Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS)  and chloroplast (trnL-F) DNA sequences

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.

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A phylogenetic analysis of Epimedium (Berberidaceae) based on nuclear ribosomal DNA sequences

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2004.12.014 ◽

2005 ◽

Vol 35 (1) ◽

pp. 287-291 ◽

Cited By ~ 27

Author(s):

Ye Sun ◽

Kwok-Pui Fung ◽

Ping-Chung Leung ◽

Pang-Chui Shaw

Keyword(s):

Phylogenetic Analysis ◽

Ribosomal Dna ◽

Dna Sequences ◽

Nuclear Ribosomal Dna

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Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

Bangladesh Journal of Botany ◽

10.3329/bjb.v48i4.49058 ◽

2019 ◽

Vol 48 (4) ◽

pp. 1099-1106

Author(s):

Emre Sevindik ◽

Zehra Tuğba Murathan ◽

Sümeyye Filiz ◽

Kübra Yalçin

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Dna Sequence ◽

Dna Sequences ◽

Genomic Dna ◽

Nucleotide Composition ◽

Neighbor Joining ◽

Sequencing Data ◽

F Region ◽

Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

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A Phylogenetic Analysis of Epilobium (Onagraceae) Based on Nuclear Ribosomal DNA Sequences

Systematic Botany ◽

10.2307/2419763 ◽

1994 ◽

Vol 19 (3) ◽

pp. 363 ◽

Cited By ~ 125

Author(s):

David A. Baum ◽

Kenneth J. Sytsma ◽

Peter C. Hoch

Keyword(s):

Phylogenetic Analysis ◽

Ribosomal Dna ◽

Dna Sequences ◽

Nuclear Ribosomal Dna

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Molecular record for the first authentication of Isaria cicadae from Vietnam

Open Life Sciences ◽

10.1515/biol-2021-0074 ◽

2021 ◽

Vol 16 (1) ◽

pp. 711-718

Author(s):

Thuan Duc Lao ◽

Hanh Van Trinh ◽

Loi Vuong ◽

Luyen Tien Vu ◽

Thuy Ai Huyen Le ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genomic Dna ◽

Morphological Analysis ◽

Phylogenetic Analyses ◽

Neighbor Joining ◽

Pcr Assay ◽

Parsimony Method ◽

Maximum Parsimony Method ◽

Cordyceps Cicadae ◽

High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

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