Sains Malaysiana 51(1)(2022): 121-136

http://doi.org/10.17576/jsm-2022-5101-10

Pencirian Jujukan Genom Mitokondria Spesies Rafflesia (Rafflesiaceae) di Semenanjung Malaysia

  (Characterisation of Mitochondrial Genome Sequences of Rafflesia Species (Rafflesiaceae) in Peninsular Malaysia)

QIONG CHIN¹, MOHD-NOOR MAT-ISA^1,2, MOHD-FAIZAL ABU-BAKAR², NORFARHAN MOHD-ASSAAD³ & KIEW-LIAN WAN¹*

¹Jabatan Sains Biologi dan Bioteknologi, Fakulti Sains dan Teknologi, Universiti Kebangsaan Malaysia 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

²Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor Darul Ehsan, Malaysia

³Jabatan Fizik Gunaan, Fakulti Sains dan Teknologi, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

Received: 8 February 2021/Accepted: 25 May 2021

ABSTRAK

Rafflesia terkenal sebagai tumbuhan yang menghasilkan bunga tunggal yang terbesar di dunia. Namun, ia semakin jarang ditemui dan ialah spesies dalam bahaya. Sistem pengelasan spesies Rafflesia ialah komponen penting dalam usaha pemuliharaan lazimnya bergantung kepada pencirian morfologi bunga. Walau bagaimanapun, pendekatan molekul, termasuk yang berasaskan kepada jujukan genom mitokondria (mtDNA), berupaya menyediakan kaedah pengelasan yang lebih berkesan. Untuk meneroka kemungkinan ini, jujukan mtDNA empat spesies Rafflesia di Semenanjung Malaysia, iaitu R. cantleyi, R. azlanii, R. kerrii dan R. sharifah-hapsahiae telah dihimpun dan dicirikan dalam kajian ini. Bacaan jujukan mtDNA untuk setiap spesies kajian pada mulanya telah ditentukan masing-masing daripada set data genom keseluruhan menggunakan pendekatan pemetaan berbantukan rujukan. Proses penghimpunan secara de novo dan perancahan kemudiannya telah dijalankan ke atas bacaan jujukan yang telah dikenal pasti untuk menghasilkan jujukan mtDNA bagi R. cantleyi (441,992 pb), R. azlanii (472,723 pb), R. kerrii (500,932 pb) dan R. sharifah-hapsahiae (453,747 pb). Seterusnya, anotasi mtDNA bagi setiap spesies telah mengenal pasti sekurang-kurangnya 31 gen pengekodan protein, enam gen tRNA dan tiga rRNA. Perbandingan gen mitokondria mendapati bahawa beberapa gen seperti cob, rpl10, mttB dan ccmB mempamerkan orientasi yang berbeza dalam spesies Rafflesia yang tertentu manakala analisis penjajaran jujukan berganda menunjukkan jujukan gen nad1 adalah berbeza antara keempat-empat spesies Rafflesia yang dikaji. Analisis filogenetik dengan menggunakan jujukan bagi tujuh gen pengekodan protein yang terpelihara berupaya membezakan spesies Rafflesia yang dikaji. Kesimpulannya, hasil pencirian jujukan mtDNA menunjukkan bahawa jujukan gen mitokondria yang khusus berupaya membezakan spesies Rafflesia yang dikaji dan berpotensi untuk digunakan bagi tujuan pengenalpastian serta pengelasan spesies Rafflesia dalam usaha pemuliharaan organisma yang unik ini.

Kata kunci: Genomik perbandingan; kepelbagaian genetik; penanda molekul; Rafflesia

ABSTRACT

Rafflesia is well-known as a plant that produces the largest single flower in the world. However, it is an increasingly rare and endangered species. The Rafflesia species classification system, which is an important component in conservation efforts usually depends on the morphological characterisation of the flower. However, molecular approaches, including those based on mitochondrial genome (mtDNA) sequences, may provide a more effective classification method. To explore this possibility, mtDNA sequences of four Rafflesia species in Peninsular Malaysia, namely R. cantleyi, R. azlanii, R. kerrii and R. sharifah-hapsahiae were assembled and characterised in this study. mtDNA sequencing reads for each of the four species were initially identified from their respective whole genome data sets using the reference-assisted mapping approach. De novo assembly and scaffolding processes were then carried out on the identified mtDNA sequencing reads to produce mtDNA sequences for R. cantleyi (441,992 bp), R. azlanii (472,723 bp), R. kerrii (500,932 bp) and R. sharifah-hapsahiae (453,747 bp). Subsequently, annotation of mtDNA for each species identified at least 31 protein coding, six tRNA and three rRNA genes. Comparative gene analysis showed that several genes such as cob, rpl10, mttB and ccmB display different orientation in certain Rafflesia species while multiple sequence alignment analysis showed that the nad1 gene sequence is different between the four Rafflesia species studied. Phylogenetic analysis using seven conserved protein coding gene sequences were able to differentiate the Rafflesia species studied. In conclusion, the results of mtDNA sequence characterisation indicate that specific mitochondrial gene sequences are capable of distinguishing the Rafflesia species studied, and have the potential to be used for identification and classification of Rafflesia species in efforts to conserve this unique organism.

Keywords: Comparative genomics; genetic diversity; molecular marker; Rafflesia

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*Corresponding author; email: klwan@ukm.edu.my