[1]

Howe CJ, Barbrook AC, Koumandou VL, Nisbet RER, Symington HA, et al. 2003. Evolution of the chloroplast genome. Philosophical Transactions of the Royal Society B: Biological Sciences 358:99−107

doi: 10.1098/rstb.2002.1176
[2]

Daniell H, Lin CS, Yu M, Chang WJ. 2016. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology 17:134

doi: 10.1186/s13059-016-1004-2
[3]

Li D, Zhao C, Liu X. 2019. Complete chloroplast genome sequences of Kaempferia Galanga and Kaempferia Elegans: molecular structures and comparative analysis. Molecules 24:474

doi: 10.3390/molecules24030474
[4]

Qin M, Zhu C, Yang J, Vatanparast M, Schley R, et al. 2022. Comparative analysis of complete plastid genome reveals powerful barcode regions for identifying wood of Dalbergia odorifera and D. tonkinensis (Leguminosae). Journal of Systematics and Evolution 60:73−84

doi: 10.1111/jse.12598
[5]

Shetty SM, Md Shah MU, Makale K, Mohd-Yusuf Y, Khalid N, et al. 2016. Complete chloroplast genome sequence of Musa balbisiana corroborates structural heterogeneity of inverted repeats in wild progenitors of cultivated bananas and plantains. The Plant Genome 9:plantgenome2015.09.0089

doi: 10.3835/plantgenome2015.09.0089
[6]

Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, et al. 2006. The complete chloroplast genome sequence of Pelargonium × hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molecular Biology and Evolution 23:2175−90

doi: 10.1093/molbev/msl089
[7]

Yang J, Tang M, Li H, Zhang Z, Li D. 2013. Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evolutionary Biology 13:84

doi: 10.1186/1471-2148-13-84
[8]

Wu FH, Chan MT, Liao DC, Hsu CT, Lee YW, et al. 2010. Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biology 10:68

doi: 10.1186/1471-2229-10-68
[9]

Huang H, Shi C, Liu Y, Mao S, Gao L. 2014. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evolutionary Biology 14:151

doi: 10.1186/1471-2148-14-151
[10]

Bi Y, Zhang M, Xue J, Dong R, Du Y, et al. 2018. Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria. Scientific Reports 8:1184

doi: 10.1038/s41598-018-19591-9
[11]

Mo Z, Feng G, Su W, Liu Z, Peng F. 2018. Transcriptomic analysis provides insights into grafting union development in pecan (Carya illinoinensis). Genes 9:71

doi: 10.3390/genes9020071
[12]

Chen Y, Wang M, Zhu C, Zhao Y, Wang B, et al. 2018. Field investigation of resistance against black spot of different pecan varieties in Jintan, Changzhou. Journal of Jiangsu Forestry Science & Technology 45:26−29

doi: 10.3969/j.issn.1001-7380.2018.06.007
[13]

Wu J, Lin H, Meng C, Jiang P, Fu W. 2014. Effects of intercropping grasses on soil organic carbon and microbial community functional diversity under Chinese hickory (Carya cathayensis Sarg.) stands. Soil Research 52:575−83

doi: 10.1071/SR14021
[14]

Manos PS, Stone DE. 2001. Evolution, phylogeny, and systematics of the Juglandaceae. Annals of the Missouri Botanical Garden 88:231−69

doi: 10.2307/2666226
[15]

Thompson TE, Romberg LD. 1985. Inheritance of heterodichogamy in pecan. Journal of Heredity 76:456−58

doi: 10.1093/oxfordjournals.jhered.a110144
[16]

Zhang R, Peng F, Li Y. 2015. Pecan production in China. Scientia Horticulturae 197:719−27

doi: 10.1016/j.scienta.2015.10.035
[17]

Mo Z, Zhang J, Zhai M, Xuan J, Jia X, et al. 2013. Observation and comparison of flowering phenology of Carya illinoensis in Nanjing. Journal of Plant Resources and Environment 22:57−62

doi: 10.3969/j.issn.1674-7895.2013.01.09
[18]

Zhang R, Lv F, Zhang X, He F, Wang L. 2005. Feasibility study for extension of pecan cultivars introduced from America. Economic Forest Researches 23:1−10

[19]

Chen Y, Zhang S, Zhao Y, Mo Z, Wang W, et al. 2022. Transcriptomic analysis to unravel potential pathways and genes involved in pe can (Carya illinoinensis) resistance to Pestalotiopsis microspora. International Journal of Molecular Sciences 23:11621

doi: 10.3390/ijms231911621
[20]

Mo Z, Lou W, Chen Y, Jia X, Zhai M, et al. 2020. The chloroplast genome of Carya illinoinensis: genome structure, adaptive evolution, and phylogenetic analysis. Forests 11:207

doi: 10.3390/f11020207
[21]

Feng G, Mo Z, Peng F. 2020. The complete chloroplast genome sequence of Carya illinoinensis cv. wichita and its phylogenetic analysis. Mitochondrial DNA Part B 5:2235−36

doi: 10.1080/23802359.2020.1768925
[22]

Wang X, Rhein HS, Jenkins J, Schmutz J, Grimwood J, et al. 2020. Chloroplast genome sequences of Carya illinoinensis from two distinct geographic populations. Tree Genetics & Genomes 16:48

doi: 10.1007/s11295-020-01436-0
[23]

Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19:11−15

[24]

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19:455−77

doi: 10.1089/cmb.2012.0021
[25]

Lohse M, Drechsel O, Bock R. 2007. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics 52:267−74

doi: 10.1007/s00294-007-0161-y
[26]

Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−85

doi: 10.1093/bioinformatics/btx198
[27]

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29:4633−42

doi: 10.1093/nar/29.22.4633
[28]

Shen J, Li X, Chen X, Huang X, Jin S. 2022. The complete chloroplast genome of Carya cathayensis and phylogenetic analysis. Genes 13:369

doi: 10.3390/genes13020369
[29]

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. 2004. VISTA: computational tools for comparative genomics. Nucleic Acids Research 32:W273−W279

doi: 10.1093/nar/gkh458
[30]

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, et al. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34:3299−302

doi: 10.1093/molbev/msx248
[31]

Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. 2010. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics, Proteomics & Bioinformatics 8:77−80

doi: 10.1016/S1672-0229(10)60008-3
[32]

Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59:307−21

doi: 10.1093/sysbio/syq010
[33]

Ye L, Fu C, Wang Y, Liu J, Gao L. 2018. Characterization of the complete plastid genome of a Chinese endemic species Carya kweichowensis. Mitochondrial DNA Part B 3:492−93

doi: 10.1080/23802359.2018.1464414
[34]

Zhai D, Yao Q, Cao X, Hao Q, Ma M, et al. 2019. Complete chloroplast genome of the wild-type Hickory Carya cathayensis. Mitochondrial DNA Part B 4:1457−58

doi: 10.1080/23802359.2019.1598815
[35]

Hu Y, Chen X, Feng X, Woeste KE, Zhao P. 2016. Characterization of the complete chloroplast genome of the endangered species Carya sinensis (Juglandaceae). Conservation Genetics Resources 8:467−70

doi: 10.1007/s12686-016-0601-4
[36]

Biju VC, Shidhi PR, Vijayan S, Rajan VS, Sasi A, et al. 2019. The complete chloroplast genome of Trichopus zeylanicus, and phylogenetic analysis with Dioscoreales. The Plant Genome 12:190032

doi: 10.3835/plantgenome2019.04.0032
[37]

Liu X, Zhu G, Li D, Wang X. 2019. Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'. PLoS ONE 14:e0224038

doi: 10.1371/journal.pone.0224038
[38]

Wang W, Yu H, Wang J, Lei W, Gao J, et al. 2017. The complete chloroplast genome sequences of the medicinal plant Forsythia suspensa (Oleaceae). International Journal of Molecular Sciences 18:2288

doi: 10.3390/ijms18112288
[39]

Dong W, Xu C, Li W, Xie X, Lu Y, et al. 2017. Phylogenetic resolution in Juglans based on complete chloroplast genomes and nuclear DNA sequences. Frontiers in Plant Science 8:1148

doi: 10.3389/fpls.2017.01148
[40]

Okumura S, Sawada M, Park YW, Hayashi T, Shimamura M, et al. 2006. Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts. Transgenic Research 15:637−46

doi: 10.1007/s11248-006-9009-3
[41]

Ueda M, Nishikawa T, Fujimoto M, Takanashi H, Arimura SI, et al. 2008. Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal. Molecular Biology and Evolution 25:1566−75

doi: 10.1093/molbev/msn102
[42]

Jansen RK, Saski C, Lee SB, Hansen AK, Daniell H. 2011. Complete plastid genome sequences of three Rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Molecular Biology and Evolution 28:835−47

doi: 10.1093/molbev/msq261
[43]

Wald N, Alroy M, Botzman M, Margalit H. 2012. Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids. Nucleic Acids Research 40:7074−83

doi: 10.1093/nar/gks348
[44]

Zuo L, Shang A, Zhang S, Yu X, Ren Y, et al. 2017. The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: genome comparative and taxonomic position analysis. PLoS ONE 12:e0171264

doi: 10.1371/journal.pone.0171264
[45]

Li Y, Sylvester SP, Li M, Zhang C, Li X, et al. 2019. The complete plastid genome of Magnolia zenii and genetic comparison to Magnoliaceae species. Molecules 24:261

doi: 10.3390/molecules24020261
[46]

Liu H, Yu Y, Deng Y, Li J, Huang Z, et al. 2018. The chloroplast genome of Lilium henrici: genome structure and comparative analysis. Molecules 23:1276

doi: 10.3390/molecules23061276
[47]

Wang X, Zhou T, Bai G, Zhao Y. 2018. Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships. Scientific Reports 8:12379

doi: 10.1038/s41598-018-30398-6
[48]

Weng ML, Blazier JC, Govindu M, Jansen RK. 2014. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Molecular Biology and Evolution 31:645−59

doi: 10.1093/molbev/mst257
[49]

Singh N, Pal AK, Roy RK, Tamta S, Rana TS. 2017. Development of cpSSR markers for analysis of genetic diversity in Gladiolus cultivars. Plant Gene 10:31−36

doi: 10.1016/j.plgene.2017.05.003
[50]

Deng Q, Zhang H, He Y, Wang T, Su Y. 2017. Chloroplast microsatellite markers for Pseudotaxus chienii developed from the whole chloroplast genome of Taxus chinensis var. mairei (Taxaceae). Applications in Plant Sciences 5:1600153

doi: 10.3732/apps.1600153
[51]

Liu Q, Li X, Li M, Xu W, Schwarzacher T, et al. 2020. Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny. BMC Plant Biology 20:406

doi: 10.1186/s12870-020-02621-y
[52]

Dugas DV, Hernandez D, Koenen EJM, Schwarz E, Straub S, et al. 2015. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Scientific Reports 5:16958

doi: 10.1038/srep16958
[53]

Kim KJ, Lee HL. 2004. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research 11:247−61

doi: 10.1093/dnares/11.4.247
[54]

Downie SR, Jansen RK. 2015. A comparative analysis of whole plastid genomes from the Apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Systematic Botany 40:336−51

doi: 10.1600/036364415X686620
[55]

Lee HL, Jansen RK, Chumley TW, Kim KJ. 2007. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Molecular Biology and Evolution 24:1161−80

doi: 10.1093/molbev/msm036
[56]

Li X, Li Y, Zang M, Li M, Fang Y. 2018. Complete chloroplast genome sequence and phylogenetic analysis of Quercus acutissima. International Journal of Molecular Sciences 19:2443

doi: 10.3390/ijms19082443
[57]

Zhang J, Li R, Xiang X, Manchester SR, Lin L, et al. 2013. Integrated fossil and molecular data reveal the biogeographic diversification of the eastern Asian-eastern North American disjunct hickory genus (Carya Nutt.). PLoS ONE 8:e70449

doi: 10.1371/journal.pone.0070449