scholarly journals ANALYSIS OF nrLSU GENE TO SUPPORT IDENTIFICATION OF FUNGUS BELONGING TO Cordyceps GENUS AND CLAVICIPITACEAE FAMILY

2018 ◽  
Vol 55 (1A) ◽  
pp. 91
Author(s):  
Vu Tien Luyen
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Agarose Gel ◽  
Large Ribosomal Subunit ◽  
Pcr Product ◽  
Sequencing Method ◽  
Clear Band ◽  
Molecular Phylogenetic ◽  
Long Time ◽  
Reference Sequences

Nucleotide sequences of the nuclear large ribosomal subunit (nrLSU) have been used in fungal systematics for a long time. nrLSU was also used in Cordyceps and related genera within the Clavicipitaceae family. A previously identified sample by morphology and ITS was used in this research to analyze the ability of nrLSU to support the identification of entomopathogenic fungi. Our results show that we successfully amplified nrLSU gene using the primer pair LR0R and LR5. The PCR product on agarose gel showed a clear band at 950 bp. Sequencing method was then adopted and proofread before molecular phylogenetic analysis was applied with reference sequences obtained from the publication of Sung et al. Once again, this analysis confirms the DL0004 specimen as Cordyceps neovolkiana. 

scholarly journals Molecular phylogenetic analysis to support the identification of samples DL0038A & DL0038B belonging to Cordyceps genus

2016 ◽  
Vol 19 (1) ◽  
pp. 55-65
Author(s):  
Luyen Tien Vu ◽  
Hiep Minh Dinh ◽  
Nguyen Binh Truong ◽  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Small Subunit ◽  
Molecular Phylogenetic Analysis ◽  
Morphological Identification ◽  
Combined Analysis ◽  
Sequencing Method ◽  
Molecular Phylogenetic ◽  
Reference Sequences

In our previous publication, we have tentatively concluded that our fungal specimen DL0038A and DL0038B are Cordyceps takaomontana. In order to further support the identification, we continued to analyse the nrSSU (nuclear ribosomal small subunit) and rpb1 (largest subunit of RNA polymerase II) genes, as well as combined analysis the nrLSU (largest subunit of RNA polymerase II) together with nrSSU and rpb2 genes on these specimens in order to support the morphological identification of those fungi. The results show that we successfully amplified all genes. Sequencing method was then adopted and proofread before molecular phylogenetic analysis was applied with reference sequences obtained from the publication of Sung et al. (2007). Once again, this analysis strongly supports the DL0038A and DL0038B specimen as Cordyceps takaomontana.

Bulinus species on Madagascar: molecular evolution, genetic markers and compatibility with Schistosoma haematobium

Parasitology ◽  
2001 ◽  
Vol 123 (7) ◽  
pp. 261-275 ◽  
Author(s):  
J. R. STOTHARD ◽  
P. BRÉMOND ◽  
L. ANDRIAMARO ◽  
B. SELLIN ◽  
E. SELLIN ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Population Genetic Analysis ◽  
Basal Node ◽  
Pcr Rflp ◽  
Dna Sequence Variation ◽  
Long Time ◽  
Laboratory Infection ◽  
Species Groups ◽  
Nucleotide Divergence

Of the four species of Bulinus found on Madagascar, three species: B. obtusispira, B. liratus and B. bavayi are endemic while the fourth, B. forskalii, is probably a recent introduction from the African mainland. The evolutionary relationships of these species with Bulinus species from Africa were studied by phylogenetic analysis of DNA sequence variation at two mitochondrial loci: cytochrome oxidase subunit I (COI) and large ribosomal subunit (LSU) or 16S. The observed levels of nucleotide divergence within Bulinus were substantial but may underestimate the true levels as there was evidence of ‘saturation' of transitional substitutions at both loci. A putative secondary structure model for the sequenced segment of the 16S was developed. Subsequent phylogenetic analysis using transversional changes only for both loci, showed that there were contrasting levels of divergence within the four species groups. B. obtusispira was consistently placed within the B. africanus group, appearing ancestral to this group and was closest to the basal node within Bulinus. Together with B. bavayi, the two species appear to have been isolated on Madagascar for a long time, contrasting with both B. liratus and B. forskalii that appear more recent colonisers; however, estimate of exact times of divergence is problematic. A PCR-RFLP assay was developed to enable identification and discrimination of B. obtusispira and B. liratus using discriminatory variation within the COI. To enable population genetic analysis within B. obtusispira, microsatellite markers were developed using an enrichment method and 8 primer pairs are reported. Laboratory infection experiments using Madasgacan S. haematobium from the Mahabo area showed that certain populations of B. obtusispira, B. liratus and B. bavayi were compatible.

scholarly journals Krefftascaris (Nematoda, Ascaridoidea) from Australian Side-Necked Turtles with Description of Krefftascaris Sharpiloi SP. N. from Chelodina Rugosa

2010 ◽  
Vol 44 (1) ◽  
pp. e-1-e-11 ◽  
Author(s):  
V. Tkach ◽  
Yu. Kuzmin ◽  
S. Snyder
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
New Records ◽  
Ribosomal Subunit ◽  
Northern Territory ◽  
Nerve Ring ◽  
Subunit Gene ◽  
Molecular Phylogenetic

Krefftascaris(Nematoda, Ascaridoidea) from Australian Side-Necked Turtles with Description ofKrefftascaris SharpiloiSP. N. fromChelodina RugosaPreviously known records of ascaridoid nematodesKrefftascarisSprent, 1980 are summarized and new records of the genus reported.Krefftascaris sharpiloiTkach, Kuzmin et Snyder, sp. n. is described from specimens found in the stomach of the northern snake-necked turtleChelodina rugosacollected from two localities in Northern Territory, Australia. The new species differs from the only previously knownKrefftascarisspecies,K. parmenteriSprent, 1980, by the presence of thickened and bifurcated anterior edges of the lateral cuticular alae and a difference in the relative distance from the anterior end to the nerve ring which is 1.5 to 2 times greater inK. parmenteri.Comparison of approximately 2.100 bases of ribosomal DNA sequences This study contains first reports ofKrefftascarisinChelodina rugosa, Chelodina burrungandjii, Chelodina canniandEmydura tanybaragaand the first records of this genus in the Northern Territory, Queensland and Western Australia. Molecular phylogenetic analysis based on sequences of nuclear small ribosomal subunit gene has demonstrated close affinities betweenKrefftascarisandHeterocheilus, the type genus of the Heterocheilidae and Heterocheilinae. Parasitism of several species and genera of Heterocheilidae in crocodiles allows us to hypothesize thatKrefftascarismay have been acquired by turtles from crocodilians.

scholarly journals A New Postharvest Fruit Rot in Apple and Pear Caused by Phacidium lacerum

Plant Disease ◽  
2016 ◽  
Vol 100 (1) ◽  
pp. 32-39 ◽  
Author(s):  
M. S. Wiseman ◽  
Y. K. Kim ◽  
F. M. Dugan ◽  
J. D. Rogers ◽  
C. L. Xiao
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Morphological Characteristics ◽  
Apple Fruit ◽  
Fruit Rot ◽  
Morphological Data ◽  
Postharvest Diseases ◽  
Pear Fruit ◽  
Diseased Fruit ◽  
Molecular Phylogenetic

During surveys for postharvest diseases of apple and pear, an unknown postharvest fruit rot was observed in Washington State. The disease appeared to originate from infection of the stem and calyx tissue of the fruit or wounds on the fruit. An unknown pycnidial fungus was consistently isolated from the decayed fruit. Isolates from apple and pear were characterized and identified by molecular phylogenetic analysis and morphology. Pathogenicity of representative isolates on apple and pear fruit was tested under laboratory or field conditions. A BLAST search in GenBank showed that isolates differed from Phacidium lacerum and its synonym, Ceuthospora pinastri, by only 0 to 4 bp in sequences within part of the combined large ribosomal subunit + internal transcribed spacer + small ribosomal subunit regions. The phylogenetic analysis confirmed the taxonomic placement of the unknown fungus in the genus Phacidium, with the highest match being C. pinastri (formerly anamorphic P. lacerum) and with closely related taxa from GenBank forming congeneric clades. The fungus grew at 0 to 30°C and formed unilocular to multilocular pycnidial conidiomata on artificial media after approximately 5 to 7 days at room temperature. On potato dextrose agar incubated for a 12-h photoperiod, semi-immersed globose to subglobose pycnidial conidiomata were 250 to 1,000 μm in diameter (mean = 350), with 1 to 3 nonpapillate to slightly papillate ostioles and a buff conidial matrix. Conidia produced on phialides were 8 to 13 by 1.5 to 2.5 μm, hyaline, aseptate, cylindrical, with an abruptly tapered, typically slightly protuberant base, 2 to 3 guttules, and sometimes with a mucilaginous, flexuous, unbranched appendage which is attached to the apex of the conidium and disappears with age. Conidiogenous cells were flask shaped and 6 to 15 ×1.5 to 3 μm. Colony characteristics included felt-like aerial white mycelium, gray olivaceous at the center becoming greenish to colorless toward the margin, in concentric rings, with pycnidia forming in 5 to 7 days originating from the center of the plate. Morphological characteristics of the fungus had the greatest conformity with the description for C. pinastri. Based on molecular and morphological data, the fungus is identified as P. lacerum. ‘Fuji’ apple fruit and ‘d’Anjou’ pear fruit that were wounded, inoculated with representative isolates, and incubated at 0°C yielded the same symptoms as seen on decayed fruit collected from commercial fruit packinghouses. Stem-end rot, calyx-end rot, and wound-associated rot developed on fruit inoculated in the orchard after 3 months of cold storage. The fungus was reisolated from the diseased fruit. This is the first report of a fruit rot in apple and pear caused by P. lacerum. We propose Phacidium rot as the name of this disease.

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1190
Author(s):  
Yuqi Huang ◽  
Minghao Sun ◽  
Lenan Zhuang ◽  
Jin He
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Functional Characterization ◽  
Vertebrate Evolution ◽  
Molecular Phylogenetic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Molecular Phylogenetic ◽  
Duplication Events ◽  
Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

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