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Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China

  • Singh, J. S. The biodiversity crisis: A multifaceted review. Curr. Sci. 82(6), 638–647 (2002).

    Google Scholar 

  • Mateo-Tomás, P. & López-Bao, J. V. A nuclear future for biodiversity conservation?. Biol. Conserv. 270, 109559. https://doi.org/10.1016/j.biocon.2022.109559 (2022).

    Article 

    Google Scholar 

  • Humphreys, A. M., Govaerts, R., Ficinski, S. Z., Nic Lughadha, E. & Vorontsova, M. S. Global dataset shows geography and life form predict modern plant extinction and rediscovery. Nat. Ecol. Evol. 3(7), 1043–1047. https://doi.org/10.1038/s41559-019-0906-2 (2019).

    Article 

    Google Scholar 

  • Larsen, B. B., Miller, E. C., Rhodes, M. K. & Wiens, J. J. Inordinate fondness multiplied and redistributed: The number of species on earth and the new pie of life. Q. Rev. Biol. 92(3), 229–265. https://doi.org/10.1086/693564 (2017).

    Article 

    Google Scholar 

  • Lewin, H. A. et al. The earth BioGenome project 2020: Starting the clock. Proc. Natl. Acad. Sci. 119(4), e2115635118. https://doi.org/10.1073/pnas.211563511 (2022).

    Article 
    CAS 

    Google Scholar 

  • Prugh, L. R., Sinclair, A. R. E., Hodges, K. E., Jacob, A. L. & Wilcove, D. S. Reducing threats to species: Threat reversibility and links to industry. Conserv. Lett. 3(4), 267–276. https://doi.org/10.1111/j.1755-263X.2010.00111.x (2010).

    Article 

    Google Scholar 

  • McCune, J. L. et al. Threats to Canadian species at risk: An analysis of finalized recovery strategies. Biol. Cons. 166, 254–265. https://doi.org/10.1016/j.biocon.2013.07.006 (2013).

    Article 

    Google Scholar 

  • Dong, S. Y. Hainan tree ferns (Cyatheaceae), morphological, ecological and phytogeographical observations. Ann. Bot. Fenn. 46(5), 381–388. https://doi.org/10.5735/085.046.0502 (2009).

    Article 

    Google Scholar 

  • Liu, Y., Wujisguleng, W. & Long, C. Food uses of ferns in China: A review. Acta Soc. Bot. Pol. 81(4), 263–270. https://doi.org/10.5586/asbp.2012.046 (2012).

    Article 

    Google Scholar 

  • Korall, P., Pryer, K. M., Metzgar, J. S., Schneider, H. & Conant, D. S. Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci. Mol. Phylogenet. Evol. 39(3), 830–845. https://doi.org/10.1016/j.ympev.2006.01.001 (2006).

    Article 
    CAS 

    Google Scholar 

  • Gu, Y. F., Jiang, R. H., Liu, B. D. & Yan, Y. H. Sphaeropteris guangxiensis YF Gu & YH Yan (Cyatheaceae), a new species of tree fern from Southern China. Phytotaxa 518(1), 69–74. https://doi.org/10.11646/phytotaxa.518.1.8 (2021).

    Article 

    Google Scholar 

  • Ho, Y. W., Huang, Y. L., Chen, J. C. & Chen, C. T. Habitat environment data and potential habitat interpolation of Cyathea lepifera at the Tajen Experimental Forest Station in Taiwan. Trop. Conserv. Sci. 9(1), 153–166. https://doi.org/10.1177/194008291600900108 (2016).

    Article 

    Google Scholar 

  • Wei, X. et al. Inferring the potential geographic distribution and reasons for the endangered status of the tree fern, Sphaeropteris lepifera, in Lingnan, China using a small sample size. Horticulturae 7(11), 496. https://doi.org/10.3390/horticulturae7110496 (2021).

    Article 

    Google Scholar 

  • Ida, N., Iwasaki, A., Teruya, T., Suenaga, K. & Kato-Noguchi, H. Tree fern Cyathea lepifera may survive by its phytotoxic property. Plants 9(1), 46. https://doi.org/10.3390/plants9010046 (2019).

    Article 
    CAS 

    Google Scholar 

  • Huang, Y. M., Ying, S. S. & Chiou, W. L. Morphology of gametophytes and young sporophytes of Sphaeropteris lepifera. Am. Fern J. 90(4), 127–137. https://doi.org/10.2307/1547489 (2000).

    Article 

    Google Scholar 

  • Fu, C. H. et al. Ophiodiaporthe cyatheae gen. et sp. Nov., a diaporthalean pathogen causing a devastating wilt disease of Cyathea lepifera in Taiwan. Mycologia 105(4), 861–872. https://doi.org/10.3852/12-346 (2013).

    Article 

    Google Scholar 

  • Kirschner, R., Lee, P. H. & Huang, Y. M. Diversity of fungi on Taiwanese fern plants: Review and new discoveries. Taiwania 64(2), 163–175. https://doi.org/10.6165/tai.2019.64.163 (2019).

    Article 

    Google Scholar 

  • Farrar, D. R. Gametophyte morphology and breeding systems in ferns. In Pteridology in the New Millennium Vol. 30 (eds Chandra, S. & Srivastava, M.) 447–454 (Springer, 2003). https://doi.org/10.1007/978-94-017-2811-9_30.

    Chapter 

    Google Scholar 

  • Kuriyama, A., Kobayashi, T. & Maeda, M. Production of sporophytic plants of Cyathea lepifera, a tree fern, from in vitro cultured gametophyte. Eng. Gakkai zasshi 73(2), 140–142. https://doi.org/10.2503/jjshs.73.140 (2008).

    Article 

    Google Scholar 

  • García, M. B. Demographic viability of a relict population of the critically endangered plant Borderea chouardii. Conserv. Biol. 17(6), 1672–1680. https://doi.org/10.1111/j.1523-1739.2003.00030.x (2003).

    Article 

    Google Scholar 

  • Chen, Y. S., Deng, T., Zhou, Z. & Sun, H. Is the East Asian flora ancient or not?. Natl. Sci. Rev. 5(6), 920–932. https://doi.org/10.1093/nsr/nwx156 (2018).

    Article 

    Google Scholar 

  • Fennessy, J. et al. Response to “How many species of giraffe are there?”. Curr. Biol. 27(4), 137–138. https://doi.org/10.1016/j.cub.2016.12.045 (2017).

    Article 
    CAS 

    Google Scholar 

  • Daniell, H., Lin, C. S., Yu, M. & Chang, W. J. Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol. 17(1), 1–29. https://doi.org/10.1186/s13059-016-1004-2 (2016).

    Article 
    CAS 

    Google Scholar 

  • Asaf, S. et al. Complete chloroplast genome of Nicotiana otophora and its comparison with related species. Front. Plant Sci. 7, 843. https://doi.org/10.3389/fpls.2016.00843 (2016).

    Article 

    Google Scholar 

  • Daniell, H. et al. Green giant: A tiny chloroplast genome with mighty power to produce high-value proteins—History and phylogeny. Plant Biotechnol. J. 19(3), 430–447. https://doi.org/10.1111/pbi.13556 (2021).

    Article 
    CAS 

    Google Scholar 

  • Martin, G. E. et al. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: Evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. Ann. Bot. 113(7), 1197–1210. https://doi.org/10.1093/aob/mcu050 (2014).

    Article 
    CAS 

    Google Scholar 

  • Xu, C. et al. Comparative analysis of six Lagerstroemia complete chloroplast genomes. Front. Plant Sci. 8, 15. https://doi.org/10.3389/fpls.2017.00015 (2017).

    Article 

    Google Scholar 

  • Henriquez, C. L. et al. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae). Planta 251(3), 1–16. https://doi.org/10.1007/s00425-020-03365-7 (2020).

    Article 
    CAS 

    Google Scholar 

  • Huang, X. et al. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. Nat. Plants 8(5), 500–512. https://doi.org/10.1038/s41477-022-01146-6 (2022).

    Article 
    CAS 

    Google Scholar 

  • Dobrogojski, J., Adamiec, M. & Luciński, R. The chloroplast genome: A review. Acta Physiol. Plant. 42(6), 1–13. https://doi.org/10.1007/s11738-020-03089-x (2020).

    Article 
    CAS 

    Google Scholar 

  • Oda, K. et al. Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA: A primitive form of plant mitochondrial genome. J. Mol. Biol. 223(1), 1–7. https://doi.org/10.1016/0022-2836(92)90708-R (1992).

    Article 
    CAS 

    Google Scholar 

  • Ohyama, K. et al. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322(6079), 572–574. https://doi.org/10.1038/322572a0 (1986).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Gao, L., Yi, X., Yang, Y. X., Su, Y. J. & Wang, T. Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol. Biol. 9(1), 1–14. https://doi.org/10.1186/1471-2148-9-130 (2009).

    Article 
    CAS 

    Google Scholar 

  • Wang, T., Hong, Y., Wang, Z. & Su, Y. Characterization of the complete chloroplast genome of Alsophila gigantea (Cyatheaceae), an ornamental and CITES giant tree fern. Mitochondrial DNA Part B 4(1), 967–968. https://doi.org/10.1080/23802359.2019.1580162 (2019).

    Article 

    Google Scholar 

  • Jia, Q. et al. A “GC-rich” method for mammaliangene expression: A dominant role of non-coding DNA GC content in regulation of mammalian gene expression. Sci. China Life Sci. 53, 94–100. https://doi.org/10.1007/s11427-010-0003-x (2010).

    Article 
    CAS 

    Google Scholar 

  • Liu, H. et al. Comparative analyses of chloroplast genomes provide comprehensive insights into the adaptive evolution of Paphiopedilum (Orchidaceae). Horticulturae 8(5), 391. https://doi.org/10.3390/horticulturae8050391 (2022).

    Article 

    Google Scholar 

  • Liu, C. K., Lei, J. Q., Jiang, Q. P., Zhou, S. D. & He, X. J. The complete plastomes of seven Peucedanum plants: Comparative and phylogenetic analyses for the Peucedanum genus. BMC Plant Biol. 22(1), 1–14. https://doi.org/10.1186/s12870-022-03488-x (2022).

    Article 
    CAS 

    Google Scholar 

  • Han, H. et al. Analysis of chloroplast genomes provides insights into the evolution of agropyron. Front. Genet. 13, 832809. https://doi.org/10.3389/fgene.2022.832809 (2022).

    Article 
    CAS 

    Google Scholar 

  • Hanaoka, M., Kanamaru, K., Takahashi, H. & Tanaka, K. Molecular genetic analysis of chloroplast gene promoters dependent on SIG2, a nucleus-encoded sigma factor for the plastid-encoded RNA polymerase Arabidopsis thaliana. Nucleic Acids Res. 31(24), 7090–7098. https://doi.org/10.1093/nar/gkg935 (2003).

    Article 
    CAS 

    Google Scholar 

  • Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E. & Tabata, S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6(5), 283–290. https://doi.org/10.1093/dnares/6.5.283 (1999).

    Article 
    CAS 

    Google Scholar 

  • Tian, S. et al. Repeated range expansions and inter-/postglacial recolonization routes of Sargentodoxa cuneata (Oliv.) Rehd. et Wils. (Lardizabalaceae) in subtropical China revealed by chloroplast phylogeography. Mol. Phylogenet. Evol. 85, 238–246. https://doi.org/10.1016/j.ympev.2015.02.016 (2015).

    Article 

    Google Scholar 

  • Ohme, M., Kamogashira, T., Shinozaki, K. & Sugiura, M. Structure and cotranscription of tobacco chloroplast genes for tRNA Glu (UUC), tRNA Tyr (GUA) and tRNA Asp (GUC). Nucleic Acids Res. 13(4), 1045–1056. https://doi.org/10.1093/nar/13.4.1045 (1985).

    Article 
    CAS 

    Google Scholar 

  • Wang, Z. et al. Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species. PeerJ 8, 8251. https://doi.org/10.7717/peerj.8251 (2020).

    Article 

    Google Scholar 

  • Pop, C. et al. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Mol. Syst. Biol. 10(12), 770. https://doi.org/10.15252/msb.20145524 (2014).

    Article 
    CAS 

    Google Scholar 

  • Verma, D. & Daniell, H. Chloroplast vector systems for biotechnology applications. Plant Physiol. 145(4), 1129–1143. https://doi.org/10.1104/pp.107.106690 (2007).

    Article 
    CAS 

    Google Scholar 

  • Bock, R. Engineering plastid genomes: Methods, tools, and applications in basic research and biotechnology. Annu. Rev. Plant Biol. 66(1), 211–241. https://doi.org/10.1146/annurev-arplant-050213-040212 (2015).

    Article 
    CAS 

    Google Scholar 

  • Tang, D. et al. Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis Benth. Dev. Genes. Evol. 231(1), 1–9. https://doi.org/10.1007/s00427-020-00670-9 (2021).

    Article 
    CAS 

    Google Scholar 

  • Zhang, Y. et al. Codon usage patterns across seven Rosales species. BMC Plant Biol. 22(1), 1–10. https://doi.org/10.1186/s12870-022-03450-x (2022).

    Article 
    CAS 

    Google Scholar 

  • Li, B., Lin, F., Huang, P., Guo, W. & Zheng, Y. Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing. Biol. Res. 53(1), 1–12. https://doi.org/10.1186/s40659-020-00289-0 (2020).

    Article 
    CAS 

    Google Scholar 

  • Wang, R. et al. Genome survey sequencing of Acer truncatum Bunge to identify genomic information, simple sequence repeat (SSR) markers and complete chloroplast genome. Forests 10(2), 87. https://doi.org/10.3390/f10020087 (2019).

    Article 

    Google Scholar 

  • Zhu, M. et al. Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae. Ecol. Evol. 11(20), 14327–14340. https://doi.org/10.1002/ece3.8151 (2021).

    Article 

    Google Scholar 

  • Hong, Z. et al. Comparative analyses of five complete chloroplast genomes from the genus Pterocarpus (Fabacaeae). Int. J. Mol. Sci. 21(11), 3758. https://doi.org/10.3390/ijms21113758 (2020).

    Article 
    CAS 

    Google Scholar 

  • Ping, J. et al. Molecular evolution and SSRs analysis based on the chloroplast genome of Callitropsis funebris. Ecol. Evol. 11(9), 4786–4802. https://doi.org/10.1002/ece3.7381 (2021).

    Article 

    Google Scholar 

  • Kim, Y., Park, J. & Chung, Y. Comparative analysis of chloroplast genome of Dysphania ambrosioides (L.) Mosyakin & Clemants understanding phylogenetic relationship in genus Dysphania R. B.. Korean J. Plant Resour. 32(6), 644–668. https://doi.org/10.7732/kjpr.2019.32.6.644 (2019).

    Article 

    Google Scholar 

  • Guo, Y. Y., Yang, J. X., Li, H. K. & Zhao, H. S. Chloroplast genomes of two species of Cypripedium: Expanded genome size and proliferation of AT-biased repeat sequences. Front. Plant Sci. 12, 609729. https://doi.org/10.3389/fpls.2021.609729 (2021).

    Article 

    Google Scholar 

  • Henriquez, C. L. et al. Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae). Genomics 112(3), 2349–2360. https://doi.org/10.1016/j.ygeno.2020.01.006 (2020).

    Article 
    CAS 

    Google Scholar 

  • Dong, S. et al. Nuclear loci developed from multiple transcriptomes yield high resolution in phylogeny of scaly tree ferns (Cyatheaceae) from China and Vietnam. Mol. Phylogenet. Evol. 139, 106567. https://doi.org/10.1016/j.ympev.2019.106567 (2019).

    Article 
    CAS 

    Google Scholar 

  • Rohde, K. Latitudinal gradients in species diversity: The search for the primary cause. Oikos 65, 514–527. https://doi.org/10.2307/3545569(1992) (1992).

    Article 

    Google Scholar 

  • Raven, J. A., Beardall, J., Larkum, A. W. D. & Sánchez-Baracaldo, P. Interactions of photosynthesis with genome size and function. Philos. Trans. R. Soc. B Biol. Sci. 368, 20120264. https://doi.org/10.1098/rstb.2012.0264 (2013).

    Article 
    CAS 

    Google Scholar 

  • Barber, J., Nield, J., Morris, E. P., Zheleva, D. & Hankamer, B. The structure, function and dynamics of photosystem two. Physiol. Plant. 100(4), 817–827. https://doi.org/10.1111/j.1399-3054.1997.tb00008.x (1997).

    Article 
    CAS 

    Google Scholar 

  • Yang, Z., Wong, W. S. & Nielsen, R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22(4), 1107–1118. https://doi.org/10.1093/molbev/msi097 (2005).

    Article 
    CAS 

    Google Scholar 

  • Li, W. et al. Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros. BMC Plant Biol. 18(1), 1–11. https://doi.org/10.1186/s12870-018-1421-3 (2018).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Duan, H. et al. Comparative chloroplast genomics of the genus Taxodium. BMC Genom. 21(1), 1–14. https://doi.org/10.1186/s12864-020-6532-1 (2020).

    Article 
    CAS 

    Google Scholar 

  • Jiao, Y. et al. Complete chloroplast genomes of 14 subspecies of D. glomerata: Phylogenetic and comparative genomic analyses. Genes 13(9), 1621. https://doi.org/10.3390/genes13091621 (2022).

    Article 
    CAS 

    Google Scholar 

  • Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455–477. https://doi.org/10.1089/cmb.2012.0021 (2012).

    Article 
    CAS 

    Google Scholar 

  • Boetzer, M. & Pirovano, W. Toward almost closed genomes with GapFiller. Genome Biol. 13(6), 1–9. https://doi.org/10.1186/gb-2012-13-6-r56 (2012).

    Article 

    Google Scholar 

  • Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24(8), 1596–1599. https://doi.org/10.1093/molbev/msm092 (2007).

    Article 
    CAS 

    Google Scholar 


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