Genetic Relationships among Cultivated Species of Rhododendron L. Section Pentanthera G.Don Based on DNA Sequence Variation of the Internal Transcribed Spacer (ITS) Region

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 505f-506
Author(s):  
S.M. Scheiber ◽  
R.L. Jarret ◽  
C.D. Robacker
Keyword(s):  
Internal Transcribed Spacer ◽  
Direct Sequencing ◽  
Genetic Relationships ◽  
Morphological Characteristics ◽  
Sequence Divergence ◽  
Its Region ◽  
Distance Matrix ◽  
Sequence Comparisons ◽  
Additional Species ◽  
Bootstrap Analysis

Rhododendron section Pentanthera has traditionally been viewed as a group of closely related species due to the relative lack of distinctive morphological characteristics separating species and numerous reports in the literature of artificial and natural fertile hybrids that produce fertile progeny. Significant variation within species has created difficulties in efforts to assemble these taxa into well-defined groups. Genetic relationships among cultivated specimens of the 15 currently recognized species in Rhododendron section Pentanthera were derived from sequence comparisons of the internal transcribed spacer (ITS) region. Sequences of the entire ITS region including ITS1, ITS2, and the 5.8S subunit were generated by direct sequencing of polymerase chain reaction (PCR) amplified fragments. Rhododendron vaseyi A.Gray, Rhododendron section Rhodora (L.) G.Don was used as an outgroup. Aligned sequences of the 16 taxa resulted in 690 characters. A distance matrix of sequence divergence was calculated using Kimura's two parameter model. A bootstrap analysis was performed and a phenogram was constructed using MEGA. A phenetic assay rather than a phylogenetic analysis was performed because the ITS region contained only eight (1.16%) phylogenetically informative sites. The entire ITS region contained 41 variable sites (5.94%). Five species had identical ITS sequences. Seven additional species differed only by one or two base pair substitutions and/or the addition or deletion of one or two base pairs. R. luteum Sweet, R. occidentale A. Gray, R. molle (Blume) G.Don, and the outgroup, R. vaseyi had noticeable variation (base substitutions, additions, and deletions) compared to the other species. Divergence values among the taxa were extremely low, ranging from 0.00% to 3.51%. This molecular data, and previous hybridization studies, do not support the accepted taxonomic treatment of the section.

Two new rock-inhabiting species of Cyphellophora from karst habitats in China

Phytotaxa ◽  
2019 ◽  
Vol 397 (1) ◽  
pp. 23
Author(s):  
WEI SUN ◽  
BINGJIE LIU ◽  
RONG FU ◽  
XINGZHONG LIU ◽  
MEICHUN XIANG
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Its Region ◽  
Closely Related Species ◽  
Two New Species ◽  
Rock Inhabiting Fungi ◽  
Karst Habitats

During survey on rock-inhabiting fungi from karst habitats in Guizhou, China, two new species in Cyphellophora were discovered and identified. Phylogenetic analysis based on combined sequences of the nuclear large subunit (nucLSU) and internal transcribed spacer (ITS) region of ribosomal DNA revealed that the tested isolates, clustered into two clades that well affiliated in the genus of Cyphellophora. Morphological characteristics were also supported the estabolishment of the new species. Herewith Cyphellophora botryose sp. nov. and Cyphellophora guizhouensis sp. nov. were described and their differences from closely related species were discussed.

scholarly journals First Report of Albugo candida Causing White Rust on Lunaria annua in Italy

Plant Disease ◽  
2011 ◽  
Vol 95 (1) ◽  
pp. 72-72
Author(s):  
I. Camele ◽  
S. M. Mang ◽  
G. L. Rana
Keyword(s):  
Direct Sequencing ◽  
Morphological Characteristics ◽  
Its Region ◽  
First Report ◽  
Albugo Candida ◽  
White Rust ◽  
Landscape Plant ◽  
Average Maximum ◽  
Mother Plants ◽  
Health Progress

Money plant or annual honesty (Lunaria annua L.) is an ornamental landscape plant used in flower beds and borders and also in flower arrangements. It is a biennial plant with large, pointed, oval leaves. Plants of L. annua showing white-to-cream, blister-like lesions on leaves and siliques (2) were found in private gardens where approximately 800 plants of 1,000 (approximately 80 to 90%) that were observed showed symptoms. The disease was also found in two ornamental nurseries, although it was limited to a few mother plants because of extensive fungicide treatments. The gardens and ornamental nurseries were located in Potenza Province (Basilicata Region, southern Italy). Sporangiophores were mostly straight or arched and almost cylindrical with attenuated base and flat or rounded apex and measured 29.2 to 33.4 × 12.8 to 13.4 μm. Sporangia, produced in chains and joined by short connectives, exhibited a spherical or angular shape, were subhyaline, contained vacuoles, and had average maximum and minimum diameters ranging from 15.8 to 18.8 and 14 to 16 μm, respectively. The morphological characteristics closely resembled those reported for Albugo candida (Pers.) Kuntze (3). Sori were collected from naturally and artificially inoculated tissues of L. annua, with the aid of a stereomicroscope, and used to extract genomic DNA via a DNeasy Plant Mini DNA extraction kit (Qiagen, Hilden, Germany) according to the manufacturer's directions. The extracted DNA was used as a template for amplification of the internal transcribed spacer (ITS) region of rDNA with primer pair ITS4/DC6 (1,4) and sequenced. One sequence, GenBank Accession No. GQ328846, matched several sequences of A. candida (Pers). Kuntze (e.g., GenBank Accession Nos. GQ328837, GQ328836, GQ328835, GQ328834, and AF271231), showing 98% identity. Pathogenicity tests were performed and repeated twice. Leaves of 10 healthy seedlings of L. annua were surface cleaned during several washings with distilled water and then spray inoculated with a suspension of 103 sporangia/ml of A. candida. Five healthy seedlings were spray inoculated with the same volume of sterile water and served as controls. Inoculated seedlings were maintained in a moist chamber for 48 h at 20°C before being moved to a shaded glasshouse at 16 to 24°C and 90% relative humidity. White rust symptoms, similar to those observed in natural conditions, appeared on leaves of inoculated seedlings 10 to 14 days later, demonstrating that A. candida was the causal agent of the disease. Control plants remained symptomless. White rust has been reported on L. annua in Europe (Czech Republic, Germany, Poland, and the United Kingdom) and in the northwestern United States (3). To our knowledge, this is the first report of A. candida infecting annual honesty plant in Italy. References: (1) P. Bonants et al. Eur. J. Plant Pathol. 103:345, 1997. (2) D. Choi et al. Mycotaxon 53:261, 1995. (3) D. A. Glawe et al. Online publication. doi:10.1094/PHP-2004-0317-01-HN. Plant Health Progress, 2004. (4) T. J. White et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols. A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990.

scholarly journals First Report of Fusarium proliferatum Causing Rot of Garlic Bulbs (Allium sativum) in India

Plant Disease ◽  
2012 ◽  
Vol 96 (2) ◽  
pp. 290-290 ◽  
Author(s):  
N. Ravi Sankar ◽  
Gundala Prasad Babu
Keyword(s):  
Sodium Hypochlorite ◽  
Allium Sativum ◽  
Morphological Characteristics ◽  
Aerial Mycelium ◽  
Its Region ◽  
Fusarium Proliferatum ◽  
Distilled Water ◽  
Sequence Comparisons ◽  
First Report ◽  
Plant Pathol

In September 2009, diseased garlic bulbs (Allium sativum L. cv. Yamuna Safed) were received from producers and exporters in Hyderabad, Andra Pradesh, India. From 2009 to 2010, similar symptoms were observed on stored garlic bulbs (cvs. Yamuna Safed and Agrifound White) in Chittoor, Kadapa, and Hyderabad districts. In some locations, approximately 60% of the garlic bulbs were affected. At first, infected bulbs showed water-soaked, brown spots and then the disease progressed as small, slightly depressed, tan lesions. A total of 120 diseased samples were collected from all localities. Infected tissues were surface sterilized in 1% sodium hypochlorite for 2 min, rinsed three times in sterile distilled water, plated on potato dextrose agar (PDA), and incubated at 25°C for 7 days. Resultant fungal colonies were fast growing with white aerial mycelium and violet to dark pigments. Hyphae were septate and hyaline. Conidiophores were short, simple, or branched. Microconidia were abundant, single celled, oval or club shaped, measuring 4.5 to 10.5 × 1.3 to 2.5 μm, and borne in chains from both mono-and polyphialides. Macroconidia were not produced. On the basis of morphological characteristics, the pathogen was identified as Fusarium proliferatum (Matsushima) Nirenberg (2). Identification was confirmed by amplification of the internal transcribed spacer (ITS) region. Genomic DNA was extracted from pure cultures of an isolate, and the ITS region was amplified using the ITS4/5 primer pair. PCR amplicons of approximately 574 bp were obtained from isolates, and sequence comparisons with GenBank showed 99% similarity with F. proliferatum (Accession No. FN868470.1). Sequence from this study was submitted to GenBank nucleotide database (Accession No. AB646795). Pathogenicity tests were conducted with three isolates of the fungus following the method of Dugan et al. (1). Each assay with an isolate consisted of 10 garlic cloves disinfected in 1% sodium hypochlorite for 45 s, rinsed with sterile distilled water, and injured to a depth of 4 mm with a sterile 1-mm-diameter probe. The wounds were filled with PDA colonized by the appropriate isolate from a 5-day-old culture. Ten cloves for each tested isolate received sterile PDA as a control. The cloves were incubated at 25°C for 5 weeks; tests were repeated once. After 17 days, rot symptoms similar to the original symptoms developed on all inoculated cloves and F. proliferatum was consistently reisolated from symptomatic tissue, fulfilling Koch's postulates. No fungi were recovered from control cloves. F. proliferatum has been reported on garlic in the northwestern United States (1), Serbia (4), and Spain (3). To our knowledge, this is the first report of F. proliferatum causing rot disease on garlic bulbs in India. References: (1) F. M. Dugan et al. Plant Pathol. 52:426, 2003. (2) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell Publishing, Oxford, UK, 2006. (3) D. Palmero et al. Plant Dis. 94:277, 2010. (4) S. Stankovic et al. Eur. J. Plant Pathol. 48:165, 2007.

scholarly journals First report of Fusarium proliferatum causing stem and root rot on lucky bamboo (Dracaena braunii) in Iraq

2019 ◽  
Vol 12 (1) ◽  
pp. 1-5
Author(s):  
A.A. Lahuf
Keyword(s):  
Ribosomal Dna ◽  
Root Rot ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Its Region ◽  
Fusarium Proliferatum ◽  
Ornamental Plant ◽  
Sequence Analyses ◽  
First Report

Summary Lucky bamboo (Dracaena braunii) is a popular ornamental plant in Iraq. Individuals of this plant showing stem and root rot symptoms were observed during a survey conducted from November 2015 to February 2016 in several nurseries in Kerbala province, Iraq. Based on morphological characteristics and sequence analyses of the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), the pathogen was identified as Fusarium proliferatum. This is the first report of stem and root rot caused by F. proliferatum on lucky bamboo (D. braunii) in Iraq.

scholarly journals First Report of Alternaria alternata Causing Leaf Spot on Bruguiera gymnorrhiza in China

Plant Disease ◽  
2015 ◽  
Vol 99 (2) ◽  
pp. 286-286 ◽  
Author(s):  
Q.-L. Lin ◽  
H.-R. Su ◽  
H. He
Keyword(s):  
Leaf Spot ◽  
Direct Sequencing ◽  
Morphological Characteristics ◽  
Its Region ◽  
Average Diameter ◽  
Morphological Observation ◽  
Leaf Spot Disease ◽  
Bruguiera Gymnorrhiza ◽  
First Report ◽  
Mangrove Tree

Bruguiera gymnorrhiza (L.) Savigny is an important mangrove tree species that grows in the intertidal regions of the tropical and subtropical coastlines. In a survey conducted in March 2014, a leaf spot disease on this plant was observed in Sea View Promenade in Zhanjiang, Guangdong Province, China. Symptoms on leaves initially appeared as small circular to irregular, dark brown, necrotic, sunken spots with an average diameter of 4 to 7 mm. The spots gradually enlarged in size, becoming irregular, or remained circular with concentric rings or zones. In the latter, the spots coalesced, and the leaves withered, dried, and fell from the plants. Leaf tissues (3 × 5 mm), cut from the margins of lesions, were surface-disinfected, placed on potato dextrose agar (PDA), and incubated at 28°C with a 12-h photoperiod. Five fungi (MLL1 to MLL5) with different morphological characteristics were obtained. To fulfill Koch's postulates, wounded and nonwounded leaves were inoculated. Fresh wounds were made with a sterile needle on 10 detached leaves and 10 leaves on five living plants for fungi MLL1 to MLL5 independently. Mycelial plugs of each fungus were applied to wounded and nonwounded leaves. For the control, 10 leaves on five living plants were inoculated with agar plugs in a similar manner, to both wounded and nonwounded leaves. All treatments were incubated in a humid chamber in the dark at 28°C. Leaf spots identical to those observed in the field were observed on the wounded leaves inoculated with fungus MLL3 after 3 to 4 days, while the other four fungi and the control remained symptomless. The 10 nonwounded leaves inoculated with fungus MLL3 were also infected after 5 days. The fungus, with the same colony and conidial morphology as MLL3, was re-isolated from the affected leaves. The pathogenic test was repeated three times under the same conditions. Hyphal tips of MLL3 were transferred to PDA for morphological observation. Colonies of white-to-dark-gray mycelia, black on the underside, formed on PDA. The colonies were further identified as Alternaria sp., based on the dark brown, obclavate to obpyriform catenulate conidia with longitudinal and transverse septa tapering to a prominent beak attached in chains on a simple and short conidiophore (3). Conidia varied from 22.5 × 40.26 to 3.95 × 5.79 μm and had three to eight transverse and zero to four longitudinal septa, with a beak length of 0 to 7.25 μm. For molecular identification, PCR was carried out using internal transcribed spacer (ITS) region primers ITS1/ITS4, partial sequences of the beta tubulin gene primers Bt1a-Bt1b (1), and A. alternata species-specific primers AAF2/AAR3 (2). The PCR products were subjected to direct sequencing. The resulting sequences were compared against the GenBank nucleotide database by using a BLAST alignment, which revealed that MLL3 had 99 to 100% identity with A. alternata for the ITS, Bt1a-Bt1b, and AAF2/AAR3 regions (GenBank Accession Nos. KF669893, GQ240308, and KJ716876, respectively). Sequences for MLL3 were deposited in GenBank under accession numbers KJ767515, KJ921779, and KJ921778. According to both morphological and sequence analyses, the pathogen of the leaf spot of B. gymnorrhiza was identified as A. alternata. To our knowledge, this is the first report of A. alternata on leaves of B. gymnorrhiza in China. This pathogen could cause serious foliar damage and threaten the survival, growth, and fitness of the local B. gymnorrhiza community. References: (1) N. L. Glass and G. C. Donaldson. Appl. Environ. Microbiol. 61:1323, 1995. (2) P. Konstantinova et al. Mycol. Res. 106:23, 2002. (3) E. G. Simmons. Alternaria: An identification Manual. CBS Fungal Biodiversity Center, Utrecht, Netherlands, 2007.

PHYLOGENETIC RELATIONSHIPS IN TRICHILIA (MELIACEAE) BASED ON RIBOSOMAL ITS SEQUENCES

Phytotaxa ◽  
2016 ◽  
Vol 259 (1) ◽  
pp. 6 ◽  
Author(s):  
JAMES J. CLARKSON ◽  
TERENCE D. PENNINGTON ◽  
MARK W. CHASE ◽  
GWILYM HAYNES ◽  
RACHEL ENGSTRAND ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Sequence Divergence ◽  
Its Region ◽  
Dry Forest ◽  
Forest Species ◽  
African Species ◽  
Seasonally Dry ◽  
Amazonian Rainforest ◽  
Seasonally Dry Forest

The internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) was used to investigate phylogenetic relationships in Trichilia (Meliaceae). Analyses focused on the neotropical Trichilia and consisted of 112 accessions (95 neotropical Trichilia, 6 African Trichilia and 11 Meliaceae Outgroups). Bayesian and Parsimony approaches demonstrated that the Cuban species T. havenensis is the earliest diverging lineage in the genus. The African species of Trichilia are nested within the neotropical clade. Section Moschoxylun (primarily Amazonian rainforest species) shows significantly lower levels of sequence divergence than section Trichilia (primarily dry/ seasonally dry forest species). Recently diverged rainforest taxa have been documented in several other Angiosperm families and our results therefore confirm this phenomenon.

Analysis of Genetic Relationships in Germplasms of Mugua in China Revealed by Internal Transcribed Spacer and its Taxonomic Significance Analysis of Genetic Relationships in Germplasms of Mugua in China Revealed by Internal Transcribed Spacer and its Taxonomic Signifi cance

2010 ◽  
Vol 65 (7-8) ◽  
pp. 495-500 ◽  
Author(s):  
Bangxing Han ◽  
Huasheng Peng ◽  
Qin Yao ◽  
Yang Zhou ◽  
Ming’en Cheng ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Genetic Relationships ◽  
Distance Matrix ◽  
Its Sequences ◽  
Taxonomic Significance ◽  
Significance Analysis ◽  
Its Analysis ◽  
Genetic Distance Matrix

Genetic relationships were studied among eight species of three taxa in the genus Chaenomeles by nuclear ribosomal internal transcribed spacer (ITS) analysis. A genetic distance matrix based on ITS sequences was estimated according to the formula of Kimura-2 parameter and a neighbour-joining phenogram, which were obtained with Clustalx4.1 software. The results showed that the germplasms of Mugua originate from Ch. speciosa (Sweet) Nakai, not including Ch. sinensis (Thouin) Kochne and Ch. cathayensis (Hemsl.) Schneid. The results also showed that ‘Yao Mugua’ and ‘Ornamental Mugua’ are the most distantly related species in germplasms.

scholarly journals The Northeast Chinese species of Psathyrella (Agaricales, Psathyrellaceae)

MycoKeys ◽  
2018 ◽  
Vol 33 ◽  
pp. 85-102 ◽  
Author(s):  
Jun-Qing Yan ◽  
Tolgor Bau
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Northeast China ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Its Region ◽  
Identification Key ◽  
Line Drawings

Twenty seven species of Psathyrella have been found in Northeast China. Amongst them, P.conica, P.jilinensis, P.mycenoides and P.subsingeri are described as new species, based on studying morphological characteristics and phylogenetic analyses. Detailed morphological descriptions, line drawings and photographs of the new species are presented. Phylogenetic analysis of the nuclear ribosomal internal transcribed spacer (ITS) region and an identification key to the 27 Psathyrella species occuring in Northeast China are provided.

scholarly journals First Report of Brown Rot on Plum Caused by Monilia polystroma in China

Plant Disease ◽  
2010 ◽  
Vol 94 (4) ◽  
pp. 478-478 ◽  
Author(s):  
X. Q. Zhu ◽  
L. Y. Guo
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Brown Rot ◽  
Its Region ◽  
Apple Orchard ◽  
Monilinia Fructigena ◽  
First Report ◽  
Plant Pathol ◽  
Monilia Polystroma

In August 2008, mummies of dwarf sweet plum (Prunus aitianli) fruit covered with grayish, conidial tufts were found in an orchard in Mudanjiang City of Heilongjiang in China. Conidial masses were touched with a sterilized wire loop and streaked onto the surface of water agar (WA) plates. After incubating at 22 ± 2°C for 16 to 24 h, individual germinated spores were picked out with a sterilized scalpel blade under a microscope in a laminar flow cabinet, and transferred to potato dextrose agar (PDA) in petri dishes. Mycelium grew an average of 10.7 mm per day on PDA and formed a white-to-grayish colony with irregular, black stroma 12 days after incubation at 22 ± 2°C under 12-h light/12-h dark. The average size of stroma was 8.19 cm2 per petri dish 37 days after incubation in the dark. The conidia were one-celled, hyaline, lemon-shaped, 15.2 (10.8 to 18.9) × 10.9 (8.3 to 16.3) μm, and arranged in branched monilioid chains on inoculated apples. The PCR products of internal transcribed spacer (ITS) region 1 and 2 and 5.8S gene of the ribosomal RNA amplified with primers ITS1 and ITS4 was directly sequenced in both directions using the PCR primers. The sequence of the Monilia polystroma isolate (GenBank Accession No. GU067539) was identical to the reference isolate of M. polystroma (CBS102686), containing five nucleotides that distinguish it from Monilinia fructigena (1,3). The pathogen was identified as M. polystroma on the basis of morphological characteristics (3) and the sequence of internal transcribed spacer (ITS) region 1 and 2 and 5.8S gene of the ribosomal RNA. Pathogenicity was confirmed by inoculating surface-sterilized, mature plum and apple fruit wounded with a nail, with a mycelial plug (5 mm in diameter) of the fungus at each wound. Fruit treated with plain PDA plugs were used as a control. Inoculated fruits were placed in a sterilized moist chamber at room temperature (23 to 28°C). Fifteen plums and nine apples were used in each of two replicated tests. All inoculated fruit developed typical brown rot symptoms 4 days after inoculation, while the control fruit remained healthy. M. polystroma was reisolated from the inoculated fruit and identified by the above methods. M. polystroma was first reported on apple in Japan (3) and it was recently discovered in an apple orchard in Hungary (2). Although the occurrence of Monilinia fructicola, Monilinia laxa, and Monilinia fructigena (teleomorphs of the three Monilia spp.) in China have been documented, to our knowledge, this is the first report of the occurrence of M. polystroma in China. References: (1) C. E. Fulton et al. Eur. J. Plant Pathol. 105:495, 1999. (2) M. Petróczy and L. Palkovics. Eur. J. Plant Pathol. 125:343, 2009. (3) G. C. M. van Leeuwen et al. Mycol. Res. 106:444, 2002.

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