the named members of the Eustigmatophyceae held in culture collections as well as a number of strains identified in culture collections as Xanthophyceae, new strains with features characteristic of the Eustigmatophyceae, and published data for uncultured DNA clones. The results of these analyses show that the Eustigmatophyceae is far more diverse than generally recognized. Two major lineages are supported in the class, the previously recognized order Eustigmatales and the new clade, Goniochloridales. Additional new lineages were also resolved within each of these major lineages; however, the results of our analyses were considered insufficient for naming these subordinate clades. Several of these lineages comprised only unnamed strains or uncultured DNA clones. Overall, our results indicate that the Eustigmatophyceae is a highly diverse class, with many new species, genera, and families awaiting taxonomic treatment.

Hemichordate Molecular Phylogeny Reveals a Novel Cold-Water Clade of Harrimaniid Acorn Worms

Hemichordates are instrumental to understanding early deuterostome and chordate evolution, yet diversity and relationships within the group have been understudied. Recently, there has been renewed interest in hemichordate diversity and taxonomy, although current findings suggest that much hemichordate diversity remains to be discovered. Herein, we present a molecular phylogenetic study based on nuclear 18S rDNA sequence data, which includes 35 previously unsampled taxa and represents all recognized hemichordate families. We include mitochondrial 16S rDNA data from 66 enteropneust taxa and three pterobranch Rhabdopleura species, and recover colonial pterobranchs and solitary enteropneusts as reciprocally monophyletic taxa. Our phylogenetic results also reveal a previously unknown clade of at least four species of harrimaniid enteropneusts from cold waters, including Antarctica, the North Atlantic around Iceland and Norway, and the deep sea off Oregon. These small worms (1-5 mm in length), occur from 130 to 2950 m and are not closely related to other deep-sea harrimaniids, indicating that diversity of enteropneusts within the deep sea is broader than previously described in the literature. Discovery of this clade, as well as larger torquaratorids from Antarctica, strengthens hypotheses of close associations between Antarctic and deep-sea fauna.

Determination of Phylogenetic Relationships among <i>Eimeria</i> species, which Parasitize Cattle, on the Basis of Nuclear 18S rDNA Sequence

ABSTRACTWe analyzed almost complete 18S rDNA sequences of 10 bovine Eimeria species, namely Eimeria alabamensis, E. auburnensis, E. bovis, E. bukidnonensis, E. canadensis, E. cylindrica, E. ellipsoidalis, E. subspherica, E. wyomingensis and E. zuernii. Although these sequences showed intraspecific variation in 8 species, the sequences of each species were clustered in monophyletic groups in all species, except E. auburnensis. The sequences constituted 3 distinct clusters in a phylogenetic tree with relatively high bootstrap values; however, the members including each cluster shared no similarities in oocyst morphology.