Characterization of the complete chloroplast genome assembly of Amorphophallus yunnanensis Engler, Pflanzenr (Araceae) from southwestern China

References

• Abdullah HCL, Mehmood F, Hayat A, Sammad A, Waseem S, Waheed MT, Matthews PJ, Croat TB, Poczai P, Ahmed I. 2021. Chloroplast genome evolution in the Dracunculus clade (Aroideae, Araceae). Genomics. 113(1 Pt 1):183–192. doi:10.1016/j.ygeno.2020.12.016.
   PubMed Web of Science ®Google Scholar
• Claudel C, Buerki S, Chatrou LW, Antonelli A, Alvarez N, Hetterscheid W. 2017. Large-scale phylogenetic analysis of Amorphophallus (Araceae) derived from nuclear and plastid sequences reveals new subgeneric delineation. Botanical J Linnean Soc. 184(1):32–45. doi:10.1093/botlinnean/box013.
   Web of Science ®Google Scholar
• Deng JY, Fu RH, Compton SG, Liu M, Wang Q, Yuan C, Zhang LS, Chen Y. 2020. Sky islands as foci for divergence of fig trees and their pollinators in southwest China. Mol Ecol. 29(4):762–782. doi:10.1111/mec.15353.
   PubMed Web of Science ®Google Scholar
• Gao Y, Dong K, Xiao P, Wu W, Yin S. 2023. Complete assembly of the chloroplast genome of Amorphophallus coaetaneus S. Y. Liu & S. J. Wei 1986 (Araceae) from southwestern China. Mitochondrial DNA B Resour. 8(7):766–770. doi:10.1080/23802359.2023.2238939.
   PubMed Web of Science ®Google Scholar
• Henriquez CL, Ahmed I, Carlsen MM, Zuluaga A, Croat TB, McKain MR. 2020. Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae). Genomics. 112(3):2349–2360. doi:10.1016/j.ygeno.2020.01.006.
   PubMed Web of Science ®Google Scholar
• Hu H, Liu J, Wang B, An J, Wang Q. 2019. Characterization of the complete chloroplast genome of Amorphophallus konjac (Araceae) and its phylogenetic analysis. Mitochondrial DNA Part B. 4(1):1658–1659. doi:10.1080/23802359.2019.1606683.
   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
• Kalyaanamoorthy S, Minh BQ, Wong T, Haeseler AV, 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
• 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
• Kim J, Lee J, Choi S, Um S, Kim H, Chun HS, Nah G. 2020. The complete chloroplast genome of Typhonium giganteum (Araceae). Mitochondrial DNA B Resour. 5(3):2994–2995. doi:10.1080/23802359.2020.1797571.
   Google Scholar
• Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25(14):1754–1760. doi:10.1093/bioinformatics/btp324.
   PubMed Web of Science ®Google Scholar
• Li H, Hetterscheid WLA. 2010. Amorphophallus. Flora of China. Beijing: Science Press.
   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
• Low SL, Yu C-C, Ooi IH, Eiadthong W, Galloway A, Zhou Z-K, Xing Y-W. 2021. Extensive Miocene speciation in and out of Indochina: the biogeographic history of Typhonium sensu stricto (Araceae) and its implication for the assembly of Indochina flora. J of Sytematics Evolution. 59(3):419–428. doi:10.1111/jse.12689.
   Web of Science ®Google Scholar
• Mayo SJ, Bogner J, Boyce PC. 1997. The genera of Araceae. Kew: Royal Botanic Gardens.
   Google Scholar
• Mehmood F, Ubaid Z, Shahzadi I, Ahmed I, Waheed MT, Poczai P, Mirza B. 2020. Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica). PeerJ. 8: e9552. doi:10.7717/peerj.9552.
   PubMed Web of Science ®Google Scholar
• Michael T, Pascal L, Tommaso P, Ulbricht-Jones ES, Axel F, Ralph B, Stephan G. 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
• 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
• Quan G, Chen L. 2020. Characterization of the complete chloroplast genome sequence of Pistia stratiotes (Araceae) and its phylogenetic implications. Mitochondrial DNA B Resour. 5(3):2168–2169. doi:10.1080/23802359.2020.1768935.
   PubMed Web of Science ®Google Scholar
• Shan Y, Li J, Zhang X, Yu J. 2023. The complete mitochondrial genome of Amorphophallus albus and development of molecular markers for five Amorphophallus species based on mitochondrial DNA. Front Plant Sci. 14:1180417. doi:10.3389/fpls.2023.1180417.
   PubMed Web of Science ®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
• Wambulwa MC, Luo YH, Zhu GF, Milne R, Wachira FN, Wu ZY, Wang H, Gao LM, Li DZ, Liu J. 2022. Determinants of genetic structure in a highly heterogeneous landscape in Southwest China. Front Plant Sci. 13:779989. doi:10.3389/fpls.2022.779989.
   PubMed Web of Science ®Google Scholar
• Wang B, Mao JF, Zhao W, Wang XR. 2013. Impact of geography and climate on the genetic differentiation of the subtropical pine Pinus yunnanensis. PLoS One. 8(6):e67345. doi:10.1371/journal.pone.0067345.
   PubMed Web of Science ®Google Scholar