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 rafflesiae dan Penilaian Potensinya 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

 

Diterima: 14 Jun 2021/Diserahkan: 10 Februari 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

 

RUJUKAN

Adam, J.H., Juhari, M.A.A., Mohamed, R., Abdul Wahab, N.A., Arshad, S., Kamaruzaman, M.P., Mohd Raih, M.F. & Wan, K-L. 2016. Rafflesia tuanku-halimii (Rafflesiaceae), a new species from Peninsular Malaysia. Sains Malaysiana 45(11): 1589-1595.

Aguileta, G., De Vienne, D.M., Ross, O.N., Hood, M.E., Giraud, T., Petit, E. & Gabaldón, T. 2014. High variability of mitochondrial gene order among fungi. Genome Biology and Evolution 6(2): 451-465.

Arshad, S., Juhari, M.A.A., Talip, N., Abdul Wahab, N.A.A. & Adam, J. 2021. Anatomy and micromorphology of Tetrastigma rafflesiae (Vitaceae). Sains Malaysiana 50(4): 897-905.

Arshad, S., Juhari, M.A.A., Talip, N., Abdul Wahab, N.A.A., Fadzilah, S. & Adam, J. 2020. Comparative leaf anatomy of Tetrastigma rafflesiae (Miq.) Planchon and Tetrastigma pedunculare (Wall. ex Laws.) Planch. in Peninsular Malaysia. Sains Malaysiana 49(4): 721-729.

Álvarez, I. & Wendel, J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29(3): 417-434.

Alverson, A.J., Wei, X., Rice, D.W., Stern, D.B., Barry, K. & Palmer, J.D. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Molecular Biology and Evolution 27(6): 1436-1448.

Barkman, T.J., McNeal, J.R., Lim, S-H., Coat, G., Croom, H.B., Young, N.D. & dePamphilis, C.W. 2007. Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evolutionary Biology 7(1): 248.

Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. & Pirovano, W. 2010. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4): 578-579.

Bosi, E., Donati, B., Galardini, M., Brunetti, S., Sagot, M.-F., Lió, P., Crescenzi, P., Fani, R. & Fondi, M. 2015. MeDuSa: A multi-draft based scaffolder. Bioinformatics 31(15): 2443-2451.

Chase, M.W., Salamin, N., Wilkinson, M., Dunwell, J.M., Kesanakurthi, R.P., Haidar, N. & Savolainen, V. 2005. Land plants and DNA barcodes: Short-term and long-term goals. Philosophical Transactions of the Royal Society B: Biological Sciences 360(1462): 1889-1895.

Chen, P., Chen, L. & Wen, J. 2011. The first phylogenetic analysis of Tetrastigma (Miq.) Planch, the host of Rafflesiaceae. Taxon 60(2): 499-512.

Cho, Y., Mower, J.P., Qiu, Y.L. & Palmer, J.D. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proceedings of the National Academy of Sciences of the United States of America 101(51): 17741-17746.

Christin, P.A., Besnard, G., Edwards, E.J. & Salamin, N. 2012. Effect of genetic convergence on phylogenetic inference. Molecular Phylogenetics and Evolution 62(3): 921-927.

Corriveau, J.L. & Coleman, A.W. 1988. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. American Journal of Botany 75(10): 1443-1458.

Donnelly, K., Cottrell, J., Ennos, R.A., Vendramin, G.G., A’Hara, S., King, S., Perry, A., Wachowiak, W. & Cavers, S. 2017. Reconstructing the plant mitochondrial genome for marker discovery: A case study using Pinus. Molecular Ecology Resources 17(5): 943-954.

Duminil, J. 2014. Mitochondrial genome and plant taxonomy. Methods in Molecular Biology 1115: 121-140.

Fauron, C., Allen, J., Clifton, S. & Newton, K. 2004. Plant mitochondrial genomes. In Molecular Biology and Biotechnology of Plant Organelles, edited by Daniell, H. & Chase, C. Dordrecht: Springer. pp. 151-177.

Feliner, G.N. & Rosselló, J.A. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44(2): 911-919.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17(6): 368-376.

Fu, Y-M., Jiang, W-M. & Fu, C-X. 2011. Identification of species within Tetrastigma (Miq.) Planch. (Vitaceae) based on DNA barcoding techniques. Journal of Systematics and Evolution 49(3): 237-245.

Goremykin, V.V., Salamini, F., Velasco, R. & Viola, R. 2009. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Molecular Biology and Evolution 26(1): 99-110.

Götz, S., García-Gómez, J.M., Terol, J., Williams, T.D., Nagaraj, S.H., Nueda, M.J., Robles, M., Talón, M., Dopazo, J. & Conesa, A. 2008. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research 36(10): 3420-3435.

Govindarajulu, R., Parks, M., Tennessen, J.A., Liston, A. & Ashman, T.A. 2015. Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species. American Journal of Botany 102(4): 544-554.

Gualberto, J.M., Mileshina, D., Wallet, C., Niazi, A.K., Weber-Lotfi, F. & Dietrich, A. 2014. The plant mitochondrial genome: Dynamics and maintenance. Biochimie 100: 107-120.

Hebert, P.D.N., Cywinska, A., Ball, S.L. & DeWaard, J.R. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270(1512): 313-321.

Hollingsworth, P.M., Forrest, L.L., Spouge, J.L., Hajibabaei, M., Ratnasingham, S., van der Bank, M., Chase, M.W., Cowan, R.S., Erickson, D.L., Fazekas, A.J., Graham, S.W., James, K.E., Kim, K-J., Kress, W.J., Schneider, H., van AlphenStahl, J., Barrett, S.C.H., van den Berg, C., Bogarin, D., Burgess, K.S., Cameron, K.M., Carine, M., Chacòn, J., Clark, A., Clarkson, J.J., Conrad, F., Devey, D.S., Ford, C.S., Hedderson, T.A.J., Hollingsworth, M.L., Husband, B.C., Kelly, L.J., Kesanakurti, P.R., Kim, J.S., Kim, Y-D., Lahaye, R., Lee, H-L., Long, D.G., Madriñán, S., Maurin, O., Meusnier, I., Newmaster, S.G., Park, C-W., Percy, D.M., Petersen, G., Richardson, J.E., Salazar, G.A., Savolainen, V., Seberg, O., Wilkinson, M.J., Yi, D-K. & Little, D.P. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 106(31): 12794-12797.

Ji, T., Ji, W.W., Wang, J., Chen, H.J., Peng, X., Cheng, K.J., Qiu, D. & Yang, W.J. 2021. A comprehensive review on traditional uses, chemical compositions, pharmacology properties and toxicology of Tetrastigma hemsleyanum. Journal of Ethnopharmacology 264: 113247.

Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35(6): 1547-1549.

Langmead, B. & Salzberg, S.L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9(4): 357.

Latiff, A. 1983. Studies in Malesian Vitaceae VII. The genus Tetrastigma in the Malay Peninsula. Gardens’ Bulletin Singapore 36(2): 213-228.

Li, X., Yang, Y., Henry, R.J., Rossetto, M., Wang, Y. & Chen, S. 2015. Plant DNA barcoding: From gene to genome. Biological Reviews 90(1): 157-166.

Liu, D., Ju, J.H., Xu, X.D., Yang, J.S. & Tu, G.Z. 2002. New C-glycosylflavones from Tetrastigma hemsleyanum (Vitaceae). Acta Botanica Sinica 44(2): 227-229.

Molina, J., Hazzouri, K.M., Nickrent, D., Geisler, M., Meyer, R.S., Pentony, M.M., Flowers, J.M., Pelser, P., Barcelona, J., Inovejas, S.A., Uy, I., Yuan, W., Wilkins, O., Michel, C-I., Locklear, S., Concepcion, G.P. & Purugganan, M.D. 2014. Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae). Molecular Biology and Evolution 31(4): 793-803.

Nabholz, B., Glémin, S. & Galtier, N. 2009. The erratic mitochondrial clock: Variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evolutionary Biology 9(1): 1-13.

Nais, J. 2001. Rafflesia of the World. Sabah: Natural History Publications.

Nasihah, M., Zulhazman, H., Siti Munirah, M.Y., Wan Norqayyum Nadia, W.A. & Latiff, A. 2016. Tetrastigma hookeri (Laws.) Planch.(Vitaceae), a host plant for Rafflesia kerri Meijer in Peninsular Malaysia. Malayan Nature Journal 68: 33-39.

Nikolov, L.A., Tomlinson, P.B., Manickam, S., Endress, P.K., Kramer, E.M. & Davis, C.C. 2014. Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world’s largest flowers. Annals of Botany 114(2): 233-242.

Paterson, A.H., Freeling, M., Tang, H. & Wang, X. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372.

Qiu, Y.L., Li, L., Wang, B., Xue, J.Y., Hendry, T.A., Li, R.Q., Brown, J.W., Liu, Y., Hudson, G.T. & Chen, Z.D. 2010. Angiosperm phylogeny inferred from sequences of four mitochondrial genes. Journal of Systematics and Evolution 48(6): 391-425.

Qiu, Y.L., Li, L., Hendry, T.A., Li, R., Taylor, D.W., Issa, M.J., Ronen, A.J., Vekaria, M.L. & White, A.M. 2006. Reconstructing the basal angiosperm phylogeny: Evaluating information content of mitochondrial genes. Taxon 55(4): 837-856.

Reboud, X. & Zeyl, C. 1994. Organelle inheritance in plants. Heredity 72: 132-140.

Sievers, F. & Higgins, D.G. 2014. Clustal Omega. Current Protocols in Bioinformatics 48(1): 3-13.

Sloan, D.B., Wu, Z. & Sharbrough, J. 2018. Correction of persistent errors in Arabidopsis reference mitochondrial genomes. The Plant Cell 30(3): 525-527.

Sloan, D.B., Alverson, A.J., Chuckalovcak, J.P., Wu, M., McCauley, D.E., Palmer, J.D. & Taylor, D.R. 2012. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biology 10(1): e100124.

Smith, D.R. & Keeling, P.J. 2015. Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes. Proceedings of the National Academy of Sciences of the United States of America 112(33): 10177-10184.

Sun, Y., Moore, M.J., Zhang, S., Soltis, P.S., Soltis, D.E., Zhao, T., Meng, A., Li, X., Li, J. & Wang, H. 2016. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution. Molecular Phylogenetics and Evolution 96: 93-101.

Van de Paer, C., Bouchez, O. & Besnard, G. 2018. Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae). Molecular Ecology Resources 18(3): 407-423.

Wan Zakaria, W.N.F., Ahmad Puad, A.S., Geri, C., Zainudin, R. & Latiff, A. 2016. Tetrastigma diepenhorstii (Miq.) Latiff (Vitaceae), a new host of Rafflesia tuan-mudae Becc. (Rafflesiaceae) in Borneo. Journal of Botany 2016: Article ID. 3952323.

Wendel, J.F. & Doyle, J.J. 1998. Phylogenetic incongruence: Window into genome history and molecular evolution. In Molecular Systematics of Plants II, edited by Soltis, D.E., Soltis, P.S. & Doyle, J.J. Boston: Springer. pp. 265-296.

Wynn, E.L. & Christensen, A.C. 2019. Repeats of unusual size in plant mitochondrial genomes: Identification, incidence and evolution. G3: Genes, Genomes, Genetics 9(2): 549-559.

Xu, C., Ding, G-Q., Fu, J-Y., Meng, J., Zhang, R-H. & Lou, X-M. 2008. Immunoregulatory effects of ethyl-acetate fraction of extracts from Tetrastigma hemsleyanum Diels et. Gilg on immune functions of ICR mice. Biomedical and Environmental Sciences 21: 325-331.

Yang, X.L., Luo, J., Sun, S.B., Wang, H.Z., Wu, X.Y., Liu, H. & Peng, H.G. 1989. Study on antiviral effect of Tetrastigma hemsleyanum. Hubei Journal of Traditional Chinese Medicine 4: 40-41.

Yang, Z. & Rannala, B. 2012. Molecular phylogenetics: Principles and practice. Nature Reviews Genetics 13(5): 303-314.

Ye, J., Zhang, Y., Cui, H., Liu, J., Wu, Y., Cheng, Y., Xu, H., Huang, X., Li, S., Zhou, A., Zhang, X., Bolund, L., Chen, Q., Wang, J., Yang, H., Fang, L. & Shi, C. 2018. WEGO 2.0: A web tool for analyzing and plotting GO annotations, 2018 update. Nucleic Acids Research 46(W1): W71-W75.

Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., Wang, J., Li, S., Li, R., Bolund, L. & Wang, J. 2006. WEGO: A web tool for plotting GO annotations. Nucleic Acids Research 34(suppl. 2): W293-W297.

Zerbino, D.R. & Birney, E. 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18(5): 821-829.

 

*Pengarang untuk surat-menyurat; email: klwan@ukm.edu.my

 

 

   

   

sebelumnya