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