The complete chloroplast genome of Chrysoglossum ornatum (Epidendroideae, Orchidaceae) and its phylogenetic analysis

References

• Ai J, Wang YP, Guo HJ, Li L. 2020. The complete chloroplast genome of the monotypic genus of Bulleyia Schltr. (Orchidaceae). Mitochondrial DNA B Resour. 5(3):3663–3664. doi:10.1080/23802359.2020.1831983.
   PubMedGoogle Scholar
• Chase MW, Cameron KM, Freudenstein JV, Pridgeon AM, Salazar G, van den Berg C, Schuiteman A. 2015. An updated classification of Orchidaceae. Bot J Linn Soc. 177(2):151–174. doi:10.1111/boj.12234.
   Web of Science ®Google Scholar
• Chen J, Chen MK, Zheng QD, Ma SH, Liu ZJ, Ai Y. 2020. Chloroplast characterization and phylogenetic relationship of Cymbidium aloifolium (Orchidaceae). Mitochondrial DNA B Resour. 5(1):478–479. doi:10.1080/23802359.2019.1704656.
   PubMed Web of Science ®Google Scholar
• Chen MK, Chen J, Zhou J, Ma SH, Zheng QD, Xie TX, Ai Y. 2019. The complete chloroplast genome sequence of Habenaria ciliolaris (Orchidaceae). Mitochondrial DNA B Resour. 4(2):4132–4133. doi:10.1080/23802359.2019.1692727.
   PubMed Web of Science ®Google Scholar
• Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, Li Y, Ye J, Yu C, Li Z, et al. 2018. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 7(1):1–6. doi:10.1093/gigascience/gix120.
   Web of Science ®Google Scholar
• Christenhusz MJM, Byng JW. 2016. The number of known plants species in the world and its annual increase. Phytotaxa. 261(3):201–217. doi:10.11646/phytotaxa.261.3.1.
   Web of Science ®Google Scholar
• Daniell H, Lin CS, Yu M, Chang WJ. 2016. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 17(1):134. doi:10.1186/s13059-016-1004-2.
   PubMed Web of Science ®Google Scholar
• David P, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol. 53(5):793–808. doi:10.1080/10635150490522304.
   PubMed Web of Science ®Google Scholar
• Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15.
   Google Scholar
• Feng H, Cao T, Xu H, Liu Y, Han Y, Sun W, Liu Y. 2019. Characterization of the complete chloroplast genome of Bletilla striata (Orchidaceae: Bletilla), the herb in China. Mitochondrial DNA B Resour. 4(2):3542–3543. doi:10.1080/23802359.2019.1676177.
   PubMed Web of Science ®Google Scholar
• Green BR. 2011. Chloroplast genomes of photosynthetic eukaryotes. Plant J. 66(1):34–44. doi:10.1111/j.1365-313X.2011.04541.x.
   PubMed Web of Science ®Google Scholar
• Jiang YT, Lin RQ, Liu B, Zeng QM, Liu ZJ, Chen SP. 2019. Complete chloroplast genome of Cymbidium ensifolium (Orchidaceae). Mitochondrial DNA B Resour. 4(2):2236–2237. doi:10.1080/23802359.2019.1624637.
   PubMed Web of Science ®Google Scholar
• Jin JJ, Yu WB, Yang JB, Song Y, DePamphilis CW, Yi TS, Li DZ. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241. doi:10.1186/s13059-020-02154-5.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley D. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. doi:10.1093/molbev/mst010.
   PubMed Web of Science ®Google Scholar
• Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. doi:10.1093/bioinformatics/bts199.
   PubMed Web of Science ®Google Scholar
• Kim YK, Jo S, Cheon SH, Joo MJ, Hong JR, Kwak M, Kim KJ. 2020. Plastome evolution and phylogeny of Orchidaceae, with 24 new sequences. Front Plant Sci. 11:22. doi:10.3389/fpls.2020.00022.
   PubMed Web of Science ®Google Scholar
• Letunic I, Bork P. 2007. Interactive Tree of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 23(1):127–128. doi:10.1093/bioinformatics/btl529.
   PubMed Web of Science ®Google Scholar
• Li ZH, Jiang Y, Ma X, Li JW, Yang JB, Wu JY, Jin XH. 2020. Plastid genome evolution in the subtribe Calypsoinae (Epidendroideae, Orchidaceae). Genome Biol Evol. 12(6):867–870. doi:10.1093/gbe/evaa091.
   PubMed Web of Science ®Google Scholar
• Liu D-K, Tu X-D, Zhao Z, Zeng M-Y, Zhang S, Ma L, Zhang G-Q, Wang M-M, Liu Z-J, Lan S-R, et al. 2020. Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma-Gastrochilus clades (Orchidaceae, Aeridinae). Mol Phylogenet Evol. 145:106729. doi:10.1016/j.ympev.2019.106729.
   PubMed Web of Science ®Google Scholar
• Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C. 2023. CPGView: a package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 23(3):694–704. doi:10.1111/1755-0998.13729.
   PubMed Web of Science ®Google Scholar
• Mao SL, Zhou Y, Yuan H, Lu C, Chang H. 2018. The complete chloroplast genome sequence of Cremastra appendiculata (Orchidaceae) revealed by next-generation sequencing and phylogenetic implication. Mitochondrial DNA B Resour. 3(2):1108–1109. doi:10.1080/23802359.2018.1516122.
   PubMed Web of Science ®Google Scholar
• Miao LY, Hu C, Huang WC, Jiang K. 2019. Chloroplast genome structure and phylogenetic position of Calanthe sylvatica (Thou.) Lindl. (Orchidaceae). Mitochondrial DNA B Resour. 4(2):2625–2626. doi:10.1080/23802359.2019.1642157.
   PubMed Web of Science ®Google Scholar
• Seidenfaden G. 1983. Orchid genera in Thailand XI Cymbidieae Pfitz. Opera Bot. 72:19–21.
   Google Scholar
• Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47(W1):W65–W73. doi:10.1093/nar/gkz345.
   PubMed Web of Science ®Google Scholar
• Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352. doi:10.1093/bioinformatics/btv383.
   PubMedGoogle Scholar
• Wu X, Peng C, Li Z, Chen S. 2019. The complete plastome genome and its inference on the phylogenetic position of Bletilla formosana (Orchidaceae). Mitochondrial DNA B Resour. 4(2):3989–3990. doi:10.1080/23802359.2019.1688699.
   PubMed Web of Science ®Google Scholar
• Xiang XG, Jin WT, Li DZ, Schuiteman A, Huang WC, Li JW, Jin XH, Li ZY. 2014. Phylogenetics of tribe Collabieae (Orchidaceae, Epidendroideae) based on four chloroplast genes with morphological appraisal. PLoS One. 9(1):e87625. doi:10.1371/journal.pone.0087625.
   PubMed Web of Science ®Google Scholar
• Xie TX, Yu X, Zheng QD, Ma SH, Liu ZJ, Ai Y. 2019. The complete chloroplast genome of Tainia dunnii (Orchidaceae): genome structure and evolution. Mitochondrial DNA B Resour. 5(1):3–4. doi:10.1080/23802359.2019.1693935.
   PubMed Web of Science ®Google Scholar
• Yang J, Zhang F, Ge Y, Yu W, Xue Q, Wang M, Wang H, Xue Q, Liu W, Niu Z, et al. 2022. Effects of geographic isolation on the Bulbophyllum chloroplast genomes. BMC Plant Biol. 22(1):201. doi:10.1186/s12870-022-03592-y.
   PubMed Web of Science ®Google Scholar
• Zheng F, Pan YY, Li TZ, Chen GZ, Wu XY, Li LQ. 2019. The complete chloroplast genome of an endangered species Cymbidium mastersii (Orchidaceae). Mitochondrial DNA B Resour. 4(2):3068–3069. doi:10.1080/23802359.2019.1666047.
   PubMed Web of Science ®Google Scholar
• Zheng Q-D, Zhou J, Ma S-H, Chen M-K, Xie T-X, Chen J, Ai Y. 2019. The complete chloroplast genome sequence of Tainia cordifolia (Orchidaceae). Mitochondrial DNA B Resour. 5(1):1–2. doi:10.1080/23802359.2019.1693304.
   PubMed Web of Science ®Google Scholar
• Zhou P, Li JH, Liu YZ, Zhu ZW, Luo Y, Xiang XG. 2023. Species richness disparity in tropical terrestrial herbaceous floras: evolutionary insight from Collabieae (Orchidaceae). Mol Phylogenet Evol. 186:107860. doi:10.1016/j.ympev.2023.107860.
   PubMed Web of Science ®Google Scholar