Large Subunit Ribosomal RNA Gene Research Articles

Chloroplast Dual Divergent Promoter Plasmid for Heterologous Protein Expression in Tetraselmis suecica (Chlorophyceae, Chlorodendrales).

The eukaryotic green microalga Tetraselmis suecica is commonly used for aquaculture purposes because of its high stress tolerance and ease of culture in a wide spectrum of environments; they are therefore suitable candidates for biotechnology applications. To date, no data are available regarding chloroplast transformation vectors based on specific endogenous promoters and homologous targeting regions. We report on the identification of Tetraselmis suecica genes encoding the ribulose bisphosphate carboxylase/oxygenase large subunit protein, the photosystem II D1 protein and the ATP synthase CF1-beta subunit protein together with their untranslated regions (5'UTR, 3'UTR). The full-length ORFs of the putative genes with their regulatory sequences were obtained. We were also able to identify the downstream 3' end of the large subunit ribosomal RNA gene (23S) along with the 5S RNA end-to-end with the psbA gene on the complementary strand. The intergenic region between these genes appears to be a good target site for the integration of target proteins. Moreover, we identified a back-to-back promoter region among the rbcL and atpB genes. To assess the bidirectionality activities of both promoters, a dual reporter vector was constructed for Tetraselmis suecica transformation containing the cat and TurboGFP genes driven by the 5'rbcL/5'atpB divergent promoter. The vector included the 23S-5S and psbA nucleotide sequences as flanking regions. These flanking regions provided suitable insertionsites within the chloroplast genome forcassette integration via homologous recombination.Simultaneous expression of the chloramphenicol-resistant conferring gene and the gene coding for TurboGFP driven by 5'rbcL/5'atpB showed a potent natural bidirectional promoter as a reliable genetic tool.

Five Fungal Pathogens Are Responsible for Bayberry Twig Blight and Fungicides Were Screened for Disease Control.

Bayberry (Myrica rubra) is a commercial fruit in China. For the past seven years, twig blight disease has been attacking bayberry plantations in Shantou City, Guangdong Province, China, leading to destructive damage and financial loss. In this study, five fungal species associated with twig dieback and stem blight were identified based on morphological characteristics combined with multilocus sequence analysis (MLSA) on the internal transcribed spacer (ITS) region, partial sequences of β-tubulin (tub2), translation elongation factor 1-α (tef1-α), large subunit ribosomal RNA (LSU) and small subunit ribosomal RNA (SSU) genes, which are Epicoccum sorghinum, Neofusicoccum parvum, Lasiodiplodia theobromae, Nigrospora oryzae and a Pestalotiopsis new species P. myricae. P. myricae is the chief pathogen in fields, based on its high isolation rate and fast disease progression after inoculation. To our knowledge, this is the first study reporting the above five fungi as the pathogens responsible for bayberry twig blight. Indoor screening of fungicides indicates that Prochloraz (copper salt) is the most promising fungicide for field application, followed by Pyraclostrobin, 15% Difenoconazole + 15% Propiconazole, Difenoconazole and Myclobutanil. Additionally, Bacillus velezensis strain 3–10 and zeamines from Dickeya zeae strain EC1 could be used as potential ecofriendly alternatives to control the disease.

Identification and lipolytic activity of yeasts isolated from foods and wastes

ABSTRACT Thirty-three yeasts were isolated from palm oil industrial wastes and traditional fermented foods in Thailand. Based on the analysis of the sequences of the D1/D2 region of the large subunit ribosomal RNA gene (LSU rDNA) and their phenotypic characteristics, they were identified as Pichia kudriavzevii (11 isolates), Candida ethanolica (1 isolate), Clavispora lusitaniae (2 isolates), Ogataea polymorpha (1 isolate), Hanseniaspora opuntiae (1 isolate), Lodderomyces elongisporus (1 isolate), Saccharomyces cerevisiae (2 isolates), C. tropicalis (5 isolates), Yarrowia lipolytica (2 isolates), Magnusiomyces ingens (1 isolate), and Magnusiomyces capitatus (3 isolates), Trichosporon insectorum (1 isolate), and Trichosporon asteroides (2 isolates). Seven strains, T. insectorum 4E-1D, M. capitatus 5E-1T and 5E-2D, T. asteroides 8E-1T and 8E-1D, and Y. lipolytica Fy-12 and Fy-13, showed high lipolytic activity ranged from 5.21 ± 0.09 to 45.68 ± 2.37 U/mL. Moreover, these seven strains exhibited good lipolytic activity after culturing in the medium containing palm oil (11.79 ± 0.67 to 28.19 ± 4.84 U/mL) and soy oil (9.14 ± 1.08 to 22.97 ± 0.69 U/mL) as lipase inducers. The result of this study suggests that the palm oil industrial wastes and Thai fermented foods could be promised as the invaluable sources of lipolytic yeasts.

Two new Microascus species with spinous conidia isolated from pig farm soils in China

Abstract Two scopulariopsis-like fungi were isolated when surveying fungi in pig farm soils in China. Sexual structures of these fungi were not observed and their conidia had spinous walls. Phylogenetic analysis based on nucleotide sequences of the internal transcribed spacer 1 and 2 and intervening 5.8S ribosomal RNA gene (ITS), large subunit ribosomal RNA gene (LSU), beta-tubulin (tub2) and translation elongation factor 1-alpha (tef1) gene showed that they were new members of the genus Microascus, and the name M. aculeatus and M. spinosporus were introduced. Genetically the two new species clustered in a well-supported clade close to M. longicollis, but differed in producing relatively long branches. Morphologically M. aculeatus could be distinguished by its conidia with sparse but long spines; M. spinosporus resembled three species of the genus Scopulariopsis, S. asperula, S. brevicaulis and S. flava, but was different in the color of colony and conidia, and the form of conidiophores.

Morphological and genetic description of Moniliformis necromysi sp. n. (Archiacanthocephala) from the wild rodent Necromys lasiurus (Cricetidae: Sigmondontinae) in Brazil

A new species of Moniliformis Travassos, 1915 (Acanthocephala: Moniliformidae) is described from the hairy-tailed bolo mouse, Necromys lasiurus Lund, 1840 (Cricetidae: Sigmondontinae), captured in the Brazilian Cerrado, in Uberlândia, state of Minas Gerais, Brazil. The specimens were studied by light and scanning electron microscopy. Molecular phylogenies were inferred from partial nuclear large subunit ribosomal RNA gene sequences and partial mitochondrial cytochrome c oxidase subunit I gene. The new species is distinguished from other moniliformid species by the number of rows and number of hooks per row, size of the proboscis, size of the eggs, host species and geographical distribution. Molecular phylogenies and genetic distances analyses demonstrated that Moniliformis necromysi sp. n. forms a well-supported monophyletic group with sequences of other species of Moniliformis and is distinguished from them, which agrees with the morphological characteristics, allocating the new species to this genus and to the family Moniliformidae Van Cleave, 1924. This is the first moniliformid acanthocephalan described from a wild rodent in Brazil.

Grease Waste as a Reservoir of Lipase-Producing Yeast and Description of Limtongella siamensis gen. nov., sp. nov.

A total of 175 yeast isolates were obtained from grease samples. Based on the D1/D2 region of the large subunit (LSU) ribosomal RNA (rRNA) gene analysis, 150 yeast isolates were identified as belonging to 36 described yeast species, whereas 25 isolates required more analysis. Among the described species, Rhodotorula mucilaginosa was the only Basidiomycetous yeast, whereas 149 isolates were identified as belonging to 35 described species of 15 genera in the phylum Ascomycota, and Candida tropicalis was the most abundant species. A study of lipase production indicated that strain DMKU-JMGT1-45 showed volumetric activity of 38.89 ± 9.62 and 155.56 ± 14.70 U/mL when grown in yeast extract malt extract (YM) and YM supplemented with 1% olive oil, respectively. In addition, this strain intracellularly accumulated lipid, of which the fatty acid profile revealed the major fatty acids to be 39.9% oleic acid (C18:1), 27.61% palmitoleic acid (C16:1) and 14.97% palmitic acid (C16:0). A phylogenetic analysis of the combined multi-locus gene sequences showed that the strains DMKU-JMGT1-45T and DMKU-JMGT4-14 formed a well-separated lineage and could not be assigned to any of the currently recognized genera of the Saccharomycetales. Limtongella siamensis gen. nov., sp. nov. is therefore proposed to accommodate these two strains as members of the order Saccharomycetales.

Occurrence and Molecular Identification of Wild Yeasts from Jimma Zone, South West Ethiopia.

Yeasts are common inhabitants of most fruit trees’ rhizospheres and phyllospheres. Wild yeasts are the major driving force behind several modern industrial biotechnologies. This study focused on determining the occurrence and frequency of wild yeasts associated with domestic and wild edible tree barks, fruits, and rhizosphere soil samples collected over two seasons (i.e., spring and summer) in South West Ethiopia. A total of 182 yeast strains were isolated from 120 samples. These strains belonged to 16 genera and 27 species as identified based on the sequence analysis of the D1/D2 domain of the large subunit (26S) ribosomal RNA gene. Candida blattae, Pichia kudriavzevii, Candida glabrata, Saccharomyces cerevisiae, and Candida humilis were the most dominant yeast species isolated from the bark samples. Only Pichia kudriavzevii was regularly detected from the bark, rhizosphere, fruit, and sugarcane samples. The retrieval of yeasts from bark samples was more frequent and diverse than that of soil, fruits, and sugarcane. The frequency of detection of yeasts during the spring was significantly higher than in the summer season. However, there was no significant seasonal variation in the frequency of detection of yeast species between the rhizosphere and phyllosphere samples.

Genetic variability on worldwide populations of the scale insect Pulvinariella mesembryanthemi

The South African scale insect Pulvinariella mesembryanthemi was introduced worldwide in several coastal areas with Mediterranean climate, probably through infested plants of Carpobrotus sp. Its high host specificity and its capacity to produce severe damages in the invasive Carpobrotus sp. plants makes this insect a potential biocontrol agent. To test the efficiency and host range of insects used for biocontrol, population genetic studies can help to unravel cryptic complexes and intraspecific diversity. In this study we performed a genetic analysis including native and exotic populations of P. mesembryanthemi, through Sanger sequencing of mitochondrial (cytochrome c oxidase I, COI) and ribosomal (D2–D3 expansion segments of the large subunit ribosomal RNA gene 28S) gene fragments. Accidentally, an endosymbiont was sequenced with one of the pair of primers used. The exotic populations of the insect did not show any variability among populations for both studied genes, which suggest a common origin of all studied introduced populations. Contrastingly, native populations showed high variability and seemed to be a cryptic species complex. Moreover, the Gauteng populations (from NE South Africa) were phylogenetically the closest to the exotic ones, suggesting that the exotic populations could be original from somewhere near this area. An endosymbiont of P. mesembryanthemi was detected, and the sequenced coxA gene was similar to that of the Rickettsiaceae family from the α-Proteobacteria, and close to other insect endosymbionts. To the best of our knowledge, this was the first mention of this endosymbiont in P. mesembryanthemi, although α-Proteobacteria endosymbionts have been reported for other sap-sucking insects.

The High Diversity and Variable Susceptibility of Clinically Relevant Acremonium-Like Species in China.

Acremonium-like fungi are emerging as important opportunistic pathogens in cutaneous, subcutaneous and serious invasive infections, especially in immunocompromised and debilitated individuals, and Acremonium infections are usually resistant to antifungal therapy. Several molecular studies have demonstrated that many species in the genus Acremonium are polyphyletic, and currently, the genus is restricted to the family Bionectriaceae (Hypocreales). Molecular identification and in vitro antifungal susceptibility tests of Acremonium-like fungi isolated from human clinical specimens in China were performed in this study. Three genetic loci: the large subunit ribosomal RNA gene (LSU), ribosomal internal transcribed spacer and elongation factor 1-α (EF1-α), were used to assess their taxonomic position for correct identification among various species. The multilocus study of twenty-eight strains showed that these strains were distributed in three main lineages: egyptiacum, Cordycipitaceae and Sarocladium; Acremonium egyptiacum and Sarocladium kiliense were the main species of these strains, and three isolates were too phylogenetically distant to be considered undescribed species. Relatively low minimum inhibitory concentrations (MICs) of 0.25-2 and 0.031-0.5μg/mL were found for voriconazole and terbinafine for most species, respectively. Varied antifungal activities of ciclopirox olamine, amorolfine and posaconazole were found in our study. However, no antifungal effect of sertaconazole, itraconazole or fluconazole was observed against most strains. This is the first study on Acremonium-like species diversity by multilocus sequence analyses and antifungal susceptibility of clinically relevant isolates in China.

Metschnikowia miensis f.a., sp. nov., isolated from flowers in Mie prefecture, Japan.

Four yeast strains (RIFY 10001T, RIFY 10002, RIFY 10003, and RIFY 10004) were isolated from flowers growing in fields of mustard and broad beans in Japan. Ascospore formation was not observed. Sequence analysis of the D1/D2 domain of the large subunit ribosomal RNA (LSU rRNA) gene of the four strains indicated that they belong to the genus Metschnikowia and are closely related to Metschnikowia hawaiiana strain CBS 9146T and Metschnikowia orientalis strain CBS 10331T. The D1/D2 domain of the LSU rRNA gene and internal transcribed spacer regions of strain RIFY 10001T were 85.7% identical to those of M. hawaiiana strain CBS 9146T. All four strains were distinguished from the M. hawaiiana strain CBS 9146T by their inability to ferment glucose. Hence, these four strains are novel species and were named as Metschnikowia miensis (holotype: RIFY 10001T; isotypes: NBRC 112445T = CBS 14749T).

New morphological and genetic data of Gigantorhynchus echinodiscus (Diesing, 1851) (Acanthocephala: Archiacanthocephala) in the giant anteater Myrmecophaga tridactyla Linnaeus, 1758 (Pilosa: Myrmecophagidae).

Gigantorhynchus echinodiscus (Diesing, 1851) is a parasite of anteaters in South America. Although described by Diesing in 1851, there is still a lack of taxonomic and phylogenetic information regarding this species. In the present study, we redescribe G. echinodiscus collected from a giant anteater, Myrmecophaga tridactyla Linnaeus, 1758, from the Brazilian Cerrado (Savannah) in the State of São Paulo by light and scanning electron microscopy. In addition, phylogenies were inferred from partial DNA gene sequence of the nuclear large subunit ribosomal RNA gene (28S rRNA). We provide for the first time details of the proboscis with a crown having 18 large hooks and numerous small hooks, a lateral papilla at the base of the proboscis, a ringed pseudo-segmented body, large testes, cemented glands in pairs, and a non-segmented region in the posterior end of the body, which contributed to the diagnosis of the species. Molecular phylogenetic analyses recovered G. echinodiscus forming a well-supported monophyletic group with Mediorhynchus sp., which was congruent with morphological studies that allocate both genera within the family Gigantorhynchidae. In conclusion, the present work adds new morphological and molecular information, emphasizing the importance of adopting integrative taxonomic approaches in studies of Acanthocephala.

Molecular phylogeny of the parasitic dinoflagellate Syltodinium listii (Gymnodiniales, Dinophyceae) and generic transfer of Syltodinium undulans comb. nov. (= Gyrodinium undulans)

The parasitic dinoflagellate Syltodinium listii was investigated from the open waters of the English Channel, southern North Sea and the NW Mediterranean Sea. Syltodinium listii has been unreported since its original description in the North Sea. Cells of S. listii were able to infect copepod eggs of different species, and even nauplii, and after each infection formed up to 32 cells embedded in a mucous envelope. Infection of the same host by more than one dinoflagellate was frequent; although overall, the progeny were reduced in number. Molecular phylogeny based on the small subunit ribosomal RNA (SSU rRNA) gene revealed that S. listii clusters with a group of environmental sequences from the cold North Atlantic region as a sister group of Gymnodinium aureolum. The large subunit ribosomal RNA (LSU rRNA) gene sequences of S. listii from the English Channel and cf. Gyrodinium undulans from the Mediterranean Sea were identical. Thus, we propose Syltodinium undulans comb. nov. for Gyrodinium undulans. The first internal transcribed spacer (ITS) and complete SSU rRNA gene sequences of Dissodinium pseudolunula are provided. The parasitic species of Chytriodinium, Dissodinium and Syltodinium cluster together within the family Chytriodiniaceae, including the free-living species Gymnodinium aureolum, G. corollarium and G. plasticum.

Heterocephalacria mucosa sp. nov., a new basidiomycetous yeast species isolated from a mangrove forest in Thailand.

Strains of yeast were isolated under a nitrogen-depleted culture condition from decaying tree bark (strain N-12.1) and from mangrove forest water (strain 1-7W.1) sampled at different locations within a mangrove forest site in Ranong province, Thailand. They were found to be genetically and phenotypically different from any currently recognised yeast species. Phylogenetic analysis of nucleotide sequence of three genes, the internal transcribed spacer region 1 and 2 plus 5.8S ribosomal RNA gene (ITS), D1/D2 domain of the large subunit ribosomal RNA gene (LSU D1/D2) and the small subunit of the ribosomal RNA gene (SSU), revealed that these two strains were related to but distinguished from Heterocephalacriaarrabidensis. Several distinct physiological characteristics of these two strains were detected, namely inability to assimilate glycerol, dl-lactic acid, succinic acid, citric acid, d-gluconic acid, and ability to grow well at 25 °C, which were different from those of H. arrabidensis. Accordingly, the name Heterocephalacria mucosa sp. nov., is proposed to accommodate this novel species. The MycoBank number is MB 828624.

Spencerozyma acididurans sp. nov., an acid-tolerant basidiomycetous yeast species isolated from acid mine drainage

Strain SYSU-17, representing a novel acid-tolerant yeast species which can grow at pH 2.0 weakly, was isolated from acid mine drainage collected in a tailing impoundment of the Fankou Lead/Zinc Mine, Guangdong Province, PR China. Phylogenetic analysis of strain SYSU-17 based on the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit ribosomal RNA (LSU rRNA) gene suggested that strain SYSU-17 was a novel species belonging to the genus Spencerozyma (class Microbotryomycetes, subphylum Pucciniomycotina). It differed from the type strain of the closest related species, Spencerozyma crocea CBS 2029T, by 0.7 % sequence divergence (three gaps and one nucleotide substitution out of 594 bp) in the D1/D2 domains of the LSU rRNA gene and 7.6 % sequence divergence (32 gaps and 22 nucleotide substitutions out of 714 bp) in the ITS region. In contrast to the physiological properties of S. crocea, the novel yeast species was unable to assimilate galactose, d-ribose, xylitol, succinate, d-xylose, ethanol, nitrate and nitrite. The name Spencerozyma acididurans sp. nov. is proposed and SYSU-17 is designated as the holotype.

Use of Markers to Determine Cryptosporidium Genotypes for Epidemiology Tracking and Detection.

Polymerase chain reaction (PCR) enables amplification of specific DNA fragments for the detection and tracking of Cryptosporidium spp. Newly obtained DNA are compared to an ever-growing database of Cryptosporidium sequences with uncertain or outdated metadata in primary public repositories (i.e., EMBL/DDBJ/GenBank). Here, we describe standard operating procedures to obtain DNA sequences from Cryptosporidium spp. marker genes. Small-subunit ribosomal RNA gene, large-subunit ribosomal RNA gene, and glycoprotein 60 are amplified using conventional PCR. Amplified and sequenced genes are compared to a reference library of up-to-date curated gene sequences to identify Cryptosporidium species and variants.

Occurrence of leaf spot disease caused by Neopestalotiopsis clavispora on Taxus chinensis in China

AbstractTaxus chinensis is a valuable tree with uses for timber, medicinal, ornamental and landscape purposes. Most importantly, it is a source of the anti‐cancer drug paclitaxel. In 2016, needle spot disease was observed on T. chinensis in Fujian Province of China. Five isolates of similar morphology were isolated from diseased samples. The pathogen was identified as Neopestalotiopsis clavispora based on morphological and cultural characteristics and confirmed by sequence analysis of the internal transcribed spacer region (ITS) and the large subunit ribosomal RNA gene (LSU). The pathogenicity of the isolates was confirmed by fulfilling Koch's postulates. To the best of our knowledge, this is the first report to indicate that the causal agent of needle spot disease on Chinese yew in China is N. clavispora.

First Report of Laurel Wilt Disease Caused by Raffaelea lauricola on Swamp Bay in Louisiana

In the past two decades, laurel wilt disease has significantly affected members of the Lauraceae in the southeast United States, causing widespread mortality of native redbay (Persea borbonia (L.) Spreng), and incidence of infections in avocado (Persea americana Mill.), sassafras (Sassafras albidum L.) and swamp bay (Persea palustris [Raf.] Sarg.) (Fraedrich et al., 2008, 2015, Olatinwo, et al. 2019). Laurel wilt is a vascular disease caused by Raffaelea lauricola (T.C. Harr., Fraedrich & Aghayeva), a fungus vectored by a non-native ambrosia beetle Xyleborus glabratus Eichhoff (Fraedrich et al. 2008). In August 2020, we investigated the mortality of a spicebush shrub (Lindera benzoin L.) (3.8 cm diameter at root collar, two m height) located ca. 17 mi northeast of Colfax, Grant Parish, Louisiana (31.750263° N, -92.643694° W). Evaluation of the dead shrub revealed brown, persistent foliage, and black vascular discoloration of the sapwood, typical symptoms of laurel wilt (Fig. S1). Although, beetle holes were observed on the sapwood, no beetle was found in galleries at the time. In the laboratory, a fungus consistently isolated from surface-sterilized sapwood tissues plated on potato dextrose agar (PDA) was identified as R. lauricola based on the morphological characteristics of the isolate (i.e., mucoid growth, conidiophores, and oblong/ovoid shape conidia [Harrington et al. 2008]). The fungal isolate was denoted as SB1. The identity of the fungus was confirmed by positive PCR amplification of the large subunit ribosomal RNA gene region using species-specific primers; rab-lsu-rl_F: CCCTCGCGGCGTATTATAG and rab-lsu-rl_R: GCGGGGCTCCTACTCAAA (Olatinwo, unpublished). The sequence of the isolate SB1 (GenBank Accession no. MW207371) showed 100% homology to the R. lauricola strain CBS 127349 sequence (GenBank Accession no. MH877933). The pathogenicity of SB1 on spicebush was evaluated on four healthy shrubs (average: 1 m height and 40 mm in diameter) at the location from which the original detection was made. Stems of two spicebush shrubs were inoculated with SB1 agar plugs from a 14-day old culture on PDA, while plain PDA plugs were used on the remaining two shrubs as non-inoculated controls. Agar plugs were placed in 5 mm (0.2 in) diameter hole punched on the bark with cork-borer as described by Mayfield et al (2008). After six weeks, the R. lauricola inoculated shrubs were wilted with noticeable blackened tissue discoloration in the sapwood, while the control trees remained healthy (Fig. S2). Raffaelea lauricola was re-isolated from tissue of the two inoculated, symptomatic shrubs, but not from the control trees. The sequence of the re-isolated R. lauricola isolate, denoted as SB3 (GenBank Accession no. MW207372), showed 100% homology to the R. lauricola strain CBS 127349 and isolate SB1. This first documentation of laurel wilt on spicebush in Louisiana is significant because, spicebush berries, leaves, and twigs are food sources for forest animals, birds, and insects including whitetail deer and spicebush swallowtail (Papilio troilus L.). Since its first report on sassafras in 2014 (Fraedrich et al. 2015), laurel wilt has spread across Louisiana on sassafras and swamp bay (Olatinwo et al. 2019) and has been confirmed in14 parishes. This report shows the relentless nature of the disease, as the pathogen moves from one vulnerable host to the next, expanding into new locations and threatening forest ecosystems across the southern United States.

New evidence of nematode-endosymbiont bacteria coevolution based on one new and one known dagger nematode species of Xiphinema americanum-group (Nematoda, Longidoridae).

Three populations of Xiphinema primum n. sp. and two populations of X. pachtaicum were recovered from natural forests and cultural regions of northern Iran. Both species belong to the X. americanum-group and were characterized by their morphological, morphometric and molecular data. The new species, which was recovered in three locations, belongs to the X. brevicolle-complex and is characterized by 2124–2981 μm long females with a widely rounded lip region separated from the rest of the body by a depression, 103–125 μm long odontostyle, two equally developed genital branches with endosymbiont bacteria inside the ovary, which are visible under light microscope (LM), vulva located at 51.8–58.0%, the tail is 26–37 μm long with a bluntly rounded end and four juvenile developmental stages. It was morphologically compared with nine similar species viz. X. brevicolle, X. diffusum, X. incognitum, X. himalayense, X. luci, X. parabrevicolle, X. paramonovi, X. parataylori and X. taylori. The second species, X. pachtaicum, was recovered in two geographically distant points close to city of Amol. Molecular phylogenetic studies of the new species were performed using partial sequences of the D2-D3 expansion segments of the large subunit ribosomal RNA gene (LSU rDNA D2-D3), the internal-transcribed spacer rDNA (ITS = ITS1+5.8S+ITS2), and the mitochondrial cytochrome c oxidase I gene (COI mtDNA) regions. The Iranian population of X. pachtaicum was also phylogenetically studied based upon its LSU rDNA D2-D3 sequences. Both species were also inspected for their putative endosymbiont bacteria. Candidatus Xiphinematobacter sp. was detected from two examined populations of the new species, whereas the second endosymbiont bacterium, detected from three examined isolates of X. pachtaicum, was related to the plant and fungal endosymbionts of the family Burkholderiaceae. The phylogenetic analyses of the two endosymbiont bacteria were performed using partial sequences of 16S rDNA. In cophylogenetic analyses, significant levels of cophylogenetic signal were observed using both LSU rDNA D2-D3 and COI mtDNA markers of the host nematodes and 16S rDNA marker of the endosymbiont bacteria.

Basidiobolus haptosporus-like fungus as a causal agent of gastrointestinal basidiobolomycosis.

Basidiobolus species were isolated from colonic biopsy samples of patients with gastrointestinal basidiobolomycosis (GIB) in southern Saudi Arabia. Isolated fungi were initially identified using classical mycological tools and confirmed by sequence analysis of the large subunit ribosomal RNA gene. Phenotypic tests revealed zygomycete-like fungi which conform to those of Basidiobolus species. Five sequenced strains formed a monophyletic clade in the 28S ribosomal RNA gene phylogenetic tree. They shared 99.97% similarity with B. haptosporus and 99.97% with B. haptosporus var. minor, and relatively lower similarity with B. ranarum (99.925%). The study suggests a new and a serious causal agent of GIB related to Basidiobolus haptosporus. These isolates are not related to B. ranarum, which is commonly linked to this disease.

Genetic diversity and metapopulation structures of two intertidal species along the coast of Zhejiang, China: implications for conservation

To priority areas for conservation in the coast of Zhejiang, this study attempts to map the spatial patterns of the intra-specific genetic diversity of two intertidal species, Septifer virgatus and Tetraclita japonica, using the sequences of mitochondrial DNA cytochrome oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA) genes. In total, 129 and 112 specimens were collected from 12 and 11 populations for S. virgatus and T. japonica, respectively. These two species revealed congruent population historical signals, including (1) high levels of haplotype diversity and low values of nucleotide diversity, (2) post-LGM expansion, (3) the lack of population genetic structure, sharing haplotypes over all sampling populations, (4) gene flow connections, and (5) migration directions. Largely, all results supported that all sampling populations could be divided into two main metapopulations, exhibiting a northern and southern distribution. The north metapopulation could be considered as a marine protected area. The genetic patterns of the two species should be considered in the management and conservation in the islands along the Zhejiang, China.