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

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.

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Genetic Diversity of Archaea in Deep-Sea Hydrothermal Vent Environments

Genetics ◽

10.1093/genetics/152.4.1285 ◽

1999 ◽

Vol 152 (4) ◽

pp. 1285-1297 ◽

Cited By ~ 3

Author(s):

Ken Takai ◽

Koki Horikoshi

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Deep Sea ◽

Hydrothermal Vent ◽

Small Subunit ◽

Molecular Phylogenetic Analysis ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Rdna Sequencing ◽

Molecular Phylogenetic

Abstract Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.

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Asproinocybaceae fam. nov. (Agaricales, Agaricomycetes) for Accommodating the Genera Asproinocybe and Tricholosporum, and Description of Asproinocybe sinensis and Tricholosporum guangxiense sp. nov

Journal of Fungi ◽

10.3390/jof7121086 ◽

2021 ◽

Vol 7 (12) ◽

pp. 1086

Author(s):

Guang-Fu Mou ◽

Tolgor Bau

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Small Subunit ◽

Internal Transcribed Spacer Region ◽

Independent Family ◽

New Family ◽

Family Level ◽

Molecular Phylogenetic

Asproinocybe and Tricholosporum are not well known, and their placement at the family level remains undetermined. In this study, we conducted molecular phylogenetic analyses based on nuc rDNA internal transcribed spacer region (ITS) and nuc 28S rDNA (nrLSU), and a dataset with six molecular markers (ITS, LSU, RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2), 18S nuclear small subunit ribosomal DNA (nrSSU), and translation elongation factor 1-alpha (TEF1-α)) using Bayesian (BA) and Maximum Likelihood (ML) methods, we found that the species of Asproinocybe and Tricholosporum formed an independent family-level clade (0.98/72). Asproinocybaceae fam. nov., a new family, is established here for accommodating this clade. Two new species, Asproinocybe sinensis and Tricholosporum guangxiense, from subtropical and tropical karst areas of China, are also described here.

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

Vietnam Journal of Science and Technology ◽

10.15625/2525-2518/55/1a/12385 ◽

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.

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Ophiocordyceps highlandensis, a new entomopathogenic fungus from Yunnan, China

Phytotaxa ◽

10.11646/phytotaxa.204.4.5 ◽

2015 ◽

Vol 204 (4) ◽

pp. 287 ◽

Cited By ~ 5

Author(s):

Zhu L. Yang ◽

Jiao Qin ◽

Chengfeng Xia ◽

Qun Hu ◽

Qing-Qing Li

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Molecular Evidence ◽

Line Drawings ◽

Phylogenetic Placement ◽

Genes Encoding ◽

Molecular Phylogenetic ◽

A New Species

A new species of Ophiocordycipitaceae, Ophiocordyceps highlandensis, from southwestern China is described using morphological and molecular evidence. It is morphologically characterized by the combination of the following characters: dark-brown to blackish stromata on larvae of Scarabaeidae, fully immersed perithecia with non-protruding ostioles, 3-septate filiform ascospores breaking easily into four part-spores (20) 33–55 × 1.5–2 μm and a hymeniform cortex layer of stipe. Molecular phylogenetic analyses using DNA nucleotide sequences of the nuclear ribosomal small subunit, and the genes encoding the largest subunit of RNA polymerase II and the second-largest subunit of RNA polymerase II indicated that O. highlandensis was related to O. konnoana, O. barnesii, O. nigrella, O. ravenelii and O. superficialis. Ophiocordyceps highlandensis and its related species were all characterized by dark-brown stromata and an affinity for melolonthid larval hosts. A description, line drawings, phylogenetic placement and comparison with allied taxa are presented.

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Biosystematic studies on the genusPolygonatum (Convallariaceae) IV. Molecular phylogenetic analysis based on restriction site mapping of the chloroplast genetrnK

Feddes Repertorium ◽

10.1002/fedr.4921080306 ◽

1997 ◽

Vol 108 (3-4) ◽

pp. 159-168

Author(s):

M. N. Tamura ◽

A. E. Schwarzbach ◽

S. Kruse ◽

R. Reski

Keyword(s):

Phylogenetic Analysis ◽

Restriction Site ◽

Molecular Phylogenetic Analysis ◽

Site Mapping ◽

Molecular Phylogenetic ◽

Restriction Site Mapping

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Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽

10.3390/genes12081190 ◽

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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