Nuclear rRNA Gene Research Articles

Melitapanda, a new species of Melitidae (Crustacea, Amphipoda) from Japan.

A new intertidal species of the melitid amphipod, Melitapanda, from the Wakayama Prefecture, Japan, is identified and described. Melitapanda sp. nov. differs from the similar M.koreana and M.nagatai by its black-and-white body color, well-developed anterodistal projection of the male gnathopod 1 propodus, and telson armature. Molecular phylogenetic analyses based on the nuclear 28S rRNA and mitochondrial COI genes support that M.panda sp. nov. is closely related to M.koreana and M.nagatai.

Trematode metacercariae parasitic in the estuarine crustacean Cyathura muromiensis Nunomura, 1974 (Peracarida: Isopoda: Anthuroidea)

This is the first report of trematodes parasitic in the estuarine isopod crustacean Cyathura muromiensis, and the fourth report from anthuroid isopods worldwide. From 52 of 54 host individuals collected qualitatively on the tidal flat of the Muromi River estuary, Fukuoka, Japan, 389 cysts of metacercariae were extracted (sample prevalence = 96.3 %). Host individuals contained from one to 71 metacercarial cysts. The range in cyst diameter was 172.3–252.1 μm, and the distribution of cyst sizes contained only one component. Cysts occurred in pereonites 2–7 and the pleon of the host, but not in the head, pereonite 1, or telson. There was no correlation between the number of cysts and host sex or size. Sequences of the nuclear “ITS1 region,” from the 3´ region of 18S rRNA to the 5´ region of internal transcribed spacer I gene (ITS1), from five cysts ranging in size from nearly the lowest diameter to the greatest diameter in our sample showed p-distances of 0.0–0.2 %, suggesting that all cysts obtained were conspecific. A phylogenetic reconstruction based on nuclear 28S rRNA gene sequences showed that the trematode belongs in the genus Microphallus. The definitive host of our trematode species is likely a bird, since the definitive hosts of microphallids are chiefly birds, and birds are known to prey on Cyathura isopods.

Multi-metal tolerant Porostereum umbrinoalutaceum isolated from Pleurotus ostreatus fruit body showing root colonization, growth promotion of chilli (Capsicum annuum L.) plant and antagonism against fungal pathogens.

Mushroom associated microbes could be utilized to improve crop productivity providing nutrients, plant growth promoting substances, production of hydrolytic enzymes and protecting plant from biotic and abiotic stress. An endophyte designated as KUFC101 was isolated from fruit body of Pleurotus ostreatus and identified as Porostereum umbrinoalutaceum based on nuclear-rRNA gene sequence analysis. Growth in different culture media, metal tolerance, biochemical characterization and effect on chilli plant growth promotion were studied. The isolate showed best growth in Malt extract medium and least growth in synthetic media. It could tolerate toxic metals (Mg, Ca, Fe, Cu, Mn, Zn and Cd each at 100ppm concentration). It produced amylase, cellulase, chitinase, pectinase, catecholate type of siderophore and indole acetic acid, and inhibited growth of Alternaria solani and Penicillium citrinum. It could colonize in the rhizosphere of chilli plant and influence growth of chilli plant by improving biomass and metabolite content. Porostereum umbrinoalutaceum KUFC101 could be utilized in formulation of biofertiliser under sustainable agricultural system.

From ctenophores to scyphozoans: parasitic spillover of a burrowing sea anemone

Most host-parasite associations are explained by phylogenetically conservative capabilities for host utilization, and therefore parasite switches between distantly related hosts are rare. Here we report the first evidence of a parasitic spillover of the burrowing sea anemone Edwardsiella carnea from the invasive ctenophore Mnemiopsis leidyi to two scyphozoan hosts: the native Mediterranean barrel jellyfish Rhizostoma pulmo and the invasive Indo-Pacific nomad jellyfish Rhopilema nomadica, collected from the Eastern Mediterranean Sea. Edwardsiella carnea planulae found in these jellyfish were identified using molecular analyses of the mitochondrial 16S and nuclear 18S rRNA genes. Overall, 93 planulae were found on tentacles, oral arms, and inside of the gastrovascular canals of the scyphomedusae, whereas no infection was observed in co-occurring ctenophores. DNA metabarcoding approach indicated seasonal presence of Edwardsiella sp. in the Eastern Mediterranean mesozooplankton, coinciding with jellyfish blooms in the region. Our findings suggest a non-specific parasitic relationship between Edwardsiella carnea and various gelatinous hosts based on shared functionality rather than evolutionary history, potentially driven by shifts in host availability due to jellyfish blooms. This spillover raises questions about the ecological impacts of parasitism on native and invasive scyphozoan hosts and the potential role of Edwardsiella in controlling their populations.

First Report of Polygonatum kingianum Leaf Spot Caused by Alternaria alternata in Kunming, China.

Polygonatum kingianum Coll. et Hemsl., a Polygonatum species in the Asparagaceae family, plays an important role in Chinese herbal medicine (Zhao et al. 2018). P. kingianum is widely planted in the Southwestern China. In September 2023, we observed a leaf spot of P. kingianum with disease incidence of 100%, and disease index reached 60 in commercial plantings in Kunming, Yunnan province, China (24.3610°N, 102.3740°E). In the initial stage of infection, symptoms manifested as a small circular brown spot. As the spots gradually expanded, they formed oval to irregular shaped lesions with grayish-white or dark-brown borders. Progressively the entire leaf withered and died. For identification of the causal agent of the leaf spot, leaf sections (5×5 mm2) were cut from the margin of the lesion and soaked in 75% ethanol for 10 s, 1% sodium hypochlorite for 3 min, washed with sterile distilled water, dried on sterilized tissue paper and placed on potato dextrose agar (PDA). The Petri dishes were then incubated at 28℃ for 3 days with a 12-h photoperiod. A predominant fungus was isolated from 95% of the samples. Three monosporic isolates were screened using a single-spore isolation method. After 4 days of incubation the colonies were white, after 7 days turned yellow-white. Conidia were black-brown, oblong or fusiform, with 3-7 transverse septa and 0-3 longitudinal septa, with dimensions of 19.5 to 49.5 × 8.7 to 17.6 µm (n = 30). Total genomic DNA of these three isolates was extracted from mycelia by the cetyltrimethylammonium bromide (CTAB) protocol. The nucleotide sequences of the elongation factor 1-alpha (EF1α), nuclear ribosomal internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit rRNA gene (LSU), 18S nuclear ribosomal small subunit rRNA gene (SSU), and the second largest subunit of nuclear DNA-directed RNA polymerase II (RPB2) gene regions were amplified using the primer pairs EF1-728F/EF1-986R (Carbone and Kohn 1999), ITS1/ITS4 (White et al. 1990), LR0R/LR5 (Schoch et al. 2012), NS1/NS4 (Schoch et al. 2012), and fRPB2-5F/fRPB2-7Cr (Liu et al. 1999), respectively. Amplicons were cloned in a pMDTM19-T vector (code no. 6013, Takara, Kusatsu, Japan) and bidirectionally sequenced. All three isolates had identical nucleotide sequences. Sequences from one isolate (PkF03) were deposited in GenBank. BLASTn analyses showed that sequences of EF1α (GenBank accession no. PP695240), ITS (PP694046), LSU (PP683406), SSU (PP683407), and RPB2 (PP695241) of isolate PkF03 were 99.6 (KP125134), 100 (KP124358), 100 (KP124510), 99.9 (KP124980), and 100% (KP124826), respectively, identical with Alternaria alternata (Fr.) Keissl. strain CBS 118815. Based on the nucleotide sequences of EF1α, ITS, LSU, SSU, and RPB2, a maximum likelihood phylogenetic tree was constructed using MEGAX with Tamura-Nei model. Isolate PkF03 was grouped in the same clade as A. alternata. According to the morphology and sequence analyses isolate PkF03 was identified as A. alternata (Woudenberg et al. 2013). To determine pathogenicity of isolate PkF03, a spore suspension (106 spores/mL) was sprayed on 1-year-old healthy leaves of P. kingianum. The control leaves were sprayed with sterile water. All plants were incubated at 28℃, 70% relative humidity, and a 12-h photoperiod. The pathogenicity tests were repeated three times with six plants in each treatment. Fifteen days post-inoculation, the inoculated leaves showed brown-yellow lesions, whereas the control leaves remained symptomless. A. alternata was reisolated from infected leaves. To our knowledge, this is the first report of A. alternata causing leaf spot on P. kingianum in Kunming, China. The results provide a scientific basis for prevention and control of the disease.

New species of Kontrimavichusia Makarikov & Binkienė, 2022 (Eucestoda: Hymenolepididae) from arvicoline rodents (Rodentia: Cricetidae) from the North Caucasus

Two previously unrecognized species attributable to the genus Kontrimavichusia Makarikov & Binkienė, 2022 in arvicoline rodents from the North Caucasus are described. Kontrimavichusia testiculata sp. nov. is described from Microtus majori (Thomas, 1906) from the northwestern Caucasus (Republic of Adygeya and Karachay-Cherkess Republic, Russia) and Kontrimavichusia hobergi sp. nov. is described from Microtus daghestanicus (Shidlovsky, 1919) from the central Caucasus (Republic of North Ossetia, Russia). Kontrimavichusia testiculata is readily distinguishable from K. asymmetrica (Janicki, 1904) and K. hobergi in having a larger number of testes (4–6 per proglottis), larger suckers and a longer cirrus and cirrus-sac. In addition, the new species differs from its congeners by the position of the cirrus-sac with regard to the poral osmoregulatory canals and position of distal end of the rostellar pouch relative to the posterior margins of the suckers. Kontrimavichusia hobergi can be readily distinguished from its congeners by the arrangement of the testes in a triangle and the position of the cirrus-sac with regard to the poral osmoregulatory canals. In addition, this previously unrecognized species differs from K. asymmetrica and K. testiculata by the smaller dimensions of the fully developed strobila and a narrower ovary. The cirrus-sac of K. hobergi is larger than that in K. asymmetrica but smaller than that in K. testiculata. We also used partial sequences of the nuclear ribosomal 28S rRNA gene and mitochondrial nad1 gen to justify the generic arrangement and independent status of these two new species which are characterized in the current manuscript.

The first report of digenean infecting short mackerel (Rastrelliger brachysoma) from Chon Buri Province, the Gulf of Thailand

Rastrelliger brachysoma (Bleeker, 1851), the short mackerel, is a dietary staple and of significant economic demand in Southeast Asia and Thailand. However, the demand for short mackerel has precipitated an overfishing crisis, leading to a depletion of fish stocks. Overfishing, coupled with parasitism, may result in a decline in the population of R. brachysoma. Digenetic trematode infection is prevalent in marine fish and has a considerable impact on the overall health of the fish. Here, to identify digenetic trematodes infecting R. brachysoma, we aim to determine the identity, prevalence, and intensity of digenean infections in R. brachysoma from the Gulf of Thailand. A total of 194 short mackerel were obtained from Chon Buri Province, where digeneans were isolated and identified. The molecular identity of the digeneans was confirmed using the nuclear 28S rRNA gene. Of the 194 short mackerel, 100% were found to be infected with digeneans, comprising of Lecithocladium, Prodistomum, Opechona, and Aphanurus. Lecithocladium was the most prevalent (98%) and had the highest intensity of infection (37 mean intensity), followed by Prodistomum (75% prevalence and 17 mean intensity). Our study thus presents the first evidence of digeneans infecting the economically important short mackerel from the Gulf of Thailand. The high infection rate of digenetic trematodes may have implications on the health of R. brachysoma, further driving their population decline. These data underscore the importance of safeguarding fisheries resources in the Gulf of Thailand, and downstream conservation efforts are crucial for evidence-based management decisions to safeguard the long-term sustainability of fish resources.

Comparative plastome and mitogenome analyses indicate that the marine prasinophyte green algae Pycnococcus provasolii and Pseudoscourfieldia marina (Pseudoscourfieldiophyceae class nov., Chlorophyta) represent morphotypes of the same species.

The marine prasinophyte green algae Pycnococcus provasolii and Pseudoscourfieldia marina represent the only extant genera and known species of the Pycnococcaceae. However, their taxonomic status needs to be reassessed, owing to the very close relationship inferred from previous sequence comparisons of individual genes. Although Py. provasolii and Ps. marina are morphologically different, their plastid rbcL and nuclear small subunit rRNA genes were observed to be nearly or entirely identical in sequence, thus leading to the hypothesis that they represent distinct growth forms or alternate life-cycle stages of the same organism. To evaluate this hypothesis, we used organelle genomes as molecular markers. The plastome and mitogenome of Ps. marina UIO 007 were sequenced and compared with those available for two isolates of Py. provasolii (CCMP 1203 and CCAP 190/2). The Ps. marina organelle genomes proved to be almost identical in size and had the same gene content and gene order as their Py. provasolii counterparts. Single nucleotide substitutions and insertions/deletions were localized using genome-scale sequence alignments. Over 99.70% sequence identities were observed in all pairwise comparisons of plastomes and mitogenomes. Alignments of both organelle genomes revealed that Ps. marina UIO 007 is closer to Py. provasolii CCAP 190/2 than are the two Py. provasolii strains to one another. Therefore, our results are not consistent with the placement of Ps. marina and Py. provasolii strains into distinct genera. We propose a taxonomic revision of the Pycnococcaceae and the erection of a new class of Chlorophyta, the Pseudoscourfieldiophyceae.

A contribution to the taxonomy and phylogeny of the genus Chaetonotus (Gastrotricha, Paucitubulatina, Chaetonotidae), with the description of a new species from Italian inland waters

Gastrotrichs of the genus Chaetonotus Ehrenberg, 1830 (Chaetonotida, Chaetonotidae) are known to be a speciose and pervasive group in both the marine and freshwater ecosystems, and recent investigations indicate that there is a significant amount of species diversity yet to be discovered. In the present study, a new species of this genus is described from two quarry lakes in northern Italy and characterized using an integrative morphological and molecular approach. Chaetonotus polites n. sp. is recognized by a rather stocky body, a five-lobed head, and the cuticular covering resolved in 13 alternating columns of partially imbricated scales, trilobed on the head and pentagonal on the trunk; each scale bears a peculiar simple, very thick, curved spine with a truncated apex. The new species is also distinguished by four putative molecular apomorphies at the 18S rRNA gene and two at the 28S rRNA gene. The location and type of these unique traits in the predicted secondary structure of the ribosomal genes is provided. The phylogenetic analysis based on concatenated sequences of three genes (the nuclear 18S and 28S rRNA genes and the mitochondrial COI gene) derived from 123 selected chaetonotidans, including the novel species, confirms that the genus Chaetonotus is a polyphyletic group, with several of its members resolved together with species of other genera. The new species forms a cluster with species of the subgenus Hystricochaetonotus Schwank 1990, suggestive of its potential stem lineage. LSIDurn:lsid:zoobank.org:pub:9A5DCE75-2EF2-41B0-863E-BB9237476F7F LSIDurn:lsid:zoobank.org:act:6C35E40A-6ED4-40C8-8A0D-DBBF33D01A07

Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Labeo catla parent populations.

Interspecific hybrids of rohu (Labeo rohita) and catla (Labeo catla) are common, especially in India due to constrained breeding. These hybrids must segregate from their wild parents as part of conservational strategies. This study intended to screen the hybrids from wild rohu and catla parents using both morphometric and molecular approaches. The carp samples were collected from Jharkhand and West Bengal, India. The correlation and regression analysis of morphometric features are considered superficial but could be protracted statistically by clustering analysis and further consolidated by nucleotide variations of one mitochondrial and one nuclear gene to differentiate hybrids from their parents. Out of 21 morphometric features, 6 were used for clustering analysis that exhibited discrete separation among rohu, catla, and their hybrids when the data points were plotted in a low-dimensional 2-D plane using the first 2 principal components. Out of 40 selected single nucleotide polymorphism (SNP) positions of the COX1 gene, hybrid showed 100% similarity with catla. Concerning SNP similarity of the 18S rRNA nuclear gene, the hybrid showed 100% similarity with rohu but not with catla; exhibiting its probable parental inheritance. Along with morphometric analysis, the SNP comparison study together points towards strong evidence of interspecific hybridization between rohu and catla, as these hybrids share both morphological and molecular differences with either parent. However, this study will help screen the hybrids from their wild parents, as a strategy for conservational management.

Skimming genomes for systematics and DNA barcodes of corals.

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

Protective effects of oyster polypeptide on cyclophosphamide-induced immunosuppressed rats.

Oyster polypeptide (OP) is a mixture of oligopeptides extracted from oysters through enzyme lysis, separation, and purification. It is associated with immunomodulatory effects, but the underlying mechanisms are not known. This study therefore combined proton nuclear magnetic resonance (1H-NMR) urinary metabolomics and 16S rRNA gene sequencing of the gut microbiome to determine the immunoprotective mechanisms of OP in rats subjected to cyclophosphamide-induced immunosuppression. Oyster polypeptide restored the body weight and the structure of spleen and thymus in rats with cyclophosphamide-induced immunosuppression. It upregulated the levels of white blood cells (WBCs), hemoglobin (HGB), platelets (PLT), red blood cells (RBCs), immunoglobulin G (IgG), immunoglobulin M (IgM), cytokines such as interleukin‑6 (IL-6) and tumor necrosis factor-α (TNF-α), and increased the numbers of CD3+ and CD4+ T cells in the immunosuppressed rats. The 1H-NMR metabolomics results showed that OP significantly reversed the levels of ten metabolites in urine, including 2-oxoglutarate, citrate, dimethylamine, taurine, N-phenylacetylglycine, alanine, betaine, creatinine, uracil, and benzoate. The 16S rRNA gene sequencing results showed that OP restored the gut microbiome homeostasis by increasing the abundance of beneficial bacteria and reducing the abundance of pathogenic bacteria. Finally, a combination of metabolomics and microbiomics found that the metabolism of taurine and hypotaurine, and the metabolism of alanine, aspartate, and glutamate were disturbed, but these metabolic pathways were restored by OP. This study demonstrated that OP had immunoprotective effects in rats with cyclophosphamide-induced immunosuppression by restoring key metabolic pathways and the gut microbiome homeostasis. Our findings provide a framework for further research into the immunoregulatory mechanisms of OP and its potential use in drugs and nutritional supplements. © 2024 Society of Chemical Industry.

Isospora and Lankesterella Parasites (Eimeriidae, Apicomplexa) of Passeriform Birds in Europe: Infection Rates, Phylogeny, and Pathogenicity.

Wild birds are common hosts to numerous intracellular parasites such as single-celled eukaryotes of the family Eimeriidae (order Eucoccidiorida, phylum Apicomplexa). We investigated the infection rates, phylogeny, and pathogenicity of Isospora and Lankesterella parasites in wild and captive passerine birds. Blood and tissue samples of 815 wild and 15 deceased captive birds from Europe were tested using polymerase chain reaction and partial sequencing of the mitochondrial cytochrome b and cytochrome c oxidase I and the nuclear 18S rRNA gene. The infection rate for Lankesterella in wild birds was 10.7% compared to 5.8% for Isospora. Chromogenic in situ hybridization with probes targeting the parasites' 18S rRNA was employed to identify the parasites' presence in multiple organs, and hematoxylin-eosin staining was performed to visualize the parasite stages and assess associated lesions. Isospora parasites were mainly identified in the intestine, spleen, and liver. Extraintestinal tissue stages of Isospora were accompanied by predominantly lymphohistiocytic inflammation of varying severity. Lankesterella was most frequently detected in the spleen, lung, and brain; however, infected birds presented only a low parasite burden without associated pathological changes. These findings contribute to our understanding of Isospora and Lankesterella parasites in wild birds.

Paratrypaea Komai & Tachikawa, 2008 (Decapoda: Axiidea: Callianassidae): more than two or three species

Abstract Paratrypaea Komai & Tachikawa, 2008 has for more than a decade been thought to contain only two species, both widespread throughout the Indo-West Pacific, or briefly three species. Molecular studies using mitochondrial 16S rRNA and 12S rRNA plus nuclear H3 and 18S rRNA genes, repeated here with samples from more individuals, have shown well separated clades within the genus. Morphological examination has found differences, especially in the form of the adult male cheliped, between the clades leading to the conclusion that Paratrypaea comprises at least eight species of which four are new and described herein. Not all closely related clades could be morphologically distinguished. Some species are narrowly and others widely distributed. The species are: P. baliensissp. nov. from Indonesia; P. bouvieri (Nobili, 1904) from the Red Sea and Indian Ocean; P. chichijimaensis (Sakai, 2015) comb. nov. from Japan; P. dworschakisp. nov. from the Hawaiian Islands; P. maldivensis (Borradaile, 1904) from the eastern Indian Ocean, Papua New Guinea, and possibly western Pacific; P. niuginiensissp. nov. from Papua New Guinea; P. rectangularis (Ngoc-Ho, 1991) from French Polynesia to the Red Sea; and P. rempiensissp. nov. from Papua New Guinea. A published partial 16S sequence from Japan has provided evidence of one more species than those proposed here. Paratrypaea cristata (Borradaile, 1910) comb. nov. remains a species inquirenda.

A new parasitic barnacle (Crustacea, Cirripedia, Rhizocephala, Mycetomorpha) from the abyssal zone in the northwestern Pacific

I describe the parasitic barnacle Mycetomorpha abyssalissp. nov. from the crangonid shrimp Sclerocrangon zenkevitchi collected from 3893–3890 m depth off the eastern coast of Iwate, Japan, northwestern Pacific. This is the first Mycetomorpha rhizocephalan from the abyssal zone and the third species in Mycetomorpha. Mycetomorpha abyssalissp. nov. differs from its congeners M. vancouverensis and M. albatrossi in (1) triangular shield lacking, (2) stalk one-quarter of length from posterior end of externa, (3) mantle opening clearly anterior to stalk, (4) different host genus, and (5) depth range much deeper. I determined partial sequences for the mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA genes and nuclear 18S rRNA and 28S rRNA genes from M. abyssalissp. nov. for future DNA barcoding and phylogeny. Kimura 2-parameter distances between M. abyssalissp. nov. and M. vancouverensis were 21.2% (16S), 0.6% (18S), and 1.5% (28S).

The invasive land flatworm Arthurdendyus triangulatus has repeated sequences in the mitogenome, extra-long cox2 gene and paralogous nuclear rRNA clusters

Using a combination of short- and long-reads sequencing, we were able to sequence the complete mitochondrial genome of the invasive ‘New Zealand flatworm’ Arthurdendyus triangulatus (Geoplanidae, Rhynchodeminae, Caenoplanini) and its two complete paralogous nuclear rRNA gene clusters. The mitogenome has a total length of 20,309 bp and contains repetitions that includes two types of tandem-repeats that could not be solved by short-reads sequencing. We also sequenced for the first time the mitogenomes of four species of Caenoplana (Caenoplanini). A maximum likelihood phylogeny associated A. triangulatus with the other Caenoplanini but Parakontikia ventrolineata and Australopacifica atrata were rejected from the Caenoplanini and associated instead with the Rhynchodemini, with Platydemus manokwari. It was found that the mitogenomes of all species of the subfamily Rhynchodeminae share several unusual structural features, including a very long cox2 gene. This is the first time that the complete paralogous rRNA clusters, which differ in length, sequence and seemingly number of copies, were obtained for a Geoplanidae.

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

BackgroundThe geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known.MethodsExperimental 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.ResultsWe 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 Sarcocystiszuoi. The phylogeny of the nuclear 18S rRNA gene placed S. muricoelognathis within the so-called S. zuoi complex, including Sarcocystisattenuati, 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.ConclusionsOur 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.Graphical

Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa.

All eight extant species ofRhabdopleuradescribed between 1869 and 2018 are provisionally accepted as valid based on a review of the literature and new data on two little-known species from the Azores. Additionally, four new species are described from the New Zealand region, increasing global diversity by 50%, and a dichotomous key to all 12 described species is provided based on morphological criteria. The distinction between colony morphologies based on erect-tube inception is regarded as particularly helpful in initial characterization of species. Erect ringed tubes are either produced directly from the surface of creeping-tubes or indirectly, i.e. a short adherent side branch from a creeping tube is interpolated between the creeping tube and an erect tube; such side branches are blind-ending. These two modes of erect-tube origination are here respectively termeddirectandindirect. Species with indirect erect-tube budding are predominant in the North Atlantic whereas species with direct erect-tube budding dominate in New Zealand waters. The only indirect-erect species from New Zealand, Rhabdopleura chathamica n. sp., was discovered on deepwater coral from 10081075 m, constituting the deepest record of the genus to date. Rhabdopleura emancipata n. sp., collected only in a detached state, constitutes a three-dimensional tangled growth that grew freely into the water columna unique morphology hitherto unknown among extant species. Owing to this growth mode, it provided a substratum for epibionts from several phyla. Rhabdopleura francesca n. sp. and Rhabdopleura decipula n. sp. are morphologically very similar but are distinguishable by their distinct placements in a phylogeny based on 16S mitochondrial and 18S nuclear rRNA genes. Phylogenetic reconstructions based on rRNA and mitochondrial genome data contribute to an updated phylogeny of all Rhabdopleura species sequenced thus far, some of which require more molecular sequences and morphological analyses for taxonomic determination.

The chloroplast and mitochondrial genomes of two Gomphonema parvulum (Bacillariophyta) environmental isolates from South Carolina (United States) and Virginia (United States).

Gomphonema parvulum is a cosmopolitan freshwater diatom that is used as an indicator in water quality biomonitoring. In this study, we report the culturing of two geographically separated isolates from southeastern North America, their morphology, and the sequencing and assembly of their mitochondrial and chloroplast genomes. Morphologically, both strains fit G. parvulum sensu lato, but the frustules from a protected habitat in South Carolina were smaller than those cited in the historic data of this species from the same location as well as a second culture from Virginia. Phylogenetic analyses using the rbcL gene placed both within a clade with G. parvulum. Genetic markers, including full chloroplast and mitochondrial genomes and the nuclear small subunit rRNA gene region were assembled from each isolate. The organellar genomes of the two strains varied slightly in size due to small differences in intergenic regions with chloroplast genomes of 121,035 bp and 121,482 bp and mitochondrial genomes of 34,639 bp and 34,654 bp. The intraspecific pairwise identities of the chloroplast and mitochondrial genomes of these two isolates were 97.9% and 95.4%, respectively. Multigene phylogenetic analysis demonstrated a close relationship between G. parvulum, Gomphoneis minuta, and Didymosphenia geminata.

Taxonomic study of the polyphyletic Dudresnaya (Dumontiaceae, Florideophyceae) with descriptions of Dudresnaya ryukyuensis sp. nov. and two new genera, Himehibirhodia and Nudresdaya

SUMMARYThe red algal genus Dudresnaya (Dumontiaceae, Gigartinales) has traditionally been a morphologically well‐defined taxon, but its molecular phylogeny has rarely been studied. To examine the phylogenetic relationships among Dudresnaya species, we generated new partial sequences of mitochondrial cox1, chloroplast rbcL and nuclear 28S rRNA genes from an undescribed Dudresnaya species from Okinawa Island, Japan, alongside five additional described species. Our phylogenetic analyses show that Dudresnaya is genetically diverse and polyphyletic. Based on molecular phylogeny and morphological data, we describe the Okinawan Dudresnaya as a new species, Dudresnaya ryukyuensis, and transferred Dudresnaya minima and Dudresnaya littleri, which were phylogenetically and morphologically distinct from the genuine Dudresnaya, to the new genera Himehibirhodia and Nudresdaya, respectively. Our phylogenetic analyses also showed that the Dumontiaceae is not a monophyletic group including the Gainiaceae and Rhizophyllidaceae (DGR complex). Considering that the DGR complex exhibits female reproductive structures and their post‐fertilization development that are similar to each other, the DGR complex appears to be recognized as the Dumontiaceae sensu lato.