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Rapid Communication

Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae

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Pages 2872-2879 | Received 03 Jun 2021, Accepted 18 Aug 2021, Published online: 09 Sep 2021

References

  • Bateman RM, Hollingsworth PM, Preston J, Yi-Bo LUO, Pridgeon AM, Chase MW. 2003. Molecular phylogenetics and evolution of Orchidinae and selected Habenariinae (Orchidaceae). Bot J Linn Soc. 142(1):1–40.
  • Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chang CC, et al. 2006. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol. 23(2):279–291.
  • Chen B, Zhang Y, Cao Y, Zheng Y, Wei Z, Zhao K, Peng D, Zhou Y. 2020. Chloroplast characterizations of a Phalaenopsis native to China, Phalaenopsis mannii (Orchidaceae). Mitochondrial DNA Part B. 5(3):3725–3726.
  • Christenhusz MJM, Byng JW. 2016. The number of known plants species in the world and its annual increase. Phytotaxa. 261(3):201–217.
  • Christenson EA. 2001. Phalaenopsis—a monograph. Portland: Timber Press.
  • Daniell H, Lin CS, Yu M, Chang WJ. 2016. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 17(1):134.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772.
  • Deng H, Zhang G-Q, Liu Z-J, Wang Y. 2015. A new species and a new combination of Phalaenopsis (Orchidaceae: Epidendroideae: Aeridinae): evidence from morphological and DNA analysis. Phytotaxa. 238(3):243–254.doi:https://doi.org/10.11646/phytotaxa.238.3.3.
  • Dixon KW, Kell SP, Barrett RL, Cribb PJ. 2003. Orchid conservation. Kota Kinabalu: Sabah Natural History Publications.
  • Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15.
  • Dressler RL. 1993. Phylogeny and classification of the orchid family. Cambridge: Cambridge University Press.
  • Gogoi K, Rinya K. 2020. Phalaenopsis arunachalensis sp. nov. (Orchidaceae: Epidendroideae: Aeridinae) A new epiphytic orchid from Arunachal Pradesh, Northeast India. Lankesteriana. 20(3):275–280.
  • Goulding SE, Olmstead RG, Morden CW, Wolfe KH. 1996. Ebb and flow of the chloroplast inverted repeat. Mol Gen Genet. 252(1–2):195–206.
  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59(3):307–321.
  • Hadi H, Razali SN, Awadh AI. 2015. A comprehensive review of the cosmeceutical benefits of Vanda species (Orchidaceae). Nat Prod Commun. 10(8):1483–1488.
  • Inda LA, Pimentel M, Chase MW. 2012. Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes. Ann Bot. 110(1):71–90.
  • Ingvarsson PK, Sarah R, Taylor DR. 2003. Molecular evolution of insertions and deletion in the chloroplast genome of silene. Mol Biol Evol. 20(11):1737–1740.
  • Jheng CF, Chen TC, Lin JY, Chen TC, Wu WL, Chang CC. 2012. The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. Plant Sci. 190:62–73.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
  • Kim HT, Kim JS, Moore MJ, Neubig KM, Williams NH, Whitten WM, Kim JH. 2015. Seven new complete plastome sequences reveal rampant independent loss of the ndh gene family across orchids and associated instability of the inverted repeat/small single-copy region boundaries. PLOS One. 10(11):e0142215.
  • Kim GB, Kwon Y, Yu HJ, Lim KB, Seo JH, Mun JH. 2016. The complete chloroplast genome of Phalaenopsis “Tiny Star”. Mitochondrial DNA Part A. 27(2):1300–1302.
  • Ko YZ, Shih HC, Tsai CC, Ho HH, Liao PC, Chiang YC. 2017. Screening transferable microsatellite markers across genus Phalaenopsis (Orchidaceae). Bot Stud. 58(1):48.
  • Lee YI, Tseng YF, Lee YC, Chung MC. 2020. Chromosome constitution and nuclear DNA content of Phalaenopsis hybrids. Sci Hortic. 262:109089.
  • Li B, Zheng Y. 2018. Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae. Sci Rep. 8(1):9285.
  • Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, et al. 2017. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. Plant J. 90(5):994–1006.
  • Lohse M, Drechsel O, Kahlau S, Bock R. 2013. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41(Web Server issue):W575–W581.
  • Magee AM, Aspinall S, Rice DW, Cusack BP, Sémon M, Perry AS, Stefanović S, Milbourne D, Barth S, Palmer JD, et al. 2010. Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res. 20(12):1700–1710.
  • Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, et al. 2014. Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae). Mol Biol Evol. 31(4):793–803.
  • Nie L, Cui Y, Wu L, Zhou J, Xu Z, Li Y, Li X, Wang Y, Yao H. 2019. Gene losses and variations in chloroplast genome of parasitic plant Macrosolen and phylogenetic relationships within Santalales. Int J Mol Sci. 20(22):5812.
  • Park J, Suh Y, Kim S. 2020. A complete chloroplast genome sequence of Gastrodia elata (Orchidaceae) represents high sequence variation in the species. Mitochondrial DNA Part B. 5(1):517–519.
  • Patel RK, Jain M. 2012. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLOS One. 7(2):e30619.
  • Schuiteman A. 2012. Nothodoritis zhejiangensis transferred to Phalaenopsis. Renziana. 2:48–50.
  • Serna-Sánchez MA, Pérez-Escobar OA, Bogarín D, Torres-Jimenez MF, Alvarez-Yela AC, Arcila-Galvis JE, Hall CF, de Barros F, Pinheiro F, Dodsworth S, et al. 2021. Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution. Sci Rep. 11(1):6858.
  • Thiel T, Michalek W, Varshney RK, Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 106(3):411–422.
  • Tsai WC, Fu CH, Hsiao YY, Huang YM, Chen LJ, Wang M, Liu ZJ, Chen HH. 2013. OrchidBase 2.0: comprehensive collection of Orchidaceae floral transcriptomes. Plant Cell Physiol. 54(2):e7.
  • Tsi ZH. 1989. New taxa of Orchidaceae from China. Bull Bot Res. 9(2):21–32.
  • Tsi ZH, Chen SC, Luo YB, Zhu GH. 1999. Flora Reipublicae Popularis Sinicae. Vol. 19. Beijing: Science Press.
  • Wang JY, Liu ZJ, Zhang GQ, Peng CC. 2019. The complete chloroplast genome sequence of Phalaenopsis lowii (Orchidaceae). Mitochondrial DNA Part B. 4(2):3569–3570.
  • Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. 2011. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol. 76(3–5):273–297.
  • Wu ZY, Raven PH, Hong DY. 2009. Flora of China. Vol. 25. Beijing and St. Louis: Science Press and Missouri Botanical Garden Press.
  • Yao J, Zhao F, Xu Y, Zhao K, Quan H, Su Y, Hao P, Liu J, Yu B, Yao M, et al. 2020. Complete chloroplast genome sequencing and phylogenetic analysis of two Dracocephalum plants. Biomed Res Int. 2020:4374801.
  • Yukawa T, Kita K. 2005. Doritis zhejiangensis (Z.H.Tsi). Acta Phytotax Geobot. 56(2):157.
  • Zeng S, Chen Z, Wu K, Zhang J, Bai C, Teixeira da Silva JA, Duan J. 2011. Asymbiotic seed germination, induction of calli and protocorm-like bodies, and in vitro seedling development of the rare and endangered Nothodoritis zhejiangensis Chinese orchid. HortScience. 46(3):460–465.
  • Zhang Y, Chen B, Zheng Y, Cao Y, Wei Z, Zhao K, Zhou Y. 2020. Characterization of the complete chloroplast genome of Phalaenopsis lobbii (Orchidaceae), an important horticultural plant in China. Mitochondrial DNA Part B. 5:3450–3451.