Alifah Nur Anzani, Irfan Martiansyah, Nia Yuliani

Studi in silico DNA barcoding pada bunga soka (Ixora)

Introduction

Studi in silico dna barcoding pada bunga soka (ixora). Telusuri studi in silico DNA barcoding bunga Soka (Ixora). Analisis kekerabatan molekuler pakai gen rbcL, trnL, matK. rbcL terbukti informatif untuk identifikasi spesies Ixora.

Abstract

Ixora merupakan genus tumbuhan dari famili Rubiaceae yang memiliki lebih dari 500 spesies. Genus ini, tersebar di area tropis Asia dan Afrika dengan keragaman terbesar tersebar di Asia Tenggara. Di Indonesia, Ixora dinamakan juga bunga Soka dan populer sebagai tanaman hias. Bunga Soka memiliki bentuk yang menarik dan warna bunga yang bervariasi. Penelitian DNA barcoding mengenai tumbuhan Ixora belum banyak dilakukan, oleh karena itu diperlukan studi awal yang bertujuan menganalisis kekerabatan Ixora dengan menggunakan sekuen gen rbcL,trnL, dan matK berbasis in silico. Metode yang dilakukan dalam DNA barcoding bunga Soka Ixora adalah dengan studi in silico menggunakan Genbank (NCBI). Sekuen DNA dikoleksi dari basis data NCBI dengan mencari nama spesies dan gen yang digunakan yaitu matK, rbcL, dan trnL. Selanjutnya data dianalisis menggunakan CLUSTAL W untuk menentukan tingkat homologi antar sekuen melalui penjajaran sekuen, identifikasi sekuen yang berpotensi sebagai barcode, dan rekosntruksi pohon filogenetik menggunakan MEGA X. Hasil studi in silico menunjukkan bahwa penjajaran dengan menggunakan lokus trnL, matK dan rbcL memiliki tingkat homologi yang relatif tinggi. Akan tetapi, gen rbcL memberikan gambaran yang informatif mengenai topologi pohon kekerabatan molekuler dari Ixora pada tingkat spesies dibandingkan dengan gen trnL dan gen matK. Selain itu, gen rbcL diketahui dapat memperlihatkan karakter spesifik dari Ixora sehingga diduga dapat dijadikan sebagai barcode untuk mengidentifikasi spesies-spesies Ixora di Kebun Raya Bogor melalui pendekatan molekuler.

Review

This study presents an *in silico* investigation into DNA barcoding for the *Ixora* genus, a diverse group within the Rubiaceae family popular as an ornamental plant in Indonesia. Acknowledging the limited prior research on *Ixora* DNA barcoding, the authors' objective was to analyze phylogenetic relationships using the standard plant barcoding markers *rbcL*, *trnL*, and *matK* gene sequences obtained from public databases. This preliminary exploration of molecular markers for species identification in *Ixora* is a relevant step towards understanding the diversity and facilitating the identification of this horticulturally important genus. The methodology involved an *in silico* approach, where DNA sequences for *matK*, *rbcL*, and *trnL* genes were retrieved from NCBI's GenBank. These sequences were then subjected to alignment using CLUSTAL W to determine homology, and phylogenetic trees were reconstructed using MEGA X. The results indicate that all three loci exhibit relatively high sequence homology. However, the *rbcL* gene emerged as the most informative marker, providing a clearer representation of molecular relationships at the species level within *Ixora* compared to *trnL* and *matK*. Consequently, the authors propose that the *rbcL* gene possesses specific characteristics that could make it a suitable DNA barcode for identifying *Ixora* species, particularly for specimens in the Bogor Botanical Garden. This *in silico* study provides a valuable initial assessment of DNA barcode efficacy for the *Ixora* genus, successfully identifying *rbcL* as a promising candidate marker. The strength of this work lies in its foundational contribution to a less-studied genus and its demonstration of an efficient *in silico* screening process. However, it is crucial to recognize that the findings are based solely on existing public data. The conclusions regarding the definitive use of *rbcL* as a barcode require rigorous experimental validation through wet-lab sequencing of actual *Ixora* samples, preferably including those from the Bogor Botanical Garden to confirm its practical applicability. Future research should prioritize expanding the dataset with new sequence data from a wider range of *Ixora* species and corroborating these molecular findings with morphological characteristics for a comprehensive and robust identification system.

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