scholarly journals Can ITS sequence data identify fungal endophytes from cultures? A case study from Rhizophora apiculata

mycosphere ◽  
2017 ◽  
Vol 8 (10) ◽  
pp. 1869-1892 ◽  
Author(s):  
M Doilom
2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.


2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.


Phytotaxa ◽  
2021 ◽  
Vol 514 (3) ◽  
pp. 247-260
Author(s):  
KASUN THAMBUGALA ◽  
DINUSHANI DARANAGAMA ◽  
SAGARIKA KANNANGARA ◽  
THENUKA KODITUWAKKU

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.


Phytotaxa ◽  
2021 ◽  
Vol 487 (1) ◽  
pp. 56-64
Author(s):  
DIANA S. MARASINGHE ◽  
SINANG HONGSANAN ◽  
SARANYAPHAT BOONMEE ◽  
NING XIE

A novel species, Micropeltis goniothalamicola and a new record Scolecopeltidium menglaense were collected from Mae Fah Luang Botanical Gardens, Thailand. Our new taxon is different from other species in Micropeltis in having relatively smaller ascomata, 6–8-spored asci and 4–5-septate ascospores covering with mucilaginous sheath. Our new record, S. menglaense is the first host recorded from Jasmine grandiflorum (Oleaceae). Morphological comparison coupled with phylogenetic analysis of combined LSU and ITS sequence data provide evidence for the new species and new host record.


Phytotaxa ◽  
2018 ◽  
Vol 369 (4) ◽  
pp. 241 ◽  
Author(s):  
CHUAN-GEN LIN ◽  
ERIC H. C. MCKENZIE ◽  
DARBHE J. BHAT ◽  
JIAN-KUI LIU ◽  
KEVIN D. HYDE ◽  
...  

A new species, Pseudodactylaria brevis, is described, illustrated and compared with other Pseudodactylaria and Dactylaria-like taxa. Evidence for the new species is provided by morphological comparison and sequence data analyses. Pseudodactylaria brevis can be distinguished from other Pseudodactylaria and Dactylaria-like species by its short hyaline conidiophores and fusiform, 1-septate hyaline conidia. Phylogenetic analysis of LSU and ITS sequence data was carried out to determine the phylogenetic placement of the species and confirm the taxonomic status of Pseudodactylariaceae.


2006 ◽  
Vol 61 (5-6) ◽  
pp. 405-412 ◽  
Author(s):  
Demet Cansaran ◽  
Sümer Aras ◽  
İrfan Kandemir ◽  
Gökhan Halıcı

Like many lichen-forming fungi, species of the genus Rhizoplaca have wide geographical distributions, but studies of their genetic variability are limited. The information about the ITS rDNA sequences of three species of Rhizoplaca from Anatolia was generated and aligned with other species from other countries and also with the data belonging to Lecanora species. The examined species were collected from the volcanic rocks of Mount Erciyes which is located in the middle of Anatolia (Turkey). The sequence data aligned with eight other samples of Rhizoplaca and six different species of Lecanora were obtained from GenBank. The results support the concept maintained by Arup and Grube (2000) that Rhizoplaca may not be a genus separate from Lecanora. According to the phylogenetic tree, Rhizoplaca melanopthalma from Turkey with two different samples of R. melanopthalma from Arizona (AF159929, AF159934) and a sample from Austria formed a group under the same branch. R. peltata and R. chrysoleuca samples from Anatolia located in two other branches of the tree formed sister groups with the samples of the same species from different countries. Although R. peltata remained on the same branch with other samples of the same species from other countries it was placed in a different branch within the group. When the three species from Anatolia were considered alone, it was noticed that Rhizoplaca melanopthalma and Rhizoplaca peltata are phylogenetically closer to each other than Rhizoplaca chrysoleuca; the morphological characteristics also support this result.


Plant Disease ◽  
2012 ◽  
Vol 96 (2) ◽  
pp. 289-289 ◽  
Author(s):  
X. Wang ◽  
J. Wang ◽  
J. Gao ◽  
L. Yang

Schisandra chinensis (Turcz.) Baill is a perennial liana belonging to the Schisandra genus of the family Magnoliaceae, which is cultivated in China as an important medicinal plant. In the summer of 2008, we observed a previously unknown foliar disease on the schisandras in Jingyu and Antu counties and the cities of Ji'an and Hunchun in Jilin Province. Symptoms appeared on the apex, margin, and center of leaves. The infection initially manifested as pale brown, small, necrotic spots on the leaves. Subsequently, these lesions became grayish brown in the center and dark brown with slight protuberances at the margins. Finally, these lesions developed concentric rings with a clear boundary separating them from the healthy tissue, were round to elliptical or irregular in shape, and had a diameter of 3 to 5 mm. In severely infected leaves, these spots eventually covered the entire leaf. Black spots (pycnidia) were produced on the infected leaf tissues in a humid environment. Fungus from infected leaf tissues was isolated on potato dextrose agar. The cultures were initially pale brown and turned dark green with age. Embedded pycnidia were generally formed after 5 days. The pycnidia were agglutinating, globose to subglobose, and measured 60.0 to 212.0 × 33.6 to 268.0 μm. Abundant conidia (4.06 to 7.2 × 1.65 to 3.53 μm) exhibiting zero to three oil droplets were produced by an 8-day-old colony; these conidia were ovoid or ellipsoidal, colorless, and aseptate; they were similar to conidia of Phoma glomerata. The internal transcribed spacer (ITS) sequence of rDNA of the isolated pathogenic strain (PG11; GenBank Accession No. GU724511) had 100% identity to P. glomerata (GenBank Accession No. HM769279). Therefore, the pathogen was identified as P. glomerata (Corda) Wollenw. & Hochapfel on the basis of morphology and ITS sequence data. To validate Koch's postulates, schisandra leaves were spray inoculated with a 2.5 × 105 conidia/ml suspension of the isolated pathogen. An equal number of healthy plants were inoculated with sterile water (control). After inoculation, 10 plants were covered with plastic bags for 3 days and maintained in a growth chamber at 25°C. After 8 days, all inoculated plants showed symptoms identical to those observed on the schisandra leaves infected in the field, whereas the controls did not show any symptoms. Reisolation of the fungi from lesions of inoculated leaves confirmed that the causal agent was P. glomerata. Diseases caused by P. glomerata have been reported on some plants (1,2). However, to our knowledge, this is the first report of leaf spot disease caused by P. glomerata on S. chinensis in China as well as in the world. References: (1) J. S. Chohan et al. Trans. Br. Mycol. Soc. 75:509, 1980. (2) T. Thomidis et al. Eur. J. Plant Pathol. 131:171,2011.


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