Resumen
Introduction: Anoectochilus formosanus is a highly valuable herb known for its efficacy in treating a wide range of diseases. However, the current methods used to differentiate this species from others within the same genus are not effective due to the high similarity in morphological characteristics and DNA barcode sequences among these species. Objective: Characterization of chloroplast (cp) genome in order to identify potential molecular markers to distinguish this plant at species or isolation levels is necessary. Methods: The complete cp genome was sequenced using next-generation sequencing technology, annotated, and compared with published cp genomes of various species within the Anoectochilus genus. Results: The complete cp genome of A. formosanus is 152 658 bp in size, consisting of a large and small copy of 82 692 bp and 17 346 bp, respectively, separated by reverse repeats of 26 310 bp. Within the cp genome, there are a total of 141 genes, including 92 protein-coding genes, 10 rRNA genes, and 39 tRNA genes. This genome contains a total of 80 simple sequence repeats, with 50 long repeats. Through phylogenetic analysis, a close relationship was observed between A. formosanus in Vietnam and A. formosanus samples originated from China (NC_061756.1). However, genomic comparisons highlighted significant differences between the two cp genomes, specifically in their reverse repeat sequences. Conclusions: These findings reveal distinct variations in the cp genome of A. formosanus in Vietnam, offering valuable insights for the taxonomy, plant identification, breeding, and conservation programs related to this herb in Vietnam.
Citas
Amiryousefi, A., Hyvönen, J., & Poczai, P. (2018). IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics, 34(17), 3030–3031.
Beier, S., Thiel, T., Münch, T., Scholz, U., & Mascher, M. (2017). MISA-web: a web server for microsatellite prediction. Bioinformatics, 33, 2583–2585.
Chen, J. R., & Shiau, Y. J. (2015). Application of internal transcribed spacers and maturase K markers for identifying Anoectochilus, Ludisia, and Ludochilus. Plant Biology, 59(3), 485-490.
Chen, Y. R., Lee, Y. H., Chang, W. M., Chen, Y. C., & Hung, M. H. (2017a). Antioxidant and anti-inflammatory properties of Anoectochilus formosanus Hayata in vitro and in vivo. Journal of Ethnopharmacology, 199, 143-152.
Chen, Y. Y., Chen, J. M., Huang, P. L., & Chung, J. D. (2017b). Evaluation of DNA barcodes for identifying closely related Orchidaceae species in Taiwan. PLoS ONE, 12(10), e0186264.
Chen, Y. Y., Chung, J. D., Lu, M. Y., & Huang, P. L. (2020). Illegal trade of Anoectochilus formosanus Hayata in Taiwan. Taiwania, 65(3), 194-196.
Daniell, H., Lin, C.S., Yu, M., & Chang, W.J. (2016). Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology, 17:134.
Dong, W., Liu, J., Yu, J., & Wang, L. (2019). DNA barcoding of Anoectochilus and Goodyera (Orchidaceae) and its application in species identification. PLoS ONE 14(1), e0210558.
Frailey, D. C., Chaluvadi, S. R., Vaughn, J. N., Coatney, C. G., & Bennetzen. J. L. (2018). Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae. BMC Plant Biology, 18:30.
Gao, C., Zhang, F., Zhang, J., Guo, S., & Shao, H. (2009). Identification of Anoectochilus based on rDNA ITS sequences alignment. International Journal of Biological Sciences, 5(7), 727-75.
Henriquez, C. L., Abdullah, Ahmed, I., Carlsen, M. M., Zuluaga, A., Croat, T. B., & McKain, M. R. (2022). Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae). Genomics, 112, 2349-2360.
Huang, Y. D., Chung, J. D., & Huang, P. L. (2019). Genetic diversity and population structure of Anoectochilus formosanus Hayata (Orchidaceae) in Taiwan. Botanical Studies, 60(1), 25.
Huang, Y., Li, L., Tang, L., & Chen, X. (2021). The influence of environmental factors on the morphology of Ludisia discolor (Orchidaceae). Plant Diversity, 43(3), 215-221.
Huynh, H. D., Nguyen, T. G., Duong, H.X., Ha, T. L., Phan. D. Y., Tran, T. T., & Do, D. G. (2019). Using some DNA barcode for the genetic analysis and identifying some species of Anoectochilus spp. Can Tho University Journal of Science, 55(1), 14-23.
Kanaka, K. K., Sukhija, N., Goli, R. C., Singh, S., Ganguly, I., Dixit, S. P., Dash, A., & Malik, A. A. (2023). On the concepts and measures of diversity in the genomics are. Current Plant Biology, 33, 100278.
Kang, Y., Deng, Z., Zang, R., & Long, W. (2017). DNA barcoding analysis and phylogenetic relationships of tree species in tropical cloud forests. Scientific Reports, 7: 12564.
Katoh, K., Rozewicki. J., & Yamada, K. D. (2019). MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 20(4), 1160–1166.
Kiew, R., & Chung, R. C. K. (1996). Taxonomic notes on the Orchidaceae of Sumatra. Gardens' Bulletin. Singapore, 48(1), 1-111.
Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., & Giegerich, R. (2001). REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22), 4633-4642.
Lei, W., Ni, D., Wang, Y., Shao, J., Wang, X., Yang, D., Wang, J., Chen, H., & Liu, C. (2016). Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus. Scientific Reports, 6: 21669.
Li, Y., Zhou, J., Chen, X., Cui, Y., Xu, Z., Li, Y., Song, J., Duan, B., & Yao, H. (2017). Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species. Scientific Reports, 7:12834.
Li, Y., Li, R., Xu, H., & Tang, Q. (2021). Anoectochilus formosanus extract exerts anti-hyperglycemic effect in diabetic rats via PI3K/Akt pathway. Journal of Ethnopharmacology, 272, 113928.
Li, C., Liu, Y., Lin, F., Zheng, Y, & Huang, P. (2022). Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). Peerj 10:13570.
Lin, C. S., Chen, J. J. W., Chiu, C. C., Hsiao, H. C. W., Yang, C. J., Jin, X. H., Leebens-Mack, J., de Pamphilis, C. W., Huang, Y. T., Yang, L. H., Chang, W. J., Kui, L., Wong, G. K. S., Hu, J. M., Wang, W., & Shih, M. C. (2017). Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant Journal, 90(5), 994-1006.
Liu, H., Ye, H., Zhang, N., Ma, J., Wang, J., Hu, G., Li, M., & Zhao, P. (2022). Comparative analyses of chloroplast genomes provide comprehensive insights into the adaptive evolution of Paphiopedilum (Orchidaceae). Horticulturae 8: 391.
Mohanta, T. K., Mishra, A. K., Khan, A., Hashem, A., Abd_Allah, E. F., & Al-Harrasi, A. (2020). Gene loss and evolution of the plastome. Genes, 11(10), 1133.
Nguyen, M. P., Trinh, T. H., Ngo, T. K. A., Widiarsih, S., & Ho, V. T. (2023a). In silico comparative analysis of the complete chloroplast genome sequences in different jewel orchid species. Nusantara Bioscience, 15(1), 12-21.
Nguyen, T. P., Phan, H. N., Do, T. D., Do, G. D., Ngo, L. H., Do, H. D. K., & Nguyen, K. T. (2023b). Polysaccharide and ethanol extracts of Anoectochilus formosanus Hayata: Antioxidant, wound-healing, antibacterial, and cytotoxic activities. Heliyon, 9(3): e13559.
Nishimaki, T., & Sato, K. (2019). An extension of the Kimura two-parameter model to the natural evolutionary process. Journal of Molecular Evolution, 87, 60-67.
Ong, B., & Lee, C. T. (2019). Diversity and conservation of jewel orchids (Anoectochilus, Goodyera, Ludisia, and Macodes) in Peninsular Malaysia. Journal of Tropical Forest Science, 31(3), 280-292.
Ren, F., Wang, L., Li, Y., Zhou, W., Xu, Z., Gou, H., Liu, Y., Gao, R., & Song, J. (2021). Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis Saxicola. Ecology and Evolution, 11, 4158–4171.
Scobeyeva, V. A., Artyushin, I. V., Krinitsina A. A., Nikitin, P. A., Antipin, M. A., Kuptsov, S. V., Belenikin, M. S., Omelchenko, D. O., Logacheva, M. D., Konorov E. A., Samoilov A. E., & Speranskaya A. S. (2021). Gene loss, pseudogenization in plastomes of genus Allium (Amaryllidaceae), and putative selection for adaptation to environmental conditions. Frontiers in Genetics, 12:674783.
Sikdar, S., Tiwari, S., Thakur, V. V., & Sapre, S. (2018). An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Fabaceae family. International Journal of Chemical Studies, 6(6), 2446-2451.
Song, W., Chen, Z., Shi, W., Han, W., Feng, Q., Shi, C., Engel, M. S., & Wang, S. (2022). Comparative analysis of complete chloroplast genomes of nine species of Litsea (Lauraceae): Hypervariable regions, positive selection, and phylogenetic relationships. Genes, 13, 1550.
Tang, H., Tang, L., Shao, S., Peng, Y., Li, L., & Lue, Y. (2021). Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution. Plant Diversity, 43(5), 350–361.
Wang, S. Y., Kuo, Y. H., Chang, H. N., Khang, P. L., Tsay, H. S., Lin, K. F., Yang, N. S., & Shyur, L. F. (2002). Profiling and characterization antioxidant activities in Anoectochilus formosanus Hayata. Journal of Agricultural and Food Chemistry, 50(7), 1859–1865.
Xu, Y., Wen, J., Su, X., & Ren, Z. (2022). Variation among the complete chloroplast genomes of the sumac species Rhus chinensis: Reannotation and comparative analysis. Genes, 13: 1936.
Ye, S., Shao, Q., & Zhang, A. (2017). Anoectochilus roxburghii: A review of its phytochemistry, pharmacology, and clinical applications. Journal of Ethnopharmacology, 209(14), 184-202.
Zhang, X., Liu, Y., Chen, Y., & Liu, Z. (2019). A comparison of DNA barcoding and morphological identification of jewel orchids (Anoectochilus, Goodyera and Ludisia). Plant Diversity, 41(5), 283-290.
Zhang, X., Liu, Y., Chen, Y., & Liu, Z. (2021). Comparative analysis of cp genomes of three jewel orchids (Ludisia discolor, Anoectochilus formosanus and Macodes petola) and molecular identification. PeerJ, 9, e11867.
Zarei, A., Ebrahimi, A., Mathur, S., & Lawson, S. (2022). The first complete chloroplast genome sequence and phylogenetic analysis of pistachio (Pistacia vera). Diversity, 14, 577.
Comentarios
Esta obra está bajo una licencia internacional Creative Commons Atribución 4.0.
Derechos de autor 2024 Revista de Biología Tropical