Sains Malaysiana 51(8)(2022): 2435-2447

http://doi.org/10.17576/jsm-2022-5108-08

 

 Characterisation of Tetrastigma rafflesiae Mitochondrial Genes and Assessment of their Potential as Sequence Markers

(Pencirian Gen Mitokondria Tetrastigma rafflesiaedan Penilaian Potensi Gen Tersebut sebagai Penanda Jujukan)

 

MOHAMAD HAFIZZUDIN-FEDELI1, MOHD-FAIZAL ABU-BAKAR2, MOHD-NOOR MAT-ISA1,2, A. LATIFF1, MOHD FIRDAUS-RAIH3,4 & KIEW-LIAN WAN1,*

 

1Department of Biological Sciences and Biotechnology, Faculty of Science and Technology,

Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

2Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, 43000 Kajang, Selangor Darul Ehsan, Malaysia

3Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

4Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

Received: 14 June 2021/Accepted: 10 February 2022

 

Abstract

Tetrastigma rafflesiae (Miq.) Planch. is a climbing plant species that is known for its unique relationship with holoparasitic plants of Rafflesiaceae. Knowledge on the mitochondrial genes of this species may contribute towards the development of molecular approaches for species identification. This study aims to identify and characterise genes from the T. rafflesiae mitochondrial genome (mitogenome) and assess their potential to discriminate different Tetrastigma species. Mitochondrial-specific sequences were first selected by mapping T. rafflesiae whole-genome sequences to mitogenomes from several reference plant species. De novo assembly of these selected sequences produced a T. rafflesiae mitogenome with a size of 336 kb. Gene annotation revealed that the T. rafflesiae mitogenome contains at least 40 protein coding genes, 20 tRNAs and two rRNAs. Phylogenetic analysis using several mitochondrial genes, namely ccmB, cob, matR, nad6 and rps3 was able to differentiate T. rafflesiae from three other Tetrastigma species, indicating the potential of these genes as species-specific sequence markers. These findings supplement additional genetic information on T. rafflesiae and may aid in the effort of species classification and conservation.

 

Keywords: Molecular markers; plant mitogenome; phylogeny; species identification

 

ABSTRAK

Tetrastigma rafflesiae (Miq.) Planch. adalah spesies tumbuhan memanjat yang terkenal kerana hubungannya yang unik dengan tumbuhan holoparasit daripada Rafflesiaceae. Pengetahuan mengenai gen mitokondria spesies ini dapat menyumbang ke arah pembangunan pendekatan molekul untuk pengecaman spesies. Kajian ini bertujuan untuk mengenal pasti dan mencirikan gen daripada genom mitokondria (mitogenom) T. rafflesiae dan menilai potensi gen tersebut dalam membezakan spesies Tetrastigma yang berbeza. Jujukan khusus mitokondria pada mulanya dipilih melalui pemetaan jujukan keseluruhan genom T. rafflesiae kepada mitogenom daripada beberapa spesies tumbuhan rujukan. Penghimpunan de novo jujukan terpilih ini menghasilkan mitogenom T. rafflesiae yang bersaiz 336 kb. Anotasi gen menunjukkan bahawa mitogenom T. rafflesiae mengandungi sekurang-kurangnya 40 gen pengekodan protein, 20 tRNA dan dua rRNA. Analisis filogenetik menggunakan beberapa gen mitokondria iaitu ccmB, cob, matR, nad6 dan rps3 berupaya membezakan T. rafflesiae daripada tiga spesies Tetrastigma yang lain lalu menunjukkan potensi kesemua gen ini sebagai penanda jujukan yang khusus bagi spesies. Penemuan ini menyumbang maklumat genetik tambahan mengenai T. rafflesiae dan boleh membantu usaha pengkelasan dan pemuliharaan spesies.

 

Kata kunci: Filogeni; mitogenom tumbuhan; penanda molekul; pengecaman spesies

 

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

 

 

 

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