scholarly journals Molecular Identification of Fungal Communities in a Soil Cultivated with Vegetables and Soil Suppressiveness toRhizoctonia solani

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Silvana Pompéia Val-Moraes ◽  
Eliamar Aparecida Nascimbem Pedrinho ◽  
Eliana Gertrudes Macedo Lemos ◽  
Lucia Maria Carareto-Alves
Keyword(s):  
Biotic Interactions ◽  
Fungal Communities ◽  
Native Forest ◽  
Metagenomic Dna ◽  
Soil Suppressiveness ◽  
Rdna Sequences ◽  
Pcr Products ◽  
Realistic View ◽  
18S Rdna Sequences ◽  
Total Dna

Fungi constitute an important part of the soil ecosystem, playing key roles in decomposition, cycling processes, and biotic interactions. Molecular methods have been used to assess fungal communities giving a more realistic view of their diversity. For this purpose, total DNA was extracted from bulk soils cultivated with tomato (STC), vegetables (SHC), and native forest (SMS) from three sites of the Taquara Branca river basin in Sumaré County, São Paulo State, Brazil. This metagenomic DNA was used as a template to amplify fungal 18S rDNA sequences, and libraries were constructed inEscherichia coliby cloning PCR products. The plasmid inserts were sequenced and compared to known rDNA sequences in the GenBank database. Of the sequenced clones, 22 were obtained from the SMS sample, 18 from the SHC sample, and 6 from the STC sample. Although most of the clone sequences did not match the sequences present in the database, individual amplified sequences matched with Glomeromycota (SMS), Fungi incertae sedis (SMS), and Neocallimastigomycota (SHC). Most of the sequences from the amplified taxa represent uncultured fungi. The molecular analysis of variance (AMOVA) indicated that fluctuations observed of haplotypes in the composition may be related to herbicide application.

scholarly journals First Report of ‘Candidatus Phytoplasma asteris’-Related Strains Infecting Lily in Mexico

Plant Disease ◽  
2008 ◽  
Vol 92 (6) ◽  
pp. 979-979 ◽  
Author(s):  
N. E. Cortés-Martínez ◽  
E. Valadez-Moctezuma ◽  
L. X. Zelaya-Molina ◽  
N. Marbán-Mendoza
Keyword(s):  
16S Rdna ◽  
The Czech Republic ◽  
First Report ◽  
Rdna Sequences ◽  
Flower Abortion ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Total Dna ◽  
Nested Pcr Assays ◽  
Symptomatic Plant

In recent years, lily (Lilium spp.) has become an important ornamental crop in diverse regions of Mexico. Since 2005, unusual symptoms have been observed on lily plants grown from imported bulbs in both greenhouse and production plots at San Pablo Ixayo, Boyeros, and Tequexquinauac, Mexico State. Symptoms included a zigzag line pattern on leaves, dwarfism, enlargement of stems, shortened internodes, leaves without petioles growing directly from bulbs, air bulbils, death of young roots, atrophy of flower buttons, and flower abortion. Symptoms were experimentally reproduced on healthy lily plants by graft inoculation. Total DNA was extracted from 50 diseased, 10 symptomless, and 10 graft-inoculated plants by the method of Dellaporta et al. (2). DNA samples were analyzed for phytoplasma presence by two different nested PCR assays. One assay employed ribosomal RNA gene primer pair P1/P7 followed by R16F2n/R16R2 (1), whereas ribosomal protein (rp) gene primer pairs rpF1/rpR1 and rp(I)F1A/rp(I)R1A (4) were used in a second assay. A DNA fragment approximately 1.2 kb long was consistently amplified from all symptomatic plant samples only by both assays. A comparative analysis of 16S rDNA sequences (Genbank Accession Nos. EF421158–EF421160 and EU124518–EU124520) and rp gene sequences (EU277012–EU277014), derived from PCR products, revealed that phytoplasma infecting lily were most similar (99.9% to 16S rDNA and 99.7% to rp) to carrot phytoplasma sp. ca2006/5 and also were similar (99.8% to 16SrDNA and 99.2% to rp) to broccoli phytoplasma sp. br273. Both carrot and broccoli phytoplasmas were classified as members of aster yellow 16S rDNA restriction fragment length polymorphism subgroup 16SrI-B (3). Although infection of lilies by aster yellows (‘Ca. phytoplasma asteris’) subgroup 16SrI-B and 16SrI-C was reported from the Czech Republic and Poland, to our knowledge, this is the first report of ‘Ca. phytoplasma asteris’-related strains associated with lily plants in Mexico. References: (1) R. F. Davis et al. Microbiol. Res. 158:229, 2003. (2) S. L. Dellaporta et al. Plant Mol. Biol. Rep. 1:19, 1983. (3) B. Duduk et al. Bull. Insectol. 60 2:341, 2007. (4) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004.

scholarly journals SEQUENCE ANALYSIS OF 18s DNA OF Melosira sp., Dunaliella sp., Isochrysis sp. AND Porphyridium sp.

2015 ◽  
Vol 2 (1) ◽  
pp. 592
Author(s):  
Lucia Kusumawati ◽  
Ruben Wahyudi ◽  
Reinhard Pinontoan ◽  
Maria Gorreti Lily Panggabean
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Rdna Sequences ◽  
Pcr Products ◽  
18S Rdna Sequences ◽  
Pcr Method ◽  
High Level

<p>Phytoplankton has high level of biodiversity. In previous years phytoplankton was identified by their morphological characters. However, their morphology might change in different environments. These difficulties can be overcome by comparing their 18S rDNA sequences. This research is aimed to verify the identity of Melosira sp., Dunaliella sp., Isochrysis sp. and Porphyridium sp. Here, PCR method was used to amplify 18s DNA sequences. Three primer pairs were used, i.e. 18S-F and 18S-R; 501F and 1700R; 18S-2F and 18S-2R. PCR products were sequenced. MEGA5 was used to make phylogenetic tree. Genus verification for Isochrysis sp., Dunaliella sp. and Melosira sp. were conducted successfully using Blast and phylogenetic tree. 18s DNA sequence of Porphyridium sp. shows an interesting result and needs further verification.</p><p><br /><strong>Keywords</strong>: Phytoplankton, Melosira sp., Dunaliella sp., Isochrysis sp., Porphyridium sp.</p>

scholarly journals Phylogeny of the Thoracican Barnacles Based on 18S rDNA Sequences

2000 ◽  
Vol 20 (2) ◽  
pp. 393-398 ◽  
Author(s):  
D. James Harris ◽  
Laura S. Maxson ◽  
Lee F. Braithwaite ◽  
Keith A. Crandall
Keyword(s):  
18S Rdna ◽  
Rdna Sequences ◽  
18S Rdna Sequences

Assessing the Biodiversity of Monoraphidium Using 18S rDNA Sequences

2002 ◽  
Vol 38 (s1) ◽  
pp. 9-9
Author(s):  
M. W. Fawley ◽  
K. P. Fawley ◽  
M. L. Dean
Keyword(s):  
18S Rdna ◽  
Rdna Sequences ◽  
18S Rdna Sequences

scholarly journals Sarcocystis Attenuati N. Sp. (Apicomplexa: Sarcocystidae) Infecting the Asian Gray Shrew, Crocidura Attenuata (Insectivora: Soricidae), in China

2021 ◽  
Author(s):  
junjie hu ◽  
Jun Sun ◽  
Yanmei Guo ◽  
Hongxia Zeng ◽  
Yunzhi Zhang ◽  
...  
Keyword(s):  
Host Specificity ◽  
Definitive Host ◽  
18S Rdna ◽  
Common Species ◽  
Molecular Characteristics ◽  
Intermediate Hosts ◽  
Parasite Life Cycle ◽  
Rdna Sequences ◽  
Transmission Electron ◽  
18S Rdna Sequences

Abstract Background: There are limited data on Sarcocystis in insectivores. The Asian gray shrew, Crocidura attenuata, is one of the most common species of insectivores in the family Soricidae distributed in South Asia and Southeast Asia. To date, Sarcocystis has never been recorded in this host.Methods: Tissues from 42 Asian gray shrews were collected in China in 2017 and 2018. Sarcocysts were observed using light (LM) and transmission electron microscopy (TEM). To complete the parasite life cycle, muscle tissues of the host infected with sarcocysts were force-fed to two beauty rat snakes, Elaphe taeniura. Individual sarcocysts from different Asian gray shrews and oocysts/sporocysts isolated from the small intestines and feces of the experimental snakes were selected for DNA extraction, and seven genetic markers, including two nuclear loci (18S rDNA and ITS1), three mitochondrial genes (cox1, cox3 and cytb), and two apicoplastic genes (rpoB and clpC), were amplified, sequenced and analyzed.Results: Sarcocysts were found in 17 of 42 (40.5%) Asian gray shrews. Under LM, the microscopic sarcocysts were exhibited saw-tooth-like protrusions measuring 3.3–4.5 μm. Ultrastructurally, the sarcocyst wall contained numerous lancet- or leaf-like villous protrusions, similar to type 9h. The experimental beauty rat snakes shed oocysts/sporcysts measuring 11.9–16.7 × 9.2–10.6 μm with a prepatent period of 10 to 11 days. Comparing these sequences with those previously deposited in GenBank revealed that the 18S rDNA sequences and cox1 sequences shared the highest similarity with those of S. scandentiborneensis recorded in tree shrews, Tuaia minor and T. tana (i.e., 97.6–98.3% and 100% identity, respectively). Phylogenetic analysis based on 18S rDNA, ITS1 or cox1 sequences revealed that this parasite formed an independent clade with Sarcocystis spp. that utilize small animals as intermediate hosts and snakes as the known or presumed definitive host. On the basis of morphological and molecular characteristics and host specificity, the parasite was proposed as a new species, named S. attenuati.Conclusions: Sarcocysts were recorded in Asian gray shrews for the first time. The sarcocysts were characterized morphologically and molecularly. The 18S rDNA and cox1 sequences of S. attenuati, named in the present study, shared the highest identities with those of S. scandentiborneensis. However, the sarcocysts of the two species of Sarcocystis were quite different under LM and TEM. Based on experimental infection, beauty rat snakes have been proven to be a definitive host of S. attenuati. As more species of Sarcocystis from insectivores and other small mammals are properly morphologically and molecularly characterized, we may gain a better understanding of the biodiversity, host specificity and evolution of Sarcocystis in the future.

scholarly journals Unexplored diversity of microscopic myxomycetes: evidence from environmental DNA

2019 ◽  
Vol 152 (3) ◽  
pp. 499-506 ◽  
Author(s):  
Oleg N. Shchepin ◽  
Martin Schnittler ◽  
Nikki H.A. Dagamac ◽  
Dmitry V. Leontyev ◽  
Yuri K. Novozhilov
Keyword(s):  
New Species ◽  
18S Rdna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Environmental Dna ◽  
Full Length ◽  
Detection Techniques ◽  
Rdna Sequences ◽  
18S Rdna Sequences ◽  
Environmental Sequences

Background and aims – Recent studies showed the position of two slime mould species with microscopic sporocarps, Echinosteliopsis oligospora and Echinostelium bisporum, within the class Myxomycetes. These minute species are seldom seen in studies based on detection of sporocarps and can easily be confused with protosteloid amoebozoans.Methods – We searched all published ePCR data sets that targeted myxomycete 18S rDNA for the presence of environmental sequences similar to E. oligospora and Echinosteliales in traditional circumscription, and performed phylogenetic analyses that included short environmental sequences and full-length 18S rDNA sequences representing all the major groups of myxomycetes.Key results – We report 19 unique sequences which are closely related to E. bisporum or E. oligospora based on sequence similarity (73.1–95.2% similarity) and which form well-supported monophyletic clades with these species in phylogenetic analyses. They may represent new species that are not yet described. Our phylogeny based on full-length 18S rDNA sequences further confirms the position of E. bisporum and E. oligospora within myxomycetes and the paraphyly of the order Echinosteliales in its traditional circumscription.Conclusions – Our results show that ePCR-based studies can reveal myxomycete taxa that often escape detection by traditional approaches, including potentially new species, and thus provide valuable new data on diversity and ecology of myxomycetes. As such, strategies for studying myxomycetes biodiversity should be revised, focusing also on molecular detection techniques in addition to the sporocarp-based ones.

Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

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