The complete chloroplast genome of Eremurus zoae Vved. (Asphodelaceae), an endemic species of Kyrgyz Republic

References

• APG IV. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc. 181(1):1–20. doi:10.1111/boj.12385.
   Web of Science ®Google Scholar
• Chase MW, Reveal JL, Fay MF. 2009. A subfamilial classification for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae. Bot J Linn Soc. 161(2):132–136. doi:10.1111/j.1095-8339.2009.00999.x.
   Web of Science ®Google Scholar
• Cho KS, Yun BK, Yoon YH, Hong SY, Mekapogu M, Kim KH, Yang TJ. 2015. Complete chloroplast genome sequence of tartary buckwheat (Fagopyrum tataricum) and comparative analysis with common buckwheat (F. esculentum). PLoS One. 10(5):e0125332. doi:10.1371/journal.pone.0125332.
   PubMed Web of Science ®Google Scholar
• Farhadi F, Avan R, Sahebkar A, Eghbali S. 2023. A comprehensive review on Eremurus species: phytochemistry, pharmacology and traditional uses. Phytochem Lett. 53:142–149. doi:10.1016/j.phytol.2022.12.002.
   Web of Science ®Google Scholar
• Fedchenko BA. 1968. Eremurus. In: komarov VL, editor. Flora of the USSR. Vol. 4. Leningrad: botanical Institute of Academy of Science; p. 27–40.
   Google Scholar
• 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. doi:10.1093/sysbio/syq010.
   PubMed Web of Science ®Google Scholar
• Han S, Ding H, Bi D, Zhang S, Yi R, Gao J, Yang J, Ye Y, Wu L, Kan X. 2022. Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales. Plants. 11(24):3544. doi:10.3390/plants11243544.
   Google Scholar
• Hedge I, Wendelbo P. 1963. Notes on the giant Asphodels of Afghanistan. J Roy Hort Soc London. 88(9):402–406.
   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
• Kalyaanamoorthy S, Minh BQ, Wong TK, Von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589. doi:10.1038/nmeth.4285.
   PubMed Web of Science ®Google Scholar
• Kamenetsky R, Rabinowitch E. 1999. Flowering response of Eremurus to post-harvest temperatures. Sci Hortic. 79(1-2):75–86. doi:10.1016/S0304-4238(98)00181-2.
   Web of Science ®Google Scholar
• Kamra K, Jung J, Kim JH. 2023. A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences. Front Plant Sci. 14:1066708. doi:10.3389/fpls.2023.1066708.
   PubMed Web of Science ®Google Scholar
• Karaman K, Polat B, Ozturk I, Sagdic O, Ozdemir C. 2011. Volatile compounds and bioactivity of Eremurus spectabilis (Ciris), a Turkish wild edible vegetable. J Med Food. 14(10):1238–1243. doi:10.1089/jmf.2010.0262.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 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.
   Google Scholar
• Kyrgyz Republic. 2006. The Red Data Book of Kyrgyz Republic. 2nd ed. Bishkek: kyrgyz Republic; p. 543.
   Google Scholar
• Lazkov G, Sennikov AN. 2015. Taxonomic corrections and new records in vascular plants of Kyrgyzstan, 4. Memoranda Societatis Pro Fauna et Flora Fennica. 91:67–83.
   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
• Lowe TM, Chan PP. 2016. TRNAscan-SE online: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44(W1):W54–W57. doi:10.1093/nar/gkw413.
   PubMed Web of Science ®Google Scholar
• Makhmudjanov D, Yusupov Z, Abdullaev D, Deng T, Tojibaev K, Sun H. 2019. The complete chloroplast genome of Eremurus robustus (Asphodelaceae). Mitochondrial DNA B Resour. 4(2):3366–3367. doi:10.1080/23802359.2019.1674198.
   PubMed Web of Science ®Google Scholar
• Minh BQ, Nguyen MA, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30(5):1188–1195. doi:10.1093/molbev/mst024.
   PubMed Web of Science ®Google Scholar
• Muhidinov ZK, Bobokalonov JT, Ismoilov IB, Strahan GD, Chau HK, Hotchkiss AT, Liu L. 2020. Characterization of two types of polysaccharides from Eremurus hissaricus roots growing in Tajikistan. Food Hydrocolloids. 105:105768. doi:10.1016/j.foodhyd.2020.105768.
   Web of Science ®Google Scholar
• Naderi Safar K, Kazempour Osaloo S, Zarrei M. 2009. Phylogeny of the genus Eremurus (Asphodelaceae) based on morphological characters in the Flora Iranica area. Iran J Bot. 15(1):27–35.
   Google Scholar
• Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. doi:10.1093/molbev/msu300.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61(3):539–542. doi:10.1093/sysbio/sys029.
   PubMed Web of Science ®Google Scholar
• Safar KN, Osaloo SK, Assadi M, Zarrei M, Mozaffar MK. 2014. Phylogenetic analysis of Eremurus, Asphodelus, and Asphodeline (Xanthorrhoeaceae-Asphodeloideae) inferred from plastid trnL-F and nrDNA ITS sequences. Biochem Syst Ecol. 56:32–39. doi:10.1016/j.bse.2014.04.015.
   Web of Science ®Google Scholar
• Shrestha B, Gilbert LE, Ruhlman TA, Jansen RK. 2020. Rampant nuclear transfer and substitutions of plastid genes in Passiflora. Genome Biol Evol. 12(8):1313–1329. doi:10.1093/gbe/evaa123.
   PubMed Web of Science ®Google Scholar
• Song W, Ji C, Chen Z, Cai H, Wu X, Shi C, Wang S. 2022. Comparative analysis the complete chloroplast genomes of nine Musa Species: genomic features, comparative analysis, and phylogenetic implications. Front Plant Sci. 13:832884. doi:10.3389/fpls.2022.832884.
   PubMed Web of Science ®Google Scholar
• Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. doi:10.1093/nar/gkx391.
   PubMed Web of Science ®Google Scholar
• Volis S, Zhang Y, Deng T, Yusupov Z. 2022. Dark-colored Oncocyclus irises in Israel analyzed by AFLP, whole chloroplast genome sequencing and species distribution modeling. Israel J Ecol Evol. 68(1–4):43–53. doi:10.1163/22244662-bja10037.
   Web of Science ®Google Scholar
• Xie DF, Yu HX, Price M, Xie C, Deng YQ, Chen JP, Yu Y, Zhou SD, He XJ. 2019. Phylogeny of Chinese Allium species in section Daghestanica and adaptive evolution of Allium (Amaryllidaceae, Allioideae) species revealed by the chloroplast complete genome. Front Plant Sci. 10:460. doi:10.3389/fpls.2019.00460.
   PubMed Web of Science ®Google Scholar
• Xinqi C, Songyun L, Jiemei X, Tamura MN. 2000. Liliaceae. Flora of China. In: Wu ZY, Raven PH, editors. Flora of China. Vol 24. Beijing and St. Louis (MO): Science Press and Missouri Botanical Garden Press. p. 73–263.
   Google Scholar
• Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355. doi:10.1111/1755-0998.13096.
   PubMed Web of Science ®Google Scholar
• Zhu Y, Xu C-h, Huang J, Li G-y, Zhou Q, Liu X-H, Sun S-q, Wang J-h 2013. Rapid discrimination of three Uighur medicine of Eremurus by FT-IR combined with 2DCOS-IR. J Mol Struct. 1069:96–102. doi:10.1016/j.molstruc.2013.11.054.
   Web of Science ®Google Scholar