Phylogenetic Analysis of Eight Malaysian Pineapple Cultivars using a Chloroplastic Marker (rbcL gene)

2013 ◽  
Vol 64 (2) ◽  
Author(s):  
Norfadilah Hamdan ◽  
Azman Abd Samad ◽  
Topik Hidayat ◽  
Faezah Mohd Salleh
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Similarity ◽  
Accurate Method ◽  
Ananas Comosus ◽  
Rbcl Gene ◽  
Ribulose Bisphosphate Carboxylase ◽  
Ribulose Bisphosphate ◽  
Parsimony Method ◽  
Bisphosphate Carboxylase ◽  
Maximum Parsimony Method

To date, Malaysian pineapple cultivars has only been characterized morphologically. A more consistent and accurate method such as biomarker is highly crucial to distinguish and establish the genetic relationship between different cultivars. In this work, we conducted a phylogenetic analysis of eight Malaysian pineapple cultivars using a chloroplastic DNA biomarker, ribulose-bisphosphate carboxylase (rbcL) gene. The rbcL gene was isolated from genomic DNA, amplified and sequenced. The rbcL gene of Ananas comosus is approximately 1100 bp. From the multialignment of eight cultivars, the percentage of sequence similarity ranged from 71.1% to 94.98% and is highly conserved throughout the sequences. Phylogenetic analysis which is carried out using maximum parsimony method revealed that the eight Malaysian pineapple cultivars can be classified into two groups. The first group consist of Yankee and Gandul cultivars while Moris, Moris Bentanggur, Moris Gajah, N36, Josaphine and Sarawak falls under the second group. Bootstrap values in some branches are low which reflect the small number of informative characters (981 are conserved, 12 are potentially informative). Formation of several group or subclades is due to its similar genetic pattern, thus supporting this classification. This study confirmed that rbcL gene is a good indicator to determine the phylogenetic relationship distinguishing the Malaysian pineapple cultivars.

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

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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