Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): Implication for DNA barcoding and population genetics

Genome

Volumn 54, Issue 8, 2011, Pages 663-673

  Kuang, Dai Yong ^a,b   Wu, Hong ^b   Wang, Ya Ling ^c   Gao, Lian Ming ^d   Zhang, Shou Zhou ^a   Lu, Lu ^a,b  

^a Shenzhen Fairylake Botanical Garden   (China)

^b SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

^c Xian Botanical Garden of Shaanxi Academy of Science   (China)

^d KUNMING INSTITUTE OF BOTANY   (China)

Author keywords

cpSSR; DNA barcoding; Magnolia kwangsiensis; plastome; RNA editing

Indexed keywords

CHLOROPLAST DNA;

ARTICLE; CHLOROPLAST; CHLOROPLAST GENOME; DNA BARCODING; DNA BASE COMPOSITION; ENDANGERED SPECIES; GENE DOSAGE; GENETICS; HIGH THROUGHPUT SEQUENCING; MAGNOLIACEAE; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE REPEAT; OPEN READING FRAME; PHYLOGENY; PLANT GENE; PLANT GENOME; POPULATION GENETICS;

BASE COMPOSITION; CHLOROPLASTS; DNA BARCODING, TAXONOMIC; DNA, CHLOROPLAST; ENDANGERED SPECIES; EVOLUTION, MOLECULAR; GENE DOSAGE; GENES, PLANT; GENETICS, POPULATION; GENOME, CHLOROPLAST; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MAGNOLIA; OPEN READING FRAMES; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID;

LIRIODENDRON TULIPIFERA; MAGNOLIA; MAGNOLIACEAE; MAGNOLIIDS; SPERMATOPHYTA;

EID: 80052008793     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g11-026     Document Type: Article

References (78)

1. Bendich A.J. 2004. Circular chloroplast chromosomes: the grand illusion. Plant Cell, 16 (7): 1661-1666. 10.1105/tpc.160771 15235123 (Pubitemid 38908766)
2. Cai Z. Penaflor C. Kuehl J.V. Leebens-Mack J. Carlson J.E. dePamphilis C.W. et al. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol. Biol. 6: 77. 10.1186/1471-2148-6-77 17020608 (Pubitemid 44662378)
3. Cho Y. Mower J.P. Qiu Y.-L. Palmer J.D. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc. Natl. Acad. Sci. U.S.A. 101 (51): 17741-17746. 10.1073/pnas.0408302101 15598738 (Pubitemid 40051957)
4. Conant G.C. Wolfe K.H. 2008. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics, 24 (6): 861-862. 10.1093/bioinformatics/btm598 18227121 (Pubitemid 351386926)
5. Covello P.S. Gray M.W. 1989. RNA editing in plant mitochondria. Nature, 341 (6243): 662-666. 10.1038/341662a0 2552326 (Pubitemid 19257319)
6. Cronn R. Liston A. Parks M. Gernandt D.S. Shen R.K. Mockler T. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36 (19): e122. 10.1093/nar/gkn502 18753151
7. Cui B.B. Li Y. Feng D.L. Liu Y. Fu X.X. 2006. A study for isolation of Populus chloroplast and cpDNA. J Baoding Teach Coll. 19 (2): 25-27. [In Chinese.]
8. Daniell H. Lee S.-B. Grevich J. Saski C. Quesada-Vargas T. Guda C. et al. 2006. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor. Appl. Genet. 112 (8): 1503-1518. 10.1007/s00122-006-0254-x 16575560
9. Deguilloux M.-F. Pemonge M.-H. Petit R.J. 2004. Use of chloroplast microsatellites to differentiate oak populations. Ann. For. Sci. 61 (8): 825-830. 10.1051/forest:2004078 (Pubitemid 40346289)
10. Doyle J.J. Morgante M. Tingey S.V. Powell W. 1998. Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine). Mol. Biol. Evol. 15 (2): 215-218. 9491617
11. Drescher A. Ruf S. Calsa T. Jr. Carrer H. Bock R. 2000. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J. 22 (2): 97-104. 10.1046/j.1365-313x.2000.00722.x 10792825 (Pubitemid 30308402)
12. Du P. Jia L. Li Y. 2009. CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics, 10: 135. 10.1186/1471-2105-10-135 19422723
13. Ebert D. Peakall R. 2009. Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol. Ecol. Resour. 9 (3): 673-690. 10.1111/j.1755-0998.2008.02319.x
14. Fiebig A. Stegemann S. Bock R. 2004. Rapid evolution of RNA editing sites in a small non-essential plastid gene. Nucleic Acids Res. 32 (12): 3615-3622. 10.1093/nar/gkh695 15240834 (Pubitemid 39157710)
15. Figlar, R.B. 2000. Proleptic branch initiation in Michelia and Magnolia subgenus Yulania provides basis for combinations in subfamily Magnoliaceae (A). In Proceedings of the International Symposium on the Family Magnoliaceae, Beijing, 2000. Edited by Y.H. Law. Science Press, Beijing. pp. 14-25.
16. Figlar R.B. Nooteboom H.P. 2004. Notes on Magnoliaceae IV. Blumea, 49: 87-100. (Pubitemid 38587748)
17. Fox M.G. Sorhannus U.M. 2003. RpoA: a useful gene for phylogenetic analysis in diatoms. J. Eukaryot. Microbiol. 50 (6): 471-475. 10.1111/j.1550-7408.2003.tb00273.x 14733439 (Pubitemid 38043094)
18. Freyer R. Kiefer-Meyer M.-C. Kössel H. 1997. Occurrence of plastid RNA editing in all major lineages of land plants. Proc. Natl. Acad. Sci. U.S.A. 94 (12): 6285-6290. 10.1073/pnas.94.12.6285 9177209 (Pubitemid 27270676)
19. Giegé P. Brennicke A. 1999. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc. Natl. Acad. Sci. U.S.A. 96 (26): 15324-15329. 10.1073/pnas.96.26.15324 10611383 (Pubitemid 30019810)
20. Goodson B.E. Santos-Guerra A. Jansen R.K. 2006. Molecular systematics of Descurainia (Brassicaceae) in the Canary Islands: biogeographic and taxonomic implications. Taxon, 55 (3): 671-682. 10.2307/25065643 (Pubitemid 44534842)
21. Goremykin V.V. Hirsch-Ernst K.I. Wölfl S. Hellwig F.H. 2003. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol. Biol. Evol. 20 (9): 1499-1505. 10.1093/molbev/msg159 12832641 (Pubitemid 37082584)
22. Gualberto J.M. Lamattina L. Bonnard G. Weil J.-H. Grienenberger J.-M. 1989. RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature, 341 (6243): 660-662. 10.1038/341660a0 2552325 (Pubitemid 19257318)
23. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
24. Hebert P.D.N. Ratnasingham S. de Waard J.R. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B Biol. Sci. 270 (Suppl. 1): S96-S99. 10.1098/rsbl.2003.0025
25. Hebert P.D.N. Penton E.H. Burns J.M. Janzen D.H. Hallwachs W. 2004. a. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. U.S.A. 101 (41): 14812-14817. 10.1073/pnas.0406166101 15465915 (Pubitemid 39410757)
26. Hebert P.D.N. Stoeckle M.Y. Zemlak T.S. Francis C.M. 2004. b. Identification of birds through DNA barcodes. PLoS Biol. 2 (10): e312. 10.1371/journal.pbio.0020312 15455034 (Pubitemid 39532927)
27. Hiesel R. Combettes B. Brennicke A. 1994. Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta. Proc. Natl. Acad. Sci. U.S.A. 91 (2): 629-633. 10.1073/pnas.91.2.629 8290575 (Pubitemid 24041455)
28. Hoch B. Maier R.M. Appel K. Igloi G.L. Kössel H. 1991. Editing of a chloroplast mRNA by creation of an initiation codon. Nature, 353 (6340): 178-180. 10.1038/353178a0 1653905 (Pubitemid 21912485)
29. Hollingsworth P.M. Forrest L.L. Spouge J.L. Hajibabaei M. Ratnasingham S. van der Bank M. CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proc. Natl. Acad. Sci. U.S.A. 106 (31): 12794-12797. 10.1073/pnas.0905845106 19666622
30. Ishii T. Mori N. Ogihara Y. 2001. Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species. Theor. Appl. Genet. 103 (6-7): 896-904. 10.1007/s001220100715 (Pubitemid 33132749)
31. Jobson R.W. Qiu Y.-L. 2008. Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biol. Direct, 3: 43. 10.1186/1745-6150-3-43 18939975
32. Kim K.-J. Lee H.-L. 2004. Complete chloroplast genome sequences from Korean Ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11 (4): 247-261. 10.1093/dnares/11.4.247 15500250 (Pubitemid 40040655)
33. Kim Y.-K. Park C.-W. Kim K.-J. 2009. Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications. Mol. Cells, 27 (3): 365-381. 10.1007/s10059-009-0047-6 19326085
34. Kress W.J. Wurdack K.J. Zimmer E.A. Weigt L.A. Janzen D.H. 2005. Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. U.S.A. 102 (23): 8369-8374. 10.1073/pnas.0503123102 15928076 (Pubitemid 40803501)
35. Kugita M. Yamamoto Y. Fujikawa T. Matsumoto T. Yoshinaga K. 2003. RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res. 31 (9): 2417-2423. 10.1093/nar/gkg327 12711687 (Pubitemid 37442110)
36. Kurtz S. Schleiermacher C. 1999. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics, 15 (5): 426-427. 10.1093/bioinformatics/15.5.426 10366664 (Pubitemid 29312632)
37. Kurtz S. Choudhuri J.V. Ohlebusch E. Schleiermacher C. Stoye J. Giegerich R. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29 (22): 4633-4642. 10.1093/nar/29.22.4633 11713313 (Pubitemid 33095024)
38. Law Y.-W. 1984. A preliminary study on the taxonomy of the family Magnoliaceae. Acta Phytotaxon. Sin. 22 (2): 89-109. [In Chinese.]
39. Li R. Li Y. Kristiansen K. Wang J. 2008. SOAP: short oligonucleotide alignment program. Bioinformatics, 24 (5): 713-714. 10.1093/bioinformatics/ btn025 18227114 (Pubitemid 351321217)
40. Liu, Y.H. (Editor). 2004. Woonyoungia Law. In Magnolias of China. Beijing Science and Technology Press, Beijing. pp. 381-383.
41. Lowe T.M. Eddy S.R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (5): 955-964. 10.1093/nar/25.5.955 9023104 (Pubitemid 27298263)
42. Maier R.M. Neckermann K. Igloi G.L. Kössel H. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251 (5): 614-628. 10.1006/jmbi.1995.0460 7666415
43. Malek O. Lättig K. Hiesel R. Brennicke A. Knoop V. 1996. RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J. 15 (6): 1403-1411. 8635473 (Pubitemid 26093476)
44. Margulies M. Egholm M. Altman W.E. Attiya S. Bader J.S. Bemben L.A. et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437 (7057): 376-380. 16056220 (Pubitemid 41613494)
45. McCauley D.E. 1995. The use of chloroplast DNA polymorphism in studies of gene flow in plants. Trends Ecol. Evol. 10 (5): 198-202. 10.1016/S0169-5347(00) 89052-7 21237002
46. Melotto-Passarin D.M. Berger I.J. Dressano K. De Martin V.F. Oliveira G.C.X. Bock R. et al. 2008. Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region. Crop Breed. Appl. Biotechnol. 8 (1): 85-95. (Pubitemid 351954504)
47. Miyamoto T. Obokata J. Sugiura M. 2002. Recognition of RNA editing sites is directed by unique proteins in chloroplasts: biochemical identification of cis-acting elements and trans-acting factors involved in RNA editing in tobacco and pea chloroplasts. Mol. Cell. Biol. 22 (19): 6726-6734. 10.1128/MCB.22.19. 6726-6734.2002 12215530
48. Mower J.P. Palmer J.D. 2006. Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol. Genet. Genomics, 276 (3): 285-293. 10.1007/s00438-006-0139-3 16862402 (Pubitemid 44268038)
49. Nguni D. Geleta M. Fatih M. Bryngelsson T. 2010. Phylogenetic analysis of the genus Sorghum based on combined sequence data from cpDNA regions and ITS generate well-supported trees with two major lineages. Ann. Bot. (Lond.), 105 (3): 471-480. 10.1093/aob/mcp305 20061309
50. Nooteboom, H.P. 2000. Different looks at the classification of the Magnoliaceae. In Proceedings of the International Symposium on the Family Magnoliaceae, Beijing, 2000. Science Press, Beijing. pp. 26-37.
51. Oldenburg D.J. Bendich A.J. 2004. Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms. J. Mol. Biol. 335 (4): 953-970. 10.1016/j.jmb.2003.11.020 14698291 (Pubitemid 38091603)
52. Petersen G. Seberg O. 1997. Phylogenetic analysis of the Triticeae (Poaceae) based on rpoA sequence data. Mol. Phylogenet. Evol. 7 (2): 217-230. 10.1006/mpev.1996.0389 9126564 (Pubitemid 127345886)
53. Petersen G. Seberg O. Baden C. 2004. A phylogenetic analysis of the genus Psathyrostachys (Poaceae) based on one nuclear gene, three plastid genes, and morphology. Plant Syst. Evol. 249 (1-2): 99-110. 10.1007/s00606-004-0196-1 (Pubitemid 39584245)
54. Powell W. Morgante M. Andre C. McNicol J.W. Machray G.C. Doyle J. et al. 1995. a. Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr. Biol. 5 (9): 1023-1029. 10.1016/S0960-9822(95)00206-5 8542278
55. Powell W. Morgante M. McDevitt R. Vendramin G.G. Rafalski J.A. 1995. b. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc. Natl. Acad. Sci. U.S.A. 92 (17): 7759-7763. 10.1073/pnas.92.17.7759 7644491
56. Presting G.G. 2006. Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Can. J. Bot. 84 (9): 1434-1443. 10.1139/b06-117
57. Provan J. Corbett G. Waugh R. McNicol J.W. Morgante M. Powell W. 1996. DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats. Proc. R. Soc. Lond. B Biol. Sci. 263 (1375): 1275-1281. 10.1098/rspb.1996.0187 8914327 (Pubitemid 26370874)
58. Provan J. Corbett G. Powell W. McNicol J.W. 1997. Chloroplast variabililty in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats. Genome, 40 (1): 104-110. 10.1139/g97-014 9061917 (Pubitemid 28126461)
59. Provan J. Powell W. Hollingsworth P.M. 2001. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol. Evol. 16 (3): 142-147. 10.1016/S0169-5347(00)02097-8 11179578 (Pubitemid 32149938)
60. Pryer K.M. Schneider H. Zimmer E.A. Banks J.A. 2002. Deciding among green plants for whole genome studies. Trends Plant Sci. 7 (12): 550-554. 10.1016/S1360-1385(02)02375-0 12475497 (Pubitemid 36725979)
61. Raubeson L.A. Peery R. Chumley T.W. Dziubek C. Fourcade H.M. Boore J.L. Jansen R.K. 2007. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics, 8: 174. 10.1186/1471-2164-8-174 17573971 (Pubitemid 47090617)
62. Ravi V. Khurana J.P. Tyagi A.K. Khurana P. 2008. An update on chloroplast genomes. Plant Syst. Evol. 271 (1-2): 101-122. 10.1007/s00606-007-0608-0
63. Shaw J. Lickey E.B. Schilling E.E. Small R.L. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 94 (3): 275-288. 10.3732/ajb.94.3.275 (Pubitemid 46955026)
64. Shinozaki K. Ohme M. Tanaka M. Wakasugi T. Hayashida N. Matsubayashi T. et al. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5 (9): 2043-2049. 16453699
65. Shiraishi S. Maeda H. Toda T. Seido K. Sasaki Y. 2001. Incomplete paternal inheritance of chloroplast DNA recognized in Chamaecyparis obtusa using an intraspecific polymorphism of the trnD-trnY intergenic spacer region. Theor. Appl. Genet. 102 (6-7): 935-941. 10.1007/s00122-001-0554-0 (Pubitemid 32532695)
66. Smith D.R. 2009. Unparalleled GC content in the plastid DNA of Selaginella. Plant Mol. Biol. 71 (6): 627-639. 10.1007/s11103-009-9545-3 19774466
67. Solexa, Inc. 2006. Protocol for whole genome sequencing using Solexa technology. BioTechniques Protocol Guide. pp. 29.
68. Sugita M. Sugiura C. Arikawa T. Higuchi M. 2004. Molecular evidence of an rpoA gene in the basal moss chloroplast genomes: rpoA is a useful molecular marker for phylogenetic analysis of mosses. Hikobia. 14 (2): 171-175. [In Japanese.]
69. Sugiura M. 1992. The chloroplast genome. Plant Mol. Biol. 19 (1): 149-168. 10.1007/BF00015612 1600166
70. Tamura K. Dudley J. Nei M. Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (8): 1596-1599. 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
71. Thurston, M.I., and Field, D. 2005. Msatfinder: detection and characterisation of microsatellites. Available from http://www.genomics.ceh.ac. uk/msatfinder/.
72. Tillich M. Lehwark P. Morton B.R. Maier U.G. 2006. The evolution of chloroplast RNA editing. Mol. Biol. Evol. 23 (10): 1912-1921. 10.1093/molbev/msl054 16835291 (Pubitemid 44412877)
73. Timme R.E. Kuehl J.V. Boore J.L. Jansen R.K. 2007. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am. J. Bot. 94 (3): 302-312. 10.3732/ajb.94.3.302 (Pubitemid 46955020)
74. Tsuji S. Ueda K. Nishiyama T. Hasebe M. Yoshikawa S. Konagaya A. et al. 2007. The chloroplast genome from alycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses. J. Plant Res. 120 (2): 281-290. 10.1007/s10265-006-0055-y 17297557 (Pubitemid 46423170)
75. Wyman S.K. Jansen R.K. Boore J.L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20 (17): 3252-3255. 10.1093/bioinformatics/bth352 15180927 (Pubitemid 39619219)
76. Xia N.H. Deng Y.F. 2002. Notes on Magnoliaceae. J. Trop Subtrop Bot. 10 (2): 128-132. [In Chinese.]
77. Xia, N.H., Liu, Y.H., and Nooteboom, H.P. 2009. Magnoliaceae. In Flora of China. Vol. 7. Missouri Botanical Garden Press and Science Press, Beijing. pp. 48.
78. Zimmer E.A. Roalson E.H. Skog L.E. Boggan J.K. Idnurm A. 2002. Phylogenetic relationships in the Gesnerioideae (Gesneriaceae) based on nrDNA ITS and cpDNA trnL-F and trnE-T spacer region sequences. Am. J. Bot. 89 (2): 296-311. 10.3732/ajb.89.2.296 (Pubitemid 34191030)