DNA Barcoding, Prey Spectrum Analysis, and Vegetative Propagation of Nepenthes mirabilis × rafflesiana, A Rarely Sighted Pitcher Plant Hybrid from Peninsular Malaysia
Abstract
A solitary female Nepenthes hybrid (Nepenthes mirabilis × rafflesiana), bearing 20-cm tall reddish pitchers, was discovered in the last remaining peat swamp forest in Johor, Peninsular Malaysia. The nothospecies (natural hybrid) is considered a very rare occurrence and has been designated as a taxon of high ecological importance, underscoring the urgent need for in-depth study and targeted conservation initiatives. To confirm its genetic identity, DNA sequencing was conducted, and the phylogenetic analysis of the internal transcribed spacer region (ITS1-5.8S-ITS2) indicated a strong genetic relationship between the hybrid (accession no. OR741796) and N. rafflesiana. Consistent with this, the ITS1 secondary structure of the hybrid exhibited a conserved folding structure similar to that of N. rafflesiana. It was recorded that the nothospecies primarily preys on hymenopterans from the family Formicidae, including at least seven genera. Furthermore, mosquito larvae from the genus Toxorhynchites were observed in both upper and lower pitchers, highlighting the pitcher plant's importance as a crucial breeding site for the predatory elephant mosquito. Given that only one living specimen of the nothospecies was discovered, we optimised a shoot-based vegetative propagation method that allowed several clones to be produced, which will be vital for the success of future reintroduction efforts. This is the first report to simultaneously address the molecular, ecological, and horticultural aspects of a Nepenthes natural hybrid in Peninsular Malaysia.
References
Adam, J.H. & Hamid, H.A., 2007. Pitcher plants (Nepenthes) recorded from Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia. International Journal of Botany, 3(1), pp.71–77. doi: 10.3923/ijb.2007.71.77
Alamsyah, F. & Ito, M., 2013. Phylogenetic analysis of Nepenthaceae, based on internal transcribed spacer nuclear ribosomal DNA sequences. Acta Phytotaxonomica et Geobotanica, 64(3), pp.113–126. doi: 10.18942/apg.KJ00008918921
Alejandro, G.J.D. et al., 2007. Conspecificity of Nepenthes alata Blco. population found in Mt. Guisguis, Zambales inferred from internal transcribed spacer (nrDNA) sequence data. Acta Manilana, 55, pp.15–21.
Alejandro, G.J.D., Madulid, R.S. & Madulid, D.A., 2008. The utility of internal transcribed spacer (nrDNA) sequence data for phylogenetic reconstruction in endemic Philippine Nepenthes L. (Nepenthaceae). The Philippine Scientist, 45, pp.99–110.
Bahadur, V. et al., 2007. Tissue culture studies in Nepenthes khasiana. ISHS Acta Horticulturae 786: International Workshop on Medicinal and Aromatic Plants, 786, pp.287–293. doi: 10.17660/ActaHortic.2008.786.35
Bazile, V. et al., 2015. Fluid physico-chemical properties influence capture and diet in Nepenthes pitcher plants. Annals of Botany, 115(4), pp.705-716. doi: 10.1093/aob/mcu266
Bednar, B.L., 1985. Nepenthes × dominii and var. intermedia. Carnivorous Plant Newsletter, 14(4), pp.105–106.
Belyakov, E.A. et al., 2022. Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing. Scientific Reports, 12(1), pp.21610. doi: 10.1038/s41598-022-25954-0
Biteau, F. et al., 2013. A simple SDS-PAGE protein pattern from pitcher secretions as a new tool to Nepenthes species (Nepenthaceae). American Journal of Botany, 100(12), pp.2478–2484. doi: 10.3732/ajb.1300145
Blanckaert, A. & Bank. C., 2018. In search of the Goldilocks zone for hybrid speciation. PLoS Genetics, 14(9), e1007613. doi: 10.1371/journal.pgen.1007613
Bolton, B., 1994. Identification guide to ant genera of the world. Harvard University Press, Cambridge.
Bunawan, H. et al., 2017. Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences. BMC Research Notes, 10(1), pp.1–6. doi: 10.1186/s13104-017-2379-1
Chin, L., Chung, A.Y. & Clarke, C., 2014. Interspecific variation in prey capture behavior by co-occurring Nepenthes pitcher plants: evidence for resource partitioning or sampling-scheme artifacts? Plant Signaling & Behavior, 9(1), e27930. doi: 10.4161/psb.27930
Clarke, C., 1998. The aquatic arthropod community of the pitcher plant, Nepenthes bicalcarata (Nepenthaceae) in Brunei. Sandakania, 11, pp.55–60.
Clarke, C.M., 2001. Nepenthes of Sumatra and Peninsular Malaysia. Natural History Publications (Borneo), Kota Kinabalu.
Coleman, A.W., 2013. Analysis of mammalian rDNA internal transcribed spacers. PLoS ONE, 8(11), e79122. doi: 10.1371/journal.pone.0079122
Danser, B.H., 1928. The Nepenthaceae of the Netherlands Indies. Bulletin du Jardin botanique de Buitenzorg, 10, pp.249–438.
Ghazalli, M.N. et al., 2020. Nepenthes latiffiana and N. domei (Nepenthaceae), two new species of pitcher plants from Terengganu, Peninsular Malaysia. Webbia, 75(1), pp.5–28. doi: 10.36253/jopt-7950
Ghazalli, M.N. et al., 2021. Laporan kajian kepelbagaian Nepenthes (Nepenthaceae) di Hutan Simpan Ayer Hitam Utara, Johor. Johor State Forestry Department, Johor.
Gilbert, K.J. et al., 2022. A semi-detritivorous pitcher plant, Nepenthes ampullaria diverges in its regulation of pitcher fluid properties. Journal of Plant Interactions, 17(1), pp.956–966. doi: 10.1080/17429145.2022.2123567
Golos, M.R. et al., 2023. Nepenthes limiana (Nepenthaceae), a new pitcher plant from the northern Titiwangsa Range of Peninsular Malaysia. Carnivorous Plant Newsletter, 52(3), pp.128–153. doi: 10.55360/cpn523.mg603
Gruber, A.R. et al., 2008. The vienna RNA websuite. Nucleic Acids Research, 36, pp.W70–W74. doi: 10.1093/nar/gkn188
Higashi, S. et al., 1993. Analysis of feeding mechanism in a pitcher of Nepenthes hybrida. Journal of Plant Research, 106, pp.47–54. doi: 10.1007/BF02344372
Hodač, L. et al., 2014. ITS polymorphisms shed light on hybrid evolution in apomictic plants: a case study on the Ranunculus auricomus complex. PLoS ONE, 9(7), e103003. doi: 10.1371/journal.pone.0103003
Hoshina, R., 2010. Secondary structural analyses of ITS1 in Paramecium. Microbes and Environments, 25(4), pp.313–316. doi: 10.1264/jsme2.ME10129
Kaplan, Z. & Fehrer, J., 2007. Molecular evidence for a natural primary triple hybrid in plants revealed from direct sequencing. Annals of Botany, 99(6), pp.1213–1222. doi: 10.1093/aob/mcm072
Kerpedjiev, P., Hammer, S. & Hofacker, I.L., 2015. Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams. Bioinformatics, 31(20), pp.3377–3379. doi: 10.1093/bioinformatics/btv372
Koetschan, C. et al., 2014. Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota). PloS ONE, 9(3), e91928. doi: 10.1371/journal.pone.0091928
Kumar, L., Shankar, P. & Kulkarni, V., 2018. Analyses of the internal transcribed rDNA spacers (ITS1 and ITS2) of Indian weevils of Odoiporus longicollis (Olivier) reveal gene flow between locations. International Journal of Tropical Insect Science, 38(4), pp.313–329. doi: 10.1017/S1742758418000231
Letsiou, S. et al., 2024. DNA Barcoding as a plant identification method. Applied Sciences, 14(4), 1415. doi: 10.3390/app14041415
Lim, G. et al., 2023. Delimitation of the Nepenthes macfarlanei group with two species described as new. In Nepenthes: the tropical pitcher plants, vol. 3. Redfern Natural History Productions, Poole, pp. 2084–2195.
Lim, R.J.Y. et al., 2019. Preliminary checklist of the inquiline and prey species of Nepenthes ampullaria pitchers across vegetation types in Singapore. Nature in Singapore, 12, pp.43–61. doi: 10.26107/NIS-2019-0006
Mansur, M., 2007. Keanekaragaman jenis Nepenthes (kantong semar) dataran rendah di Kalimantan Tengah. Berita Biologi, 8(5), pp.335–341. doi: 10.14203/beritabiologi.v8i5.1898
Maquart, P.O. et al., 2023. Description of a new species of Toxorhynchites (Diptera: Culicidae) from Nepenthes pitchers in Cambodia. Journal of Asia-Pacific Entomology, 26(2), 102064. doi: 10.1016/j.aspen.2023.102064
Marina, M.T. et al., 2018. Fauna diversity in pitcher plants at Setiam Hill, Bintulu, Sarawak, Malaysia. Sains Malaysiana, 47(1), pp.19–25. doi: 10.17576/jsm-2018-4701-03
Maryati, M., 1999. Keys to terrestrial invertebrates. Universiti Malaysia Sabah, Kota Kinabalu.
Masaoka, T. & Kobayashi, T., 2005. Natural hybridization between Pinctada fucata and Pinctada maculata inferred from internal transcribed spacer regions of nuclear ribosomal RNA genes. Fisheries Science, 71, pp.829–836. doi: 10.1111/j.1444-2906.2005.01034.x
Masters, M.T., 1881. New garden plants. Nepenthes Hookeriana. The Gardeners' Chronicle, New Series 16(417), pp.812–813.
Masters, M.T., 1882. New garden plants. Nepenthes intermedia×, Hort. Veitch. The Gardeners' Chronicle, New Series, 17(424), pp.178–179.
McPherson, S.R. & Robinson, A., 2012. Field guide to the pitcher plants of Peninsular Malaysia and Indochina. Redfern Natural History Productions, Poole.
Meimberg, H. et al., 2010. Evidence for species differentiation within the Ancistrocladus tectorius complex (Ancistrocladaceae) in Southeast Asia: a molecular approach. Plant Systematics and Evolution, 284, pp.77–98. doi: 10.1007/s00606-009-0241-1
Miguel, S., Hehn, A. & Bourgaud, F., 2018. Nepenthes: state of the art of an inspiring plant for biotechnologists. Journal of Biotechnology, 265, pp.109–115. doi: 10.1016/j.jbiotec.2017.11.014
Moran, J.A., 1999. Aspects of pitcher morphology and spectral characteristics of six Bornean Nepenthes pitcher plant species: implications for prey capture. Annals of Botany, 83(5), pp.521–528. doi: 10.1006/anbo.1999.0857
Muazam, F.N.I. et al., 2022. Development of Odonata as a nature tourism product for peat swamp ecosystem in North Ayer Hitam Forest Reserve, Johor. Journal of Sustainable Natural Resources, 3(2), pp.1–11. doi: 10.30880/jsunr.2022.03.02.001
Muhammad Jais, N.N. et al., 2022. Inventory of non-timber species in Ayer Hitam Utara Forest Reserve, Johor. Journal of Sustainable Natural Resources, 3(2), pp.34–40. doi: 10.30880/jsunr.2022.03.02.004
Murphy, B. et al., 2020. A phylogenomic analysis of Nepenthes (Nepenthaceae). Molecular Phylogenetics and Evolution, 144, 106668. doi: 10.1016/j.ympev.2019.106668
Nafisi, H., Kaveh, A. & Kazempour-Osaloo, S., 2023. Characterizing nrDNA ITS1, 5.8 S and ITS2 secondary structures and their phylogenetic utility in the legume tribe Hedysareae with special reference to Hedysarum. PLoS ONE, 18(4), e0283847. doi: 10.1371/journal.pone.0283847
Nikookar, S.H. et al., 2017. Correlation between mosquito larval density and their habitat physicochemical characteristics in Mazandaran Province, northern Iran. PLOS Neglected Tropical Diseases, 11(8), e0005835. doi: 10.1371/journal.pntd.0005835
Renner, T. & Specht C.D., 2011. A sticky situation: assessing adaptations for plant carnivory in the Caryophyllales by means of stochastic character mapping. International Journal of Plant Sciences, 172(7), pp.889–901. doi: 10.1086/660882
Riedel, M. et al., 2007. Chemical composition of epicuticular wax crystals on the slippery zone in pitchers of five Nepenthes species and hybrids. Planta, 225, pp.1517–1534. doi: 10.1007/s00425-006-0437-3
Ristiawan, H. & Hikmat, A., 2022. The prey composition of Nepenthes gymnamphora Reinw. Ex Nees at Mount Bismo, Deroduwur hiking trail, Wonosobo, Central Java. Media Konservasi, 27(3), pp.116–120. doi: 10.29244/medkon.27.3.116-120
Rosli, M.A.F. et al., 2021. UPLC-TOF-MS/MS-based metabolomics analysis reveals species-specific metabolite compositions in pitchers of Nepenthes ampullaria, Nepenthes rafflesiana, and their hybrid Nepenthes ×hookeriana. Frontiers in Plant Science, 12, 655004. doi: 10.3389/fpls.2021.655004
Saidon, N.A. et al., 2023. DNA barcoding, phylogenetic analysis and secondary structure predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana. Genes, 14(3), pp.697. doi: 10.3390/genes14030697
Sani, B.H. et al., 2000. Vegetative propagation of selected Nepenthes species. Borneo Science, 7, pp.1–9.
Scharmann, M., Wistuba, A. & Widmer, A., 2021. Introgression is widespread in the radiation of carnivorous Nepenthes pitcher plants. Molecular Phylogenetics and Evolution, 163, 107214. doi: 10.1016/j.ympev.2021.107214
Setiawan, H. et al., 2022. Prey composition and correlation between morphometry and prey biomass weight of the endemic Nepenthes bicalcarata in Kalimantan, Indonesia. Biodiversitas Journal of Biology Diversity, 23(10), pp.5453–5460. doi: 10.13057/biodiv/d231057
Siti-Suhaila, A.R. & Norwati, M., 2021. Micropropagation of Nepenthes hybrid (N. viking × N. miranda) using a temporary immersion bioreactor system, SETIS™. Journal of Tropical Forest Science, 33(4), pp.494–500. doi: 10.26525/jtfs2021.33.4.494
Takeuchi, Y. et al., 2011. In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes. PLoS ONE, 6(9), e25144. doi: 10.1371/journal.pone.0025144
Tamizi, A.A. et al., 2020a. Nepenthes malayensis (Nepenthaceae), a new species of carnivorous pitcher plant from Peninsular Malaysia. Kew Bulletin, 75, 63. doi: 10.1007/s12225-020-09918-z
Tamizi, A.A. et al., 2020b. Nepenthes ×setiuensis (Nepenthaceae), a new nothospecies of pitcher plant from montane cloud forest of Peninsular Malaysia. Malayan Nature Journal, 72, pp.27–41
Tamizi, A.A. et al., 2023a. New diversity, ex vitro propagation technique and hybrid development of pitcher plants native to Peninsular Malaysia. Buletin Teknologi MARDI, 38, pp.73–88.
Tamizi, A.A. et al., 2023b. Insights into the diversity of Nepenthes L. (Nepenthaceae) across Peninsular Malaysia, including the first sighting of an undescribed taxon with flared peristomes and quadruple-row ventral wings. Journal of Sustainable Uses of Natural Resources, 4(1), pp.10–36. doi: 10.30880/jsunr.2023.04.01.002
Tamura, K. & Nei, M., 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10(3), pp.512–526. doi: 10.1093/oxfordjournals.molbev.a040023
Tan, H.L. et al., 2022. Nepenthes berbulu (Nepenthaceae), a pitcher plant from Peninsular Malaysia with remarkably long lid bristles. Carnivorous Plant Newsletter, 52(1), pp.15–43. doi: 10.55360/cpn521.fm322
Tieng, F.Y.F. et al., 2023. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Briefings in Bioinformatics, 25(1), bbad421. doi: 10.1093/bib/bbad421
Thornhill, D.J. & Lord, J.B., 2010. Secondary structure models for the internal transcribed spacer (ITS) region 1 from symbiotic dinoflagellates. Protist, 161(3), pp.434–51. doi: 10.1016/j.protis.2009.11.004
Tsukamoto, M., 1989. Two new mosquito species from a pitcher plant of Mt. Kinabalu, Sabah, Malaysia: Culex rajah and Toxorhynchites rajah (Diptera: Culicidae). Japanese Journal of Tropical Medicine and Hygiene, 17(3), pp.215–228. doi: 10.2149/tmh1973.17.215
Wang, S. et al., 2007. Analysis of the secondary structure of ITS1 in Pectinidae: implications for phylogenetic reconstruction and structural evolution. Marine Biotechnology, 9, pp.231–242. doi: 10.1007/s10126-006-6113-6