Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

Dindin Hidayatul Mursyidin,Gusti Muhammad Zainal Ahyar,Ahmad Winarto Saputra,Aminoor Hidayat

doi:10.15294/biosaintifika.v13i2.29904

Dindin Hidayatul Mursyidin, Gusti Muhammad Zainal Ahyar + Show 2 more

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https://doi.org/10.15294/biosaintifika.v13i2.29904

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Abstract

In silico is the more comprehensive and applicable approach in supporting, both conservation and breeding programs of germplasm. The study aimed to analyze and determine the genetic diversity and relationships of 24 species of Phalaenopsis using two DNA barcoding markers, namely the rbcL and trnL-F, by in silico approach. All sequences of these markers were collected randomly from the NCBI website and analyzed using several softwares and methods, such as ClustalW and MultAlin for multiple sequence alignments and MEGA-X to determine its genetic diversity and relationships. Specifically, the genetic diversity was determined using a nucleotide diversity index and their relationships by the Maximum Likelihood method. The results showed that Phalaenopsis has a low genetic diversity of 0.24, 0.32, and 0.19, respectively. The phylogenetic analysis revealed that this orchid separated into five (for the rbcL), six (trnL-F), and seven clades (a combined one), where the closest relationship is shown by P. amboinensis vs. P. venosa, whereas the farthest by P. gibbosa vs. P. doweryensis, P. stuartiana vs. P. micholitzii, and P. celebensis vs. P. pulchra. The results have novel information on the diversity and relationships of Phalaenopsis on the in silico approach. Thus, our findings might be used in supporting the conservation and breeding program of Phalaenopsis, both locally and globally.

Highlights

Phalaenopsis, commonly known as moth orchid (Tsai et al, 2012), is the most popular orchid genus in the world (Chen et al, 2013b; Deng et al, 2015; Hsu et al, 2018)
The rbcL has a range of nucleotides of 669-718 bp, whereas the trnL-F has 568-1126 bp
According to CBOL (2009), the rbcL has a complete sequence, including approximately 1400 nucleotides coding for the large subunit protein, but the length varies slightly among flowering plants (Angiosperm)

Summary

Introduction

Phalaenopsis, commonly known as moth orchid (Tsai et al, 2012), is the most popular orchid genus in the world (Chen et al, 2013b; Deng et al, 2015; Hsu et al, 2018). The popularity of this orchid is mainly related to the characteristics of the flowers it has, both shape, color, scent, and a long-lasting blossom (Hsu et al, 2011). In Indonesia, there are more than 20 species of Phalaenopsis scattered in several large islands, including Sumatra, Java, Kalimantan, Nusa Tenggara, Sulawesi, Maluku, and Papua (Fatimah & Sukma, 2011; Rahayu et al, 2015)

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