Liao C, Downie SR, Li Q, Yu Y, He X, Zhou B. New insights into the phylogeny of Angelica and its allies (Apiaceae) with emphasis on east Asian species, inferred from nrDNA, cpDNA, and morphological evidence. Syst Bot. 2013;38(1):266–81.
Article
Google Scholar
Vasil'eva MG, Pimenov MG. Karyotaxonomical analysis in the genusAngelica (Umbelliferae). Plant Syst Evol. 1991;177(3):117–38.
Article
Google Scholar
Meng-lan S, Fa-ting P, Zehui P, Watson MF, Cannon JFM, Holmes-Smith I, et al. In: Wu ZY, Raven PH, editors. Apiaceae. Pp. 1–205 in Flora of China, vol. 14. St. Louis: Missouri Botanical Garden Press and Beijing: Science Press; 2005.
Google Scholar
Wen J. Evolution of eastern Asian and eastern north American Disjunct distributions in flowering plants. Annu Rev Ecol Syst. 1999;30(1):421–55.
Article
Google Scholar
Liao CY, Downie SR, Yu Y, He XJ. Historical biogeography of the Angelica group (Apiaceae tribe Selineae) inferred from analyses of nrDNA and cpDNA sequences. J Syst Evol. 2012;50(3):206–17.
Article
Google Scholar
Feng T, Downie S, Yu Y, Zhang X, Chen W, He X-J, et al. Molecular systematics of Angelica and allied genera (Apiaceae) from the Hengduan Mountains of China based on nrDNA ITS sequences: phylogenetic affinities and biogeographic implications. J Plant Res. 2009;122:403–14.
Article
CAS
PubMed
Google Scholar
Yuan QJ, Zhang B, Jiang D, Zhang WJ, Lin TY, Wang NH, et al. Identification of species and materia medica within Angelica L.(Umbelliferae) based on phylogeny inferred from DNA barcodes. Mol Ecol Resour. 2015;15(2):358–71.
Shan RH. In: Shan RH, Sheh ML, editors. Umbelliferae. Pp. 13–62 in Flora Reipublicae Popularis Sinicae, vol. 55(3). Beijing: Acade- mia Sinica; 1992.
Google Scholar
Ze-Hui P, Xin-Tian L, Meng-Lan S, Lang-Ran X. A study on karyotypes of eight species and geographical distribution of Angelica (Umbelliferae) in Sichuan. Acta Phytotaxonomica Sinica. 1991;29(5):431–8.
Google Scholar
Zhang QY, Xing-Jin HE, Zhang YC, Peng L, Ning WU. Study on karyotypes of six species in Angelica from Sichuan,China. Acta Bot Yunnanica. 2005;27(5):539-44.
Chen WW, He XJ, Zhang XM, Pu JX. Pollen morphology of the genus Angelica from Southwest China and its systematic evolution analysis. Acta Botan Boreali-Occiden Sin. 2007; 27(3):1364-72.
Lan SM, Su P, Pan ZH. The comparative study of pollen morphology of Angelica L. between East Asia and North America. J Plant Res Environ. 1997;6(1):41-47.
Meng D. Pollen morphology of the genus Peucedanum from Sichuan and its systematic significance. Acta Bot Boreal Occident Sin. 2004;24(12):2341-45.
Zhang QY, Xing Jin HE, Zhang YC, Luo P, Ning WU. Anatomical studies on fruits and petioles of 8 species of Angelica L.from Sichuan Province. J Wuhan Botanical Res. 2005;23(6):549-54.
Chen X, Changqi Y. The generic position of Zihua Qianhu and its comparative taxonomic studies with Korean Danggui. J Nanjing Univ. 1987;23(1):23-31.
Shneyer VS, Kutyavina NG, Pimenov MG. Systematic relationships within and between Peucedanum and Angelica (Umbelliferae–Peucedaneae) inferred from immunological studies of seed proteins. Plant Syst Evol. 2003;236(3–4):175–94.
Katz-Downie DS, Valiejo-Roman CM, Terentieva EI, Troitsky AV, Pimenov MG, Lee B, et al. Towards a molecular phylogeny of Apiaceae subfamily Apioideae: additional information from nuclear ribosomal DNA ITS sequences. Plant Syst Evol. 1999;216(3–4):167–95.
Article
CAS
Google Scholar
Downie S, Katz-Downie D. A molecular phylogeny of apiaceae subfamily apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences. Am J Bot. 1996;83(2):234–51.
Spalik K, Reduron JP, Downie SR. The phylogenetic position of Peucedanum sensu lato and allied genera and their placement in tribe Selineae (Apiaceae, subfamily Apioideae). Plant Syst Evol. 2004;243(3):189–210.
Article
Google Scholar
Xue HJ. Taxonomic study of Angelica from East Asia: Inferences from ITS sequences of nuclear ribosomal DNA. Acta Phytotaxonomica Sinica. 2007;45(6):783–95.
Article
Google Scholar
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
Gurusamy R, Park S. The complete chloroplast genome sequence of ampelopsis: Gene Organization, comparative analysis, and phylogenetic relationships to other angiosperms. Front Plant Sci. 2016;7:341.
Wang H-X, Liu H, Moore MJ, Landrein S, Liu B, Zhu Z-X, et al. Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l. (Dipsacales). Mol Phylogenet Evol. 2020;142:106641.
Article
PubMed
Google Scholar
Xu C, Dong W, Li W, Lu Y, Xie X, Jin X, et al. Comparative analysis of six Lagerstroemia complete chloroplast genomes. Front Plant Sci. 2017;8:15.
Dong W, Chao X, Tao C, 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.
Article
Google Scholar
Dong W, Xu C, Li D, Jin X, Li R, Lu Q, et al. Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). PeerJ. 2016;4:e2699.
Article
PubMed
PubMed Central
Google Scholar
Ruhlman T, Lee S-B, Jansen RK, Hostetler JB, Tallon LJ, Town CD, et al. Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics. 2006;7(1):222.
Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). New Phytol. 2014; 204(3):693-703.
Perdereau A, Klaas M, Barth S, Hodkinson TR. Plastid genome sequencing reveals biogeographical structure and extensive population genetic variation in wild populations of Phalaris arundinacea L. In North-Western Europe. GCB Bioenergy. 2017;9(1):46–56.
Spooner DM, Ruess H, Iorizzo M, Senalik D, Simon P. Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid. Am J Bot. 2017;104(2):296–312.
Wang H, Liu H, Moore M, Landrein S, Liu B, Zhu Z, et al. Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l.(Dipsacales). Mol Phylogenet Evol. 2019;142:106641.
Article
PubMed
Google Scholar
Yao G, Jin J, Li H-T, Yang J-B, Mandala V, Croley M, et al. Plastid phylogenomic insights into the evolution of Caryophyllales. Mol Phylogenet Evol. 2019;134:74-86.
Liu D, Tu X-D, Zhao Z, Zeng M-Y, Zhang S, Ma L, et al. Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae). Mol Phylogenet Evol. 2020;145:106729.
Article
PubMed
Google Scholar
Zhang H, Wei R, Xiang Q-P. Plastome-based phylogenomics resolves the placement of the sanguinolenta group in the spikemoss of lycophyte (Selaginellaceae). Mol Phylogenet Evol. 2020;106788.
Zhang R, Wang Y-H, Jin J, Moore M, Zhang S-D, Chen S-Y, et al. Exploration of plastid Phylogenomic conflict yields new insights into the deep relationships of Leguminosae. Syst Biol. 2020;69(4):613-22.
Kim KJ, Lee HL. Widespread occurrence of small inversions in the chloroplast genomes of land plants. Mol Cell. 2005;19(1):104–13.
CAS
Google Scholar
Sajjad A, Khan AL, Khan AR, Muhammad W, Kang SM, Khan MA, et al. Complete chloroplast genome of Nicotiana otophora and its comparison with related species. Front Plant Sci. 2016;7:843.
Yang Y, Zhou T, Duan D, Yang J, Feng L, Zhao G. Comparative analysis of the complete chloroplast genomes of five Quercus species. Front Plant Sci. 2016;07:959.
Downie SR, Katz-Downie DS, Watson MF. A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: towards a suprageneric classification of subfamily Apioideae. Am J Bot. 2000;87(2):273–92.
Article
CAS
PubMed
Google Scholar
Zhou J, Gong X, Downie SR, Peng H. Towards a more robust molecular phylogeny of Chinese Apiaceae subfamily Apioideae: additional evidence from nrDNA ITS and cpDNA intron (rpl16 and rps16) sequences. Mol Phylogenet Evol. 2009;53(1):56–68.
Article
CAS
PubMed
Google Scholar
Downie SR, Spalik K, Katz-Downie DS, Reduron J-P. Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences. Plant Diversity Evol. 2010;128(1–2):111–36.
Article
Google Scholar
Gong X, Liu ZW, Downie SR, Peng H, Zhou J. A molecular phylogeny of Chinese Apiaceae subfamily Apioideae inferred from nuclear ribosomal DNA internal transcribed spacer sequences. Taxon. 2008;57(2):402-416.
Downie SR, Spalik K, Katz-Downie DS, Reduron JP. Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences. Plant Diversity Evol. 2010;128(1):111–36.
Article
Google Scholar
Li R, Ma PF, Wen J, Yi TS. Complete sequencing of five Araliaceae chloroplast genomes and the phylogenetic implications. PLoS One. 2013;8(10):e78568.
Xue S, Shi T, Luo W, Ni X, Iqbal S, Ni Z, et al. Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina. Horticulture Res. 2019;6(1):89.
Article
Google Scholar
Bock R, Knoop V, editors. Genomics of chloroplasts and mitochondria, Adv. Photosyn Resp, vol. 35. Dordrecht: Springer Netherlands; Dordrecht; 2012. p. 1–458.
Plunkett GM, Downie SR. Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae. Syst Bot. 2000;25(4):648–67 620.
Article
Google Scholar
Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology. 2020;21(1):241.
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R, et al. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017;45(1):W6–W11.
Greiner S, Lehwark P, Bock R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019;47(W1):W59–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thiel T, Michalek W, Varshney R, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical Appl Genet. 2003;106(3):411–22.
Article
CAS
Google Scholar
Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394–403.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amiryousefi A, Hyvönen J, Poczai P. IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018;34(17):3030–1.
Article
CAS
PubMed
Google Scholar
Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 2016;34(3):772–3.
Google Scholar
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35(21):4453–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539–42.
Article
PubMed
PubMed Central
Google Scholar