The first complete chloroplast genome in Engelhardia sensu stricto, Engelhardia hainanensis Chen: genome characterization and its phylogenetic relationships within the family Juglandaceae

References

• Blume CL. 1851. Museum botanicum Lugduno-Batavum, sive, Stirpium exoticarum novarum vel minus cognitarum ex vivis aut siccis brevis expositio et descriptio. Lugdunum Batavorum: Nabu Press; p. 286.
   Google Scholar
• Chen PY. 1981. Two new species of Engelhardia from Hainan Island. Acta Phytotaxon Sin. 19(2):250–252.
   Google Scholar
• Dong WP, Xu C, Li WQ, Xie XM, Lu YZ, Liu YL, Jin XB, Suo ZL. 2017. Phylogenetic resolution in Juglans based on complete chloroplast genomes and nuclear DNA sequences. Front Plant Sci. 8:1148.
   PubMed Web of Science ®Google Scholar
• Hu YH, Woeste KE, Zhao P. 2017. Completion of the chloroplast genomes of five Chinese Juglans and their contribution to chloroplast phylogeny. Front Plant Sci. 7:1955.
   PubMed Web of Science ®Google Scholar
• Hu YH, Yan J, Feng XJ, Dang M, Woeste KE, Zhao P. 2017. Characterization of the complete chloroplast genome of wheel wingnut (Cyclocarya paliurus), an endemic in China. Conserv Genet Resour. 9(2):273–275.
   Web of Science ®Google Scholar
• Iljinskaya IA. 1993. Alfaropsis, a new genus of the Juglandaceae. Bot Zhurn. 78:79–83.
   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.
   PubMed Web of Science ®Google Scholar
• Jin L, Zhou GH, He ML, Yang ZY, Yan HJ. 2020. The complete plastome and phylogenetic analysis of Rhoiptelea chiliantha (Juglandaceae). Mitochondrial DNA Part B. 5(3):3091–3092.
   PubMed Web of Science ®Google Scholar
• Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 20(4):1160–1166.
   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. 28:1647–1649.
   PubMed Web of Science ®Google Scholar
• Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 35(21):4453–4455.
   PubMed Web of Science ®Google Scholar
• Letunic I, Bork P. 2016. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44(W1):W242–W245.
   PubMed Web of Science ®Google Scholar
• Ling LZ, Zhang SD. 2020. Characterization of the complete chloroplast genome of Engelhardia roxburghiana (Juglandaceae). Mitochondrial DNA Part B. 5:250–251.
   Web of Science ®Google Scholar
• Liu LX, Li R, Worth JRP, Li X, Li P, Cameron KM, Fu CX. 2017. The complete chloroplast genome of Chinese bayberry (Morella rubra, Myricaceae): implications for understanding the evolution of Fagales. Front Plant Sci. 8:968.
   PubMed Web of Science ®Google Scholar
• Liu M, Lu JS, Li Y, Zhang LS. 2021. Complete chloroplast genome of Engelhardtia fenzlii (Juglandaceae). Mitochondrial DNA Part B. 6(1):288–289.
   PubMed Web of Science ®Google Scholar
• Liu SY, Ni Y, Li JL, Zhang XY, Yang HY, Chen HM, Liu C. 2023. CPGView: a package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 23(3):694–704.
   PubMed Web of Science ®Google Scholar
• Loureiro JD. 1790. Flora Cochinchinensis. Ulyssipo: Typis et expensis Academicis; p. 548.
   Google Scholar
• Lu AM, Stone DE, Grauke LJ. 1999. Juglandaceae. In Wu ZY, Raven PH, editors. Flora of China. Vol. 4. Beijing & St. Louis: Science Press & Missouri Botanical Garden Press; p. 277–285.
   Google Scholar
• Meng HH, Zhang CY, Low SL, Li L, Shen JY, Zhang Y, Huang PH, Zhou SS, Tan YH, Li J. 2022. Two new species from Sulawesi and Borneo facilitate phylogeny and taxonomic revision of Engelhardia (Juglandaceae). Plant Diversity. 44(6):552–564.
   Google Scholar
• Mu XY, Tong L, Sun M, Zhu YX, Wen J, Lin QW, Liu B. 2020. Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data. Mol Phylogenet Evol. 147:106802.
   PubMed Web of Science ®Google Scholar
• Shen JS, Li XQ, Chen X, Huang XL, Jin SH. 2022. The complete chloroplast genome of Carya cathayensis and phylogenetic analysis. Genes. 13(2):369.
   PubMed Web of Science ®Google Scholar
• Shi LC, Chen HM, Jiang M, Wang LQ, Wu X, Huang LF, Liu C. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47:W65–W73.
   PubMed Web of Science ®Google Scholar
• Song YG, Li Y, Meng HH, Fragnière Y, Ge BJ, Sakio H, Yousefzadeh H, Bétrisey S, Kozlowski G. 2020. Phylogeny, taxonomy, and biogeography of Pterocarya (Juglandaceae). Plants. 9:1524.
   Web of Science ®Google Scholar
• Walter T. 1788. Flora Caroliniana. p. 236. London: John Fraser.
   Google Scholar
• Xi JW, Lv SB, Zhang WP, Zhang JB, Wang KT, Guo HB, Hu J, Yang Y, Wang JH, Xia GH, et al. 2022. Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus. Front Plant Sci. 13:990064.
   PubMed Web of Science ®Google Scholar
• Yan H, Zhang JS, Ye JF, Guo CC, Xiang XG. 2021. Characterization of the complete chloroplast genome of Pterocarya macroptera var. delavayi (Juglandaceae). Mitochondrial DNA Part B. 6(4):1344–1345.
   PubMed Web of Science ®Google Scholar
• Zhai M, Jia XD, Zhang JY, Guo ZR, Xuan JP. 2021. Characterization of the complete chloroplast genome of Carya laciniosa (F. Michx.) G. Don (Juglandaceae). Mitochondrial DNA Part B. 6(3):1261–1262.
   PubMed Web of Science ®Google Scholar
• Zhang CY, Ling Low S, Song YG, Nurainas KG, Van Do T, Li L, Zhou SS, Tan YH, Cao GL, et al. 2020. Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae). Mol Phylogenet Evol. 152:106918.
   PubMed Web of Science ®Google Scholar
• Zhang BW, Xu LL, Li N, Yan PC, Jiang XH, Woeste KE, Lin K, Renner SS, Zhang DY, Bai WN. 2019. Phylogenomics reveals an ancient hybrid origin of the Persian walnut. Mol Biol Evol. 36(11):2451–2461.
   PubMed Web of Science ®Google Scholar
• Zhao TT, Wang GX, Ma QH, Liang LS, Yang Z. 2020. Multilocus data reveal deep phylogenetic relationships and intercontinental biogeography of the Eurasian-North American genus Corylus (Betulaceae). Mol Phylogenet Evol. 142:106658.
   PubMed Web of Science ®Google Scholar
• Zhou HJ, Hu YH, Ebrahimi A, Liu PL, Woeste K, Zhao P, Zhang SX. 2021. Whole genome based insights into the phylogeny and evolution of the Juglandaceae. BMC Ecol Evol. 21(1):1–16.
   PubMedGoogle Scholar
• Zhu CC, Shi FH, Wang M, Zhao YQ, Chen Y, Geng GM. 2019. The complete chloroplast genome of a variety of Castanea mollissima ‘Hongli’ (Fagaceae). Mitochondrial DNA Part B. 4(1):993–994.
   Web of Science ®Google Scholar