Advertisement

Science China Life Sciences

, Volume 56, Issue 2, pp 189–198 | Cite as

Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species

  • XiWen Li
  • HuanHuan Gao
  • YiTao Wang
  • JingYuan Song
  • Robert Henry
  • HeZhen Wu
  • ZhiGang Hu
  • Hui Yao
  • HongMei Luo
  • Kun Luo
  • HongLin Pan
  • ShiLin ChenEmail author
Open Access
Research Paper
First Online:

Abstract

Magnolia grandiflora is an important medicinal, ornamental and horticultural plant species. The chloroplast (cp) genome of M. grandiflora was sequenced using a 454 sequencing platform and the genome structure was compared with other related species. The complete cp genome of M. grandiflora was 159623 bp in length and contained a pair of inverted repeats (IR) of 26563 bp separated by large and small single copy (LSC, SSC) regions of 87757 and 18740 bp, respectively. A total of 129 genes were successfully annotated, 18 of which included introns. The identity, number and GC content of M. grandiflora cp genes were similar to those of other Magnoliaceae species genomes. Analysis revealed 218 simple sequence repeat (SSR) loci, most composed of A or T, contributing to a bias in base composition. The types and abundances of repeat units in Magnoliaceae species were relatively conserved and these loci will be useful for developing M. grandiflora cp genome vectors. In addition, results indicated that the cp genome size in Magnoliaceae species and the position of the IR border were closely related to the length of the ycf1 gene. Phylogenetic analyses based on 66 shared genes from 30 species using maximum parsimony (MP) and maximum likelihood (ML) methods provided strong support for the phylogenetic position of Magnolia. The availability of the complete cp genome sequence of M. grandiflora provides valuable information for breeding of desirable varieties, cp genetic engineering, developing useful molecular markers and phylogenetic analyses in Magnoliaceae.

Keywords

intron inverted repeats SSR phylogenetics 
Download to read the full article text

Supplementary material

11427_2012_4430_MOESM1_ESM.pdf (365 kb)
Supplementary material, approximately 365 KB.

References

  1. 1.
    Verma D, Daniell H. Chloroplast vector systems for biotechnology applications. Plant Physiol, 2007, 145: 1129–1143PubMedPubMedCentralCrossRefGoogle Scholar
  2. 2.
    Clegg M T, Gaut B S, Learn G H, et al. Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci USA, 1994, 91: 6795–6801PubMedPubMedCentralCrossRefGoogle Scholar
  3. 3.
    Shinozaki K, Ohme M, Tanaka M, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J, 1986, 5: 2043–2049PubMedPubMedCentralGoogle Scholar
  4. 4.
    Ohyama K, Fukuzawa H, Kohchi T, et al. Chloroplast gene organization deduced from complete sequence of Liverwort Marchantia polymorpha chloroplast DNA. Nature, 1986, 322: 572–574CrossRefGoogle Scholar
  5. 5.
    Terada R, Urawa H, Inagaki Y, et al. Efficient gene targeting by homologous recombination in rice. Nat Biotechnol, 2002, 20: 1030–1034PubMedCrossRefGoogle Scholar
  6. 6.
    Kane N, Sveinsson S, Dempewolf H, et al. Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Am J Bot, 2012, 99: 320–329PubMedGoogle Scholar
  7. 7.
    Zhang Y J, Ma P F, Li D Z. High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae). PLoS One, 2011, 6: e20596PubMedPubMedCentralCrossRefGoogle Scholar
  8. 8.
    Kanevski I, Maliga P, Rhoades D F, et al. Plastome engineering of ribulose-1, 5-bisphosphate carboxylase/oxygenase in tobacco to form a sunflower large subunit and tobacco small subunit hybrid. Plant Physiol, 1999, 119: 133–142PubMedPubMedCentralCrossRefGoogle Scholar
  9. 9.
    Craig W, Lenzi P, Scotti N, et al. Transplastomic tobacco plants expressing a fatty acid desaturase gene exhibit altered fatty acid profiles and improved cold tolerance. Transgenic Res, 2008, 17: 769–782PubMedCrossRefGoogle Scholar
  10. 10.
    Jansen K J, Zhengqiu C, Linda A R, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA, 2007, 104: 19369–19374PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Xu F, Rudall P J. Comparative floral anatomy and ontogeny in Magnoliaceae. Plant Syst Evol, 2006, 258: 1–15CrossRefGoogle Scholar
  12. 12.
    Yamada T, Imaichi R, et al. The outer integument and funicular outgrowth complex in the ovule of Magnolia grandiflora (Magnoliaceae). J Plant Res, 2003, 116: 189–198PubMedCrossRefGoogle Scholar
  13. 13.
    Kim S, Park C W, Kim Y D, et al. Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences. Am J Bot, 2001, 88: 717–728PubMedCrossRefGoogle Scholar
  14. 14.
    Sauquet H, Doyle J A, Scharaschkin T, et al. Phylogenetic analysis of Magnoliales and Myristicaceae based on multiple data sets: implications for character evolution. Bot J Linn Soc, 2003, 142: 125–186CrossRefGoogle Scholar
  15. 15.
    Fu D L. Notes on Yulania Spach. J Wuhan Bot Res, 2001, 19: 191–198Google Scholar
  16. 16.
    Wang Q, Wang Z Z, Li Y L. Study on tissue culture of Magnolia grandiflora L.. Northwest Pharm J, 2001, 16: 11–13Google Scholar
  17. 17.
    Lee S, Chappell J. Biochemical and genomic characterization of terpene synthases in Magnolia grandiflora. Plant Physiol, 2008, 147: 1017–1033PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Wang Z G, Wu C Q, Wang C Y, et al. Effect of Magnolia grandifore oil on lipid metabolism in hyperlipoidemic rat. Chin Trad Patent Med, 2010, 32: 1679–1682Google Scholar
  19. 19.
    Li X W, Hu Z G, Lin X H, et al. High-throughput pyrosequencing of the complete chloroplast genome of Magnolia officinalis and its application in species identification. Acta Pharm Sin, 2012, 47: 124–130Google Scholar
  20. 20.
    Cai Z Q, Penaflor C, Kuehl J V, et al. Complete plastid genome sequence of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol, 2006, 6: 77PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Xu J W, Feng D J, Song G S, et al. The first introns in rice EPSP synthase enhance exogenous gene expression. Science China Ser C-Life Sci, 2003, 33: 224–230Google Scholar
  22. 22.
    Fukuzawa H, Kohchi T, Shirai H, et al. Coding sequences for chloroplast ribosomal protein S12 from the liverwort Marchantia polymorpha, are separated far apart on the different DNA Strand. FEBS Lett, 1986, 198: 11–15CrossRefGoogle Scholar
  23. 23.
    Kim K J, Lee H L. Complete chloroplast genome sequences from Korean Ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res, 2004, 11: 247–261PubMedCrossRefGoogle Scholar
  24. 24.
    Kuang D Y, Wu H, Wang Y L, et al. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome, 2011, 54: 663–673PubMedCrossRefGoogle Scholar
  25. 25.
    Xu G X, Guo C C, Shan H Y, et al. Divergence of duplicate genes in exon-intron structure. Proc Natl Acad Sci USA, 2012, 109: 1187–1192PubMedPubMedCentralCrossRefGoogle Scholar
  26. 26.
    Kaundun S S, Matsumoto S. Heterologous nuclear and chloroplast microsatellite amplification and variation in tea Camellia sinensis. Genome, 2002, 45: 1041–1048PubMedCrossRefGoogle Scholar
  27. 27.
    Jiao Y, Jia H M, Li X W, et al. Development of simple sequence repeat (SSR) markers from a genome survey of Chinese Bayberry (Myrica rubra). BMC Genomics, 2012, 13: 201PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Ravi V, Khurana J P, Tyagi A K, et al. An update on chloroplast genomes. Plant Syst Evol, 2008, 271: 101–122CrossRefGoogle Scholar
  29. 29.
    Michael J M, Soltis, P S, Bell C D, et al. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci USA, 2010, 107: 4623–4628CrossRefGoogle Scholar
  30. 30.
    Azuma H, Thien L B, Kawano S. Molecular phylogeny of Magnolia (Magnoliaceae) inferred from cpDNA sequences and evolutionary divergence of the floral scents. J Plant Res, 1999, 112: 291–306CrossRefGoogle Scholar
  31. 31.
    Azuma H, Thien L B, Kawano S. Molecular phylogeny of Magnolia based on chloroplast DNA sequence data (trnK intron, psbA-trnH and atpB-rbcL intergenic spacer regions) and floral scent chemistry. In: Liu Y H, Fan H M, eds. Proceedings of the International Symposium on the Family Magnoliaceae. Beijing: Science Press, 2000. 219–227Google Scholar
  32. 32.
    Azuma H, Garcia-Franco J G, Rico-Gray V, et al. Molecular phylogeny of the Magnoliaceae: the biogeography of tropical and temperate disjunctions. Am J Bot, 2001, 88: 2275–2285PubMedCrossRefGoogle Scholar
  33. 33.
    Ueda K, Yamashita J, Tamura M N. Molecular phylogeny of the Magnoliaceae. In: Liu Y H, Fan H M, eds. Proceedings of the International Symposium on the Family Magnoliaceae. Beijing: Science Press, 2000. 205–209Google Scholar
  34. 34.
    Wang Y L, Zhang S Z, Cui T C. The utility of trnL intron and trnL-trnF IGS in phylogenetic analysis of Magnoliaceae. Acta Bot Boreali-Occident Sin, 2003, 23: 247–252Google Scholar
  35. 35.
    Wang Y L, Li Y, Zhang S Z, et al. The utility of matk gene in the phylogenetic analysis of the genus Magnolia. Acta Phytotaxon Sin, 2006: 135–147Google Scholar

Copyright information

© The Author(s) 2013

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  • XiWen Li
    • 1
    • 3
  • HuanHuan Gao
    • 1
    • 2
  • YiTao Wang
    • 3
  • JingYuan Song
    • 1
  • Robert Henry
    • 4
  • HeZhen Wu
    • 2
  • ZhiGang Hu
    • 2
  • Hui Yao
    • 1
  • HongMei Luo
    • 1
  • Kun Luo
    • 1
  • HongLin Pan
    • 2
  • ShiLin Chen
    • 1
    • 5
    Email author
  1. 1.Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesBeijingChina
  2. 2.Faculty of PharmacyHubei University of Chinese MedicineWuhanChina
  3. 3.Institute of Chinese Medical ScienceUniversity of MacaoMacaoChina
  4. 4.Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneAustralia
  5. 5.Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina

Personalised recommendations