scholarly journals Diversity of Phytoplasmas Associated with Several Plants in Western Java-Indonesia

2018 ◽  
Vol 17 (4) ◽  
pp. 303-312
Author(s):  
Ariny PRASETYA ◽  
Kikin Hamzah MUTAQIN ◽  
Meity Suradji SINAGA ◽  
Giyanto GIYANTO
Keyword(s):  
Classification Scheme ◽  
Phylogenetic Analyses ◽  
Nucleotide Sequences ◽  
Bermuda Grass ◽  
Similarity Coefficients ◽  
Reliable Identification ◽  
Field Crops ◽  
Blast Analysis ◽  
White Leaf ◽  
Symptomatic Plant

Diseases caused by phytoplasmas have been reported in field crops, ornamentals, and weeds in Indonesia. However, most of phytoplasmas have not been subjected to further identification and thus, they remain unaffiliated with proper classification scheme. More reliable identification of phytoplasmas mostly rely on molecular methods. The aim of this study was to characterize the phytoplasma as the causal agent of naturally infected plants in western Java-Indonesia based on their 16S rRNA nucleotide sequences. Plant exhibiting phytoplasmal symptoms were observed and taken for further molecular examination. Eight plant species from three families in Bogor, Tangerang, and Bekasi, i.e. peanut, soybean, snakebean, Opuntia sp., betung bamboo, apus bamboo, Bermuda grass, and digitaria grass (Digitaria fuscescens) have been observed and taken as samples for further molecular examination. Nested-PCR with primer pairs P1/P7 followed by R16F2n/R16R2 resulted in amplification of products of approximately 1.2 kb from all symptomatic plant samples tested. BLAST analysis of the nucleotide sequences, phylogenetic analyses, and similarity coefficients derived from RFLP in silico revealed that there were association of a phytoplasma of 16SrII-A subgroup with phytoplasmas identified in peanut, soybean, and snakebean. Such an association showed witches’ broom symptoms; 16SrII-C with Opuntia sp. causing proliferation and mosaics; and phytoplasmas displaying yellowing and little leaf of two kinds of bamboos and white leaf of Bermuda grass and digitaria grass that were closely related to 16SrXIV-A subgroup. To our knowledge, this is the first report molecular identification of 16SrXIV-A associated with apus bamboo and digitaria grass in Indonesia.

scholarly journals ‘Candidatus Phytoplasma cynodontis’, the phytoplasma associated with Bermuda grass white leaf disease

2004 ◽  
Vol 54 (4) ◽  
pp. 1077-1082 ◽  
Author(s):  
Carmine Marcone ◽  
Bernd Schneider ◽  
Erich Seemüller
Keyword(s):  
16S Rdna ◽  
Cynodon Dactylon ◽  
Phylogenetic Analyses ◽  
Species Level ◽  
Bermuda Grass ◽  
Taxonomic Assignment ◽  
Rdna Sequences ◽  
Putative Species ◽  
White Leaf ◽  
Major Branch

Bermuda grass white leaf (BGWL) is a destructive, phytoplasmal disease of Bermuda grass (Cynodon dactylon). The causal pathogen, the BGWL agent, differs from other phytoplasmas that cluster in the same major branch of the phytoplasma phylogenetic clade in <2·5 % of 16S rDNA nucleotide positions, the threshold for assigning species rank to phytoplasmas under the provisional status ‘Candidatus’. Thus, the objective of this work was to examine homogeneity of BGWL isolates and to determine whether there are, in addition to 16S rDNA, other markers that support delineation of the BGWL agent at the putative species level. Phylogenetic analyses revealed that the 16S rDNA sequences of BGWL strains were identical or nearly identical. Clear differences that support separation of the BGWL agent from related phytoplasmas were observed within the 16S–23S rDNA spacer sequence, by serological comparisons, in vector transmission and in host-range specificity. From these results, it can be concluded that the BGWL phytoplasma is a discrete taxon at the putative species level, for which the name ‘Candidatus Phytoplasma cynodontis' is proposed. Strain BGWL-C1 was selected as the reference strain. Phytoplasmas that are associated with brachiaria white leaf, carpet grass white leaf and diseases of date palms showed 16S rDNA and/or 16S–23S rDNA spacer sequences that were identical or nearly identical to those of the BGWL phytoplasmas. However, the data available do not seem to be sufficient for a proper taxonomic assignment of these phytoplasmas.

Phylogenetic analyses of nucleotide sequences confirm a unique plant intercontinental disjunction between tropical Africa, the Caribbean, and the Hawaiian Islands

2009 ◽  
Vol 123 (1) ◽  
pp. 57-65 ◽  
Author(s):  
Sandra Namoff ◽  
Quentin Luke ◽  
Francisco Jiménez ◽  
Alberto Veloz ◽  
Carl E. Lewis ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Hawaiian Islands ◽  
Nucleotide Sequences ◽  
Tropical Africa ◽  
The Caribbean

scholarly journals 'Candidatus Phytoplasma sacchari’, a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease

2020 ◽  
Author(s):  
Kiran Kirdat ◽  
Bhavesh Tiwarekar ◽  
Vipool Thorat ◽  
Shivaji Sathe ◽  
Yogesh Shouche ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Indian Subcontinent ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Genome Sequences ◽  
Phytoplasma Strain ◽  
White Leaf

Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with ‘Ca. Phytoplasma cynodontis’ strain BGWL-C1 followed by 97.65 % similarity with ‘Ca. P. oryzae’ strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to ‘Ca. P. cynodontis’, were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon ‘Candidatus Phytoplasma sacchari’ is proposed.

scholarly journals Suspected zoonotic transmission of rotavirus group A in Danish adults

2011 ◽  
Vol 140 (6) ◽  
pp. 1013-1017 ◽  
Author(s):  
S. E. MIDGLEY ◽  
C. K. HJULSAGER ◽  
L. E. LARSEN ◽  
G. FALKENHORST ◽  
B. BÖTTIGER
Keyword(s):  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Geographical Area ◽  
Nucleotide Sequences ◽  
Zoonotic Transmission ◽  
Adult Patients ◽  
Epidemiological Features ◽  
Group A Rotaviruses ◽  
Group A ◽  
Stool Samples

SUMMARYGroup A rotaviruses infect humans and a variety of animals. In July 2006 a rare rotavirus strain with G8P[14] specificity was identified in the stool samples of two adult patients with diarrheoa, who lived in the same geographical area in Denmark. Nucleotide sequences of the VP7, VP4, VP6, and NSP4 genes of the identified strains were identical. Phylogenetic analyses showed that both Danish G8P[14] strains clustered with rotaviruses of animal, mainly, bovine and caprine, origin. The high genetic relatedness to animal rotaviruses and the atypical epidemiological features suggest that these human G8P[14] strains were acquired through direct zoonotic transmission events.

Clavibacter XYLI subsp. cynodontis. [Descriptions of Fungi and Bacteria].

1991 ◽  
Author(s):  
J. F. Bradbury
Keyword(s):  
Host Range ◽  
Geographical Distribution ◽  
Sugar Cane ◽  
Cynodon Dactylon ◽  
Bermuda Grass ◽  
Artificial Inoculation ◽  
Mechanical Transmission ◽  
Ecological Significance ◽  
Sudan Grass ◽  
White Leaf

Abstract A description is provided for Clavibacter XYLI subsp. cynodontis. Information is included on the disease caused by the organism, its transmission, geographical distribution, and hosts. HOST: Cynodon dactylon, where it is limited to the xylem. It also multiplies in the xylem of sugar cane and a Sudan grass-sorghum hybrid when artificially inoculated, but symptoms are not produced (61, 4328). Further host range not yet recorded. DISEASE: Bermuda grass stunting disease. Natural occurrences so far discovered have been in combination with mycoplasma-like organisms thought to cause white leaf and witches' broom symptoms. The presence of the bacterium causes considerably more severe symptoms. The full ecological significance of this bacterium has not yet been evaluated, but a further stress is usually required to produce noticeable symptoms. GEOGRAPHICAL DISTRIBUTION: Taiwan, USA (Florida). TRANSMISSION: So far only mechanical transmission, by artificial inoculation, is known. Cutting blades and possibly grazing animals are likely to spread the infection.

Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification

The Auk ◽  
2021 ◽  
Author(s):  
Jeremy J Kirchman ◽  
Nancy Rotzel McInerney ◽  
Thomas C Giarla ◽  
Storrs L Olson ◽  
Elizabeth Slikas ◽  
...  
Keyword(s):  
Confidence Intervals ◽  
Geographic Distribution ◽  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Nucleotide Sequences ◽  
Museum Specimens ◽  
Multispecies Coalescent ◽  
Evolutionary Studies ◽  
Age Estimates

Abstract The rails (Family Rallidae) are the most diverse and widespread group in the Gruiformes. Their extensive fossil history, global geographic distribution, and tendency to rapidly evolve flightless species on islands make them an attractive subject of evolutionary studies, but the rarity of modern museum specimens of so many rail species has, until recently, limited the scope of molecular phylogenetics studies. As a result, the classification of rails remains one of the most unsettled among major bird radiations. We extracted DNA from museum specimens of 82 species, including 27 from study skins collected as long ago as 1875, and generated nucleotide sequences from thousands of homologous ultra-conserved elements (UCEs). Our phylogenetic analyses, using both concatenation and multispecies coalescent approaches, resulted in well-supported and highly congruent phylogenies that resolve the major lineages of rails and reveal several currently recognized genera to be polyphyletic. A fossil-calibrated time tree is well-resolved and supports the hypothesis that rails split into 2 major lineages (subfamilies Himantornithinae and Rallinae) ~34 mya, but clade age estimates have wide confidence intervals. Our results, combined with results of other recently published phylogenomics studies of rails and other Gruiformes, form the basis for a proposed classification of the Rallidae that recognizes 40 genera in 9 tribes.

Molecular identification of ‘CandidatusPhytoplasma cynodontis’ associated with Bermuda grass white leaf disease in India

2008 ◽  
Vol 57 (4) ◽  
pp. 770-770 ◽  
Author(s):  
S. K. Snehi ◽  
M. S. Khan ◽  
S. K. Raj ◽  
S. Mall ◽  
M. Singh ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Bermuda Grass ◽  
Leaf Disease ◽  
White Leaf ◽  
White Leaf Disease

scholarly journals Draft Genome Sequences of Two Phytoplasma Strains Associated with Sugarcane Grassy Shoot (SCGS) and Bermuda Grass White Leaf (BGWL) Diseases

2020 ◽  
Vol 33 (5) ◽  
pp. 715-717 ◽  
Author(s):  
Kiran Kirdat ◽  
Bhavesh Tiwarekar ◽  
Vipool Thorat ◽  
Nitin Narawade ◽  
Dhiraj Dhotre ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Bermuda Grass ◽  
Whole Genome ◽  
Genome Sequences ◽  
Taxonomic Level ◽  
Phytoplasma Strain ◽  
White Leaf

We performed whole-genome sequencing of two phytoplasmas associated with sugarcane grassy shoot (SCGS) and Bermuda grass white leaf diseases. These are the first draft genomes of SCGS phytoplasma (strain SCGS) and ‘Candidatus Phytoplasma cynodontis’ (strain LW01) and may help to delineate these phytoplasmas at a finer taxonomic level.

scholarly journals Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups

2007 ◽  
Vol 57 (8) ◽  
pp. 1855-1867 ◽  
Author(s):  
Wei Wei ◽  
Robert E. Davis ◽  
Ing-Ming Lee ◽  
Yan Zhao
Keyword(s):  
16S Rrna ◽  
Classification Scheme ◽  
Rflp Analysis ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Wide Range

Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.

scholarly journals Chromosome Sizes of Phytoplasmas Composing Major Phylogenetic Groups and Subgroups

1999 ◽  
Vol 89 (9) ◽  
pp. 805-810 ◽  
Author(s):  
C. Marcone ◽  
H. Neimark ◽  
A. Ragozzino ◽  
U. Lauer ◽  
E. Seemüller
Keyword(s):  
Pigeon Pea ◽  
Bermuda Grass ◽  
Phylogenetic Groups ◽  
Aster Yellows ◽  
White Leaf ◽  
Wide Range ◽  
Dna Elements ◽  
Sugarcane White Leaf ◽  
Elm Yellows ◽  
Size Heterogeneity

Chromosome sizes of 71 phytoplasmas belonging to 12 major phylogenetic groups including several of the aster yellows subgroups were estimated from electrophoretic mobilities of full-length chromosomes in pulsed-field gels. Considerable variation in genome size, from 660 to 1,130 kilobases (kb), was observed among aster yellows phytoplasmas. Chromosome size heterogeneity was also observed in the stolbur phytoplasma group (range 860 to 1,350 kb); in this group, isolate STOLF contains the largest chromosome found in a phytoplasma to date. A wide range of chromosome sizes, from 670 to 1,075 kb, was also identified in the X-disease group. The other phytoplasmas examined, which included members of the apple proliferation, Italian alfalfa witches' broom, faba bean phyllody, pigeon pea witches' broom, sugarcane white leaf, Bermuda grass white leaf, ash yellows, clover proliferation, and elm yellows groups, all have chromosomes smaller than 1 megabase, and the size ranges within each of these groups is narrower than in the aster yellows, stolbur, and X-disease groups. The smallest chromosome, ≈530 kb, was found in two Bermuda grass white leaf phytoplasma isolates. This not only is the smallest mollicute chromosome found to date, but also is the smallest chromosome known for any cell. More than one large DNA band was observed in several phytoplasma preparations. Possible explanations for the occurrence of more than one band may be infection of the host plant by different phytoplasmas, the presence of more than one chromosome in the same organism, or the presence of large extrachromosomal DNA elements.

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