Asaf S, Khan AL, Khan AR, Waqas M, Kang SM, Khan MA, Lee SM, Lee IJ (2016) Complete chloroplast genome of Nicotianaotophora and its comparison with related species. Front Plant Sci 7:843–854
Article
PubMed
PubMed Central
Google Scholar
Chen JH, Hao ZD, Xu HB, Yang LM, Liu GX, Sheng Y, Zheng C, Zheng WW, Chen TL, Shi JS (2015) The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng. Front Plant Sci 6:447
PubMed
PubMed Central
Google Scholar
Choi KS, Chung MG, Park SJ (2016) The complete chloroplast genome sequences of three Veroniceae species (Plantaginaceae): comparative analysis and highly divergent regions. Front Plant Sci 7:342–355
Google Scholar
Ding YJ, Zhang JH, Lu YF, Lin EP, Lou LH, Tong ZK (2015) Development of EST-SSR markers and analysis of genetic diversity in natural populations of endemic and endangered plant Phoebe chekiangensis. Biochem Syst Ecol 63:183–189
Article
CAS
Google Scholar
Dong WP, Liu H, Xu C, Zuo YJ, Chen Z, Zhou SL (2014) A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs. BMC Genet 15:138–145
Article
PubMed
PubMed Central
Google Scholar
Douglas SE (1990) Plastid evolution: origins, diversity, trends. Curr Opin Genet Dev 8:655–661
Article
Google Scholar
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273–W279
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao L, Yi X, Yang YX, Su YJ, Wang T (2009) Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol Biol 9:130–142
Article
PubMed
PubMed Central
Google Scholar
Hegde VR, Dai P, Ladislaw C, Patel MG, Puar MS, Pachter JA (1997) D4 dopamine receptor-selective compounds from the Chinese plant Phoebe chekiangensis. Bioorg Med Chem Lett 9:1207–1212
Article
Google Scholar
Huang H, Shi C, Liu Y, Mao SY, Gao LZ (2014) Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol Biol 14:151–167
Article
PubMed
PubMed Central
Google Scholar
Ingvarsson PK, Ribstein S, Taylor DR (2003) Molecular evolution of insertions and deletion in the chloroplast genome of Silene. Mol Biol Evol 20:1737–1740
Article
CAS
PubMed
Google Scholar
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780
Article
CAS
PubMed
PubMed Central
Google Scholar
Khakhlova O, Bock R (2006) Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J 46:85–94
Article
CAS
PubMed
Google Scholar
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 Res 11:247–261
Article
CAS
PubMed
Google Scholar
Kim JS, Jung JD, Lee JA, Park HW, Oh KH, Jeong WJ, Choi DW, Liu JR (2006) Complete sequence and organization of the cucumber (Cucumis sativus L cv. Baekmibaekdadagi) chloroplast genome. Plant Cell Rep 25:334–340
Article
CAS
PubMed
Google Scholar
Korotkova N, Nauheimer L, Ter-Voskanyan H, Allgaier M, Borsch T (2014) Variability among the most rapidly evolving plastid genomic regions is lineage-specific: implications of pairwise genome comparisons in Pyrus (Rosaceae) and other angiosperms for marker choice. PLoS ONE 11:e112998
Article
Google Scholar
Kuang DY, Wu H, Wang YL, Gao LM, Zhang SZ, Lu L, Bonen L (2011) Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome 54:663–673
Article
PubMed
Google Scholar
Kurtz S, Schleiermacher C (1999) REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15:426–427
Article
CAS
PubMed
Google Scholar
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452
Article
CAS
PubMed
Google Scholar
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. Curr Genet 52:267–274
Article
CAS
PubMed
Google Scholar
Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA 104:19363–19368
Article
PubMed
PubMed Central
Google Scholar
Nie XJ, Lv SZ, Zhang YX (2012) Complete chloroplast genome sequence of a major invasive species Crofton Weed (Ageratina adenophora). PLoS ONE 7:e36869
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84–100
Article
PubMed
PubMed Central
Google Scholar
Pauwels M, Vekemans X, Gode C, Frerot H, Castric V, Saumitou-Laprade P (2012) Nuclear and chloroplast DNA phylogeography reveals vicariance among European populations of the model species for the study of metal tolerance Arabidopsis halleri (Brassicaceae). New Phytol 193:916–928
Article
CAS
PubMed
Google Scholar
Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15:8–15
Article
CAS
Google Scholar
Qian J, Song JY, Gao HH (2013) The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS ONE 8:e57607
Article
CAS
PubMed
PubMed Central
Google Scholar
Rohwer JG (2000) Toward a phylogenetic classification of the Lauraceae: evidence from matK sequences. Syst Bot 25:60–71
Article
Google Scholar
Särkinen T, George M (2013) Predicting plastid marker variation: can complete plastid genomes from closely related species help? PLoS ONE 11:e82266
Article
Google Scholar
Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:686–689
Article
Google Scholar
Song Y, Dong WP, Liu B, Xu C, Yao X, Gao J, Corlett RT (2015) Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae. Front Plant Sci 6:662–669
PubMed
PubMed Central
Google Scholar
Song Y, Yao X, Tan YH, Gan Y, Richard TC (2016) Complete chloroplast genome sequence of the avocado: gene organization, comparative analysis, and phylogenetic relationships with other Lauraceae. Can J Forest Res 46:1293–1301
Article
Google Scholar
Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N (2010) The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res 17:11–22
Article
CAS
PubMed
Google Scholar
Terakami S, Matsumura Y, Kurita K, Kanamori H, Katayose Y, Yamamoto T (2012) Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis. Tree Genet Genomes 8:1–14
Article
Google Scholar
Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L). Theor Appl Genet 106:411–422
Article
CAS
PubMed
Google Scholar
Uthaipaisanwong P, Chanprasert J, Shearman J (2012) Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq). Gene 500:172–180
Article
CAS
PubMed
Google Scholar
Wang MX, Cui LC, Feng KW, Deng PC, Du XH, Wan FH, Song WN, Nie XJ (2015) Comparative analysis of Asteraceae chloroplast genomes: structural organization, RNA editing and evolution. Plant Mol Biol Rep 33:1526–1538
Article
CAS
Google Scholar
Wicke S, Schneeweiss GM, Müller KF, Quandt D (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76:273–297
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu ZY, Peter HR, Hong DY (2008) Flora of China. Science press, Beijing
Google Scholar
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255
Article
CAS
PubMed
Google Scholar
Xu Q, Xiong G, Li P, He F, Huang Y, Wang K, Li ZH, Hua JP (2012) Analysis of complete nucleotide sequences of 12 gossypium chloroplast genomes: origin and evolution of allotetraploids. PLoS ONE 8:e37128
Article
Google Scholar
Yang M, Zhang XW, Liu GM, Yin YX, Chen KF, Yun QZ, Zhao DJ, Al-Mssallem IS, Yu J (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L). PLoS ONE 5:e12762
Article
PubMed
PubMed Central
Google Scholar
Yang J, Yue M, Niu C, Ma XF, Li ZH (2017) Comparative analysis of the complete chloroplast genome of four endangered herbals of Notopterygium. Genes 8:124
Article
PubMed Central
Google Scholar
Yao X, Tang P, Li Z, Li D, Liu Y, Huang H (2015) The first complete chloroplast genome sequences in Actinidiaceae: genome structure and comparative analysis. PLoS ONE 10:e0129347
Article
PubMed
PubMed Central
Google Scholar
Zeng SY, Zhou T, Han K, Yang YC, Zhao JH, Liu ZL (2017) The complete chloroplast genome sequences of six Rehmannia species. Genes 8:103
Article
PubMed Central
Google Scholar
Zhang Q, Li J, Zhao Y, Korba SS, Han Y (2012a) Evaluation of genetic diversity in Chinese wild apple species along with apple cultivars using SSR markers. Plant Mol Biol Rep 30:539–546
Article
CAS
Google Scholar
Zhang R, Zhou ZC, Jin GQ, Wang SH, Wang XH (2012b) Genetic diversity and differentiation within three species of the family Lauraceae in southeast China. Biochem Syst Ecol 44:317–324
Article
CAS
Google Scholar
Zhang YJ, Du LW, Liu A, Chen JJ, Wu L, Hu WM, Zhang W, Kim KH, Lee SC, Yang TJ, Wang Y (2016) The complete chloroplast genome sequences of five Epimedium species: lights into phylogenetic and taxonomic analyses. Front Plant Sci 7:306–317
PubMed
PubMed Central
Google Scholar
Zhao Y, Yin J, Guo H (2015) The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Front Plant Sci 5:696–707
PubMed
PubMed Central
Google Scholar