Cheng H, Li JF, Zhang H, Cai BH, Gao ZH, Qiao YS, Mi L. The complete chloroplast genome sequence of strawberry (Fragaria X ananassa Duch.) and comparison with related species of Rosaceae. Peerj. 2017:5.
Dong W, Xu C, Cheng T, Lin K, Zhou S. Sequencing angiosperm plastid genomes made easy: a complete set of universal primers and a case study on the phylogeny of Saxifragales. Genome Biol Evol. 2013;5(5):989–97.
Article
PubMed
PubMed Central
Google Scholar
Dong WP, Liu J, Yu J, Wang L, Zhou SL. Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding. PLoS One. 2012:7(4).
Twyford AD, Ness RW. Strategies for complete plastid genome sequencing. Mol Ecol Resour. 2017;17(5):858–68.
Article
PubMed
Google Scholar
Dong W, Xu C, Wu P, Cheng T, Yu J, Zhou S, Hong D-Y. Resolving the systematic positions of enigmatic taxa: manipulating the chloroplast genome data of Saxifragales. Mol Phylogenet Evol. 2018;126:321–30.
Article
CAS
PubMed
Google Scholar
Li W, Liu Y, Yang Y, Xie X, Lu Y, Yang Z, Jin X, Dong W, Suo Z. Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros. BMC Plant Biol. 2018;18(1):210.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dong W, Xu C, Li W, Xie X, Lu Y, Liu Y, Jin X, Suo Z. Phylogenetic resolution in Juglans based on complete chloroplast genomes and nuclear DNA sequences. Front Plant Sci. 2017;8:1148.
Article
PubMed
PubMed Central
Google Scholar
Liu HS, Su ZH, Yu SQ, Liu JL, Yin XJ, Zhang GW, Liu W, Li B. Genome comparison reveals mutation hotspots in the chloroplast genome and phylogenetic relationships of Ormosia species. Biomed Res Int. 2019;2019.
Meng J, Li XP, Li HT, Yang JB, Wang H, He J. Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species. Molecules. 2018:23(5).
Mader M, Pakull B, Blanc-Jolivet C, Paulini-Drewes M, Bouda ZHN, Degen B, Small I, Kersten B. Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses. Int J Mol Sci. 2018:19(3).
Yang Z, Zhao TT, Ma QH, Liang LS, Wang GX. Comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus (Betulaceae) species. Front Plant Sci. 2018;9.
Dong W, Liu J, Yu J, Wang L, Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One. 2012;7(4):e35071.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peng HS, Wang DQ. The history and differentiation of raw Atractylodes commodity in successive ages. Zhonghua Yi Shi Za Zhi. 2007;37(1):15–8.
PubMed
Google Scholar
Kohjyouma M, Nakajima S, Namera A, Shimizu R, Mizukami H, Kohda H. Random amplified polymorphic DNA analysis and variation of essential oil components of Atractylodes plants. Biol Pharm Bull. 1997;20(5):502–6.
Article
CAS
PubMed
Google Scholar
Ge YF, Hang YY, Xia B, Wei YL. Sequencing of trnL-F and analysis of interspecific genetic relationship of five medicinal species in Atractylodes DC. J Plant Resour Environ. 2007;16:12–6.
CAS
Google Scholar
Peng HS, Yuan Q, Li Q, Huang L. Molecular systematics of genus Atractylodes (Compositae, Cardueae): evidence from internal transcribed spacer (ITS) and trnL-F sequences. Int J Mol Sci. 2012;13(11):14623–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zou XX, Huang LQ, Cui GH, Yuan QJ, Peng Y, Liu Y, Xiao PG. Genetic relationships of Atractylodes plants. Acta Pharm Sin. 2009;44(6):680–6.
CAS
Google Scholar
Lu RS, Li P, Qiu YX. The complete chloroplast genomes of three Cardiocrinum (Liliaceae) species: comparative genomic and phylogenetic analyses. Front Plant Sci. 2016;7:2054.
PubMed
Google Scholar
Wicke S, Schneeweiss GM, De Pamphilis CW, Muller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol. 2011;76(3–5):273–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KD, Wolf PG, Duffy AM, Karol KG. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC Genomics. 2010;11:143.
Article
PubMed
PubMed Central
Google Scholar
Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Muller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 2007;104(49):19369–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu C, Dong W, Li W, Lu Y, Xie X, Jin X, Shi J, He K, Suo Z. Comparative analysis of six Lagerstroemia complete chloroplast genomes. Front Plant Sci. 2017;8(15):15.
PubMed
PubMed Central
Google Scholar
Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M, Chen N. Development of chloroplast genomic resources for Oryza species discrimination. Front Plant Sci. 2017;8:1854.
Article
PubMed
PubMed Central
Google Scholar
Graham SW, Reeves PA, Burns ACE, Olmstead RG. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int J Plant Sci. 2000;161(6):S83–96.
Article
CAS
Google Scholar
Gandhi SG, Awasthi P, Bedi YS. Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family. Bioinformation. 2010;5(1):16–20.
Article
PubMed
PubMed Central
Google Scholar
Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M. Comparative chloroplast genomes of Sorghum species: sequence divergence and phylogenetic relationships. Biomed Res Int. 2019;2019:11.
Google Scholar
Ahmed I, Biggs PJ, Matthews PJ, Collins LJ, Hendy MD, Lockhart PJ. Mutational dynamics of aroid chloroplast genomes. Genome Biol Evol. 2012;4(12):1316–23.
Article
PubMed
PubMed Central
Google Scholar
Tian DC, Wang Q, Zhang PF, Araki H, Yang SH, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature. 2008;455(7209):105–U170.
Article
CAS
PubMed
Google Scholar
Hollister JD, Ross-Ibarra J, Gaut BS. Indel-associated mutation rate varies with mating system in flowering plants. Mol Biol Evol. 2010;27(2):409–16.
Article
CAS
PubMed
Google Scholar
Viljoen E, Odeny DA, Coetzee MPA, Berger DK, Rees DJG: Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. J Mol Evol 2018.
Cai C-N, Ma H, Ci X-Q, Conran JG, Li J: Comparative phylogenetic analyses of Chinese Horsfieldia (Myristicaceae) using complete chloroplast genome sequences. J Syst Evol 2019, n/a(n/a).
Shi Z. On the nomenclature of Chinese drug “Cangzhu”. Acta Phytotaxon Sin. 1981;19(3):318–22.
Google Scholar
Xu GF, Yu YL, Liu J, Wang LX. Observations on the morphological charcter of Atractylodes japonica Koidz. Et Kitam J Jiamusi Med Coll. 1993;16:15–7.
Google Scholar
Lee C, Wen J. Phylogeny of Panax using chloroplast trnC–trnD intergenic region and the utility of trnC–trnD in interspecific studies of plants. Mol Phylogenet Evol. 2004;31(3):894–903.
Article
CAS
PubMed
Google Scholar
Shaw J, Lickey EB, Beck JT, Farmer SB, Liu WS, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot. 2005;92(1):142–66.
Article
CAS
PubMed
Google Scholar
Gao G, Tang Z, Wang Q, Gou X, Ding C, Zhang L, Zhou Y, Yang R. Phylogeny and maternal donor of Kengyilia (Triticeae: Poaceae) based on chloroplast trnT–trnL sequences. Biochem Syst Ecol. 2014;57:102–7.
Article
CAS
Google Scholar
Li JL, Wang S, Yu J, Wang L, Zhou SL. A modified CTAB protocol for plant DNA extraction. Chinese Bulletin of Botany. 2013;48(1):72–8.
Article
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
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. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9.
Article
PubMed
PubMed Central
Google Scholar
Huang DI, Cronk QCB. Plann: a command-line application for annotating plastome sequences. Applications in Plant Sciences. 2015;3(8):1500026.
Article
Google Scholar
Lohse M, Drechsel O, Bock R. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 2007;52(5–6):267–74.
Article
CAS
PubMed
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rambaut A: Se-Al: sequence alignment editor. Version 2.0. 1996:http://tree.bio.ed.ac.uk/software/seal/.
Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008;9(4):299–306.
Article
CAS
PubMed
Google Scholar
Wang XW, Wang L. GMATA: an integrated software package for genome-scale SSR mining, marker development and VIewing. Front Plant Sci. 2016;7.
Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451–2.
Article
CAS
PubMed
Google Scholar
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17(4):540–52.
Article
CAS
PubMed
Google Scholar
Zhang D, Gao F, Jakovlic I, Zou H, Zhang J, Li WX, Wang GT. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 2020;20(1):348–55.
Article
PubMed
Google Scholar
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Article
CAS
PubMed
Google Scholar
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539–42.
PubMed
PubMed Central
Google Scholar