Lithocarpus encleisocarpus (Korth.) A. Camus - A newly recorded from Vietnam and its phylogenetic relationship based on genome-wide SNPs
Main Article Content
Abstract
A newly recorded Lithocarpus (Fagaceae) species for the flora of Vietnam, namely Lithocarpus encleisocarpus (Korth.) A.Camus was reported in this study. This species is most morphologically similar to L. dahuoaiensis Ngoc & L.V. Dung in having a completely entire leaf margin, solitary cupule, long stalks of fruits, deeply cup-shaped or turbinate cupules, with several horizontal filiform lines, but it differs from the latter by having cupules almost completely covering the nut, surface of the cupule densely fulvous tomentose by stellate hairs, secondary veins 8-10 pairs. This study provides the phylogenetic relationship of L. encleisocarpus with its close species based on genome-wide SNPs. Taxonomic treatment, photographs, information on distribution and habitat, and the GenBank accession number for DNA barcodes of the species are also provided.
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
References
Ban, N. T. (2005). Fagaceae. In N. T. Ban (Eds.), Checklist of plant species of Vietnam 2. (pp. 227–271). Agricultural Publishing House, Hanoi.
Barnett, E.C. (1944) Keys to the Species Groups of Quercus, Lithocarpus, and Castanopsis of Eastern Asia, with Notes on their Distribution. Transactions of the Botanical Society of Edinburgh, 34(1), 159–204. doi: 10.1080/13594864409441557
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Camus, A. (1931). Sur quelques genres de Fagacees. Riviera Scientifique, 18, 37–42.
Camus, A. (1938). Fagacées nouvelles de l’asie orientale. Notulae systematicae (Paris), 6(4), 178–185.
Camus, A. (1942). Fagacées asiatiques nouvelles. Bulletin du Muséum National d’Histoire Naturelle Series, II 14(5), 357–360.
Camus, A. (1943). Lithocarpus (Fagacées) nouveaux d’Annam. Bulletin de la Société Botanique de France 90(4–6), 84–85. https://doi.org/10.1080/00378941.1943.10837497
Camus, A. (1945). Espèces et variétés nouvelles du genre Lithocarpus. Bulletin de la Société Bota nique de France 92(4–6), 82–84. https://doi.org/10.1080/00378941.1945.10834409
Camus, A. (1948). Les Chênes: Monographie du genres Quercus et Lithocarpus. Chênes Atlas (Vol. 3). Paul Lechevalier & fils.
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool set for population genomics. Molecular Ecology, 22, 3124–3140. https://doi.org/10. 1111/mec.12354
Darriba, D., Taboada, G.L., Doallo, R., & Posada, D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9(8), e772. https://doi.org/10.1038/nmeth.2109
Doyle, J.J., Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11–15.
Dunning, L. T. & Savolainen, V. (2010). Broad-scale amplification of matK for DNA barcoding plants, a technical note. Botanical Journal of the Linnean Society, 164, 1–9.
Ho, P. H. (2003). An Illustrated Flora of Vietnam (Vol. 2). Young Publishing House, Ho Chi Minh City.
Huang, C.J., Zhang, Y.T., Bartholomew, B. (1999). Fagaceae. In W. Zhengyi, P. H. Raven, H. Deyuan, (Eds.), Flora of China. Volume 4, (pp. 333–369). http://www.efloras.org
Kress, W. J., Erickson, D. L., Jones, F. A., Swenson, N. G., Perez, R., Sanjur, O., & Bermingham, E. (2009). Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences, 106, 18621–18626.
Manos, P.S., Cannon, C.H., Oh, S.H. (2008) Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of Western North America: Recognition of a new genus, Notholithocarpus. Madroño, 55, 181–190. doi: 10.3120/0024-9637-55.3.181
Ngoc, N.V., Dung, L.V., Tagane, S., Binhm, H.T., Son, H.T., Trung, V.Q., & Yahara, T. (2016). Lithocarpus dahuoaiensis (Fagaceae), a new species from Lam Dong Province, Vietnam. PhytoKeys, 69, 23–30. https://doi.org/10.3897/phytokeys.69.9821
Ngoc, N. V., Hung, N. V., Binh, H. T., Tagane, S., Toyama, H., Son, H.T., Ha, T.V., & Yahara, T. (2018) Lithocarpus vuquangensis (Fagaceae), a new species from Vu Quang National Park, Vietnam. PhytoKeys, 95, 15–25. https://doi.org/10.3897/phytokeys.95.21832
Ngoc, N.V., Binh, H.T., Nagahama, A., Tagane, S., Toyama, H., Matsuo, A., Suyama, Y., & Yahara, T. (2021). Morphological and molecular evidence reveals three new species of Lithocarpus (Fagaceae) from Bidoup-Nui Ba National Park, Vietnam. PhytoKeys, 186, 73–92. https://doi.org/10.3897/phytokeys.186.69878
Phengklai, C. (2008) Fagaceae. In T. Santisuk, K. Larsen, (Eds.), Flora of Thailand 9(3) (pp. 179–410). The Forest Herbarium, Bangkok.
Rochette, N. C., Rivera-Colon, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology, 28, 4737–4754. https://doi.org/10.1111/mec.15253
Rohwer, J. G., Li, J., Rudolph, B., Schmidt, S. A., van der Werrf, H., & Li, H. W. (2009). Is Persea (Lauraceae) monophyletic? Evidence from nuclear ribosomal ITS sequences. Taxon, 58, 1153–1167.
Stamatakis, A. (2014). RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (Oxford, England), 30(9), 1312–1313. https://doi. org/10.1093/bioinformatics/btu033
Strijk, J., Sirimongkol, S., Rueangruea, S., Ritphet, N., & Chamchumroon, V. (2014a). Lithocarpus orbicarpus (Fagaceae), a new species of Stone Oak from Phang Nga province, Thailand. PhytoKeys, 34, 33–46. doi: 10.3897/phytokeys.34.6429
Strijk, J. S., Rueangruea, S., Sirimongkol, S., & Suddee, S. (2014b). Lithocarpus corneus (Fagaceae), a new record for the Flora of Thailand. Thai Forest Bulletin (Botany), 42, 1–5.
Strijk, J. S., & Son, H. T. (2019). Lithocarpus gigantophyllus (Fagaceae), a new record from Loei province (Thailand). Thai Forest Bulletin (Botany), 47(2), 145–151.
The Plant List. (2013). Version 1.1. Published on the Internet. http://www.theplantlist.org/
Suyama, Y., & Matsuki, Y. (2015). MIG-seq: An effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Scientific Reports, 5, e16968. https://doi.org/10.1038/srep16963
Suyama, Y., Hirota, S.K., Matsuo, A., Tsunamoto, Y., Mitsuyuki, C., Shimura, A., & Okano, K. (2021). Complementary combination of multiplex high-throughput DNA sequencing for molecular phylogeny. Ecological Research, 1–11. https://doi.org/10.1111/14401703. 12270
Takata, K., Taninaka, H., Nonakam M., Iwasem F., Kikuchi, T., Suyama, Y., Nagai, S., & Yasuda, N. (2019). Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (An thozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype. PeerJ, 7, e7769. https://doi.org/10.7717/peerj.7769
Toyama, H., Kajisa, T., Tagane, S., Mase, K., Chhang, P., Samreth, V., Ma, V., Sokh, H., Ichihasi ,R., Onoda, Y., Mizoue, N., & Yahara, T. (2015) Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom, Cambodia. Philosophical Transactions of the Royal Society B. Biological Sciences, 370(1662), 1–13. https:// doi.org/10.1098/rstb.2014.0008.