The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Martin, Guillaume ^a   Baurens, Franc Christophe ^a   Cardi, Céline ^a   D'Hont, Angélique ^a   Aury, Jean Marc ^b  

^a UMR AGAP   (France)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; ARTICLE; BANANA; CHLOROPLAST GENOME; CONTROLLED STUDY; DNA TRANSFER; EVOLUTION; GENE SEQUENCE; INVERTED REPEAT; MONOCOT; NDHA GENE; NDHH GENE; NONHUMAN; PHYLOGENY; PLANT GENE; PLASTID; RPS15 GENE; SIMPLE SEQUENCE REPEAT; YCF1 GENE;

ALLELES; CODON; EVOLUTION, MOLECULAR; GENES, PLANT; GENETIC MARKERS; GENOME, CHLOROPLAST; LIKELIHOOD FUNCTIONS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; MUSA; PHYLOGENY; PLASTIDS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; TRIPLOIDY;

LILIOPSIDA; MAGNOLIOPHYTA; MUSA; MUSA ACUMINATA; POALES; ZINGIBERALES;

EID: 84879525964     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067350     Document Type: Article

References (63)

1. Bendich AJ, (2004) Circular Chloroplast Chromosomes: The Grand Illusion. The Plant Cell Online 16: 1661-1666 doi:10.1105/tpc.160771.
2. Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, et al. (2006) The Complete Chloroplast Genome Sequence of Pelargonium × hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants. Molecular Biology and Evolution 23: 2175-2190 doi:10.1093/molbev/msl089.
3. Palmer JD (1991) Plastid chromosomes: structure and evolution. In: Bogorad L, Vasil I, editors. Cell Culture and Somatic Cell Genetics of Plants. San Diego: Academic Press. 5-53.
4. Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants. In: Henry RJ, editor. Plant diversity and evolution: genotypic and phenotypic variation in higher plants. Cambridge: CAB International. 45-68.
5. Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, et al. (2001) Many Parallel Losses of infA from Chloroplast DNA during Angiosperm Evolution with Multiple Independent Transfers to the Nucleus. The Plant Cell Online 13: 645-658 doi:10.1105/tpc.13.3.645.
6. Guisinger M, Chumley T, Kuehl J, Boore J, Jansen R, (2010) Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae. J Mol Evol 70: 149-166 doi:10.1007/s00239-009-9317-3.
7. Downie SR, Palmer JD (1992) Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In: Soltis PS, Soltis DE, Doyle JJ, editors. Molecular systematics of plants. New York: Chapman and Hall. 14-35.
8. Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences 104: 19369-19374 doi:10.1073/pnas.0709121104.
9. Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, et al. (2010) Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1. Annals of the Missouri Botanical Garden 97: 584-616 doi:10.3417/2010023.
10. Logacheva MD, Penin AA, Samigullin TH, Vallejo-Roman CM, Antonov AS, (2007) Phylogeny of flowering plants by the chloroplast genome sequences: in search of a "lucky gene.". Biochemistry Moscow 72: 1324-1330 doi:10.1134/S0006297907120061.
11. D'Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488: 213-217 doi:10.1038/nature11241.
12. Fauré S, Noyer J-L, Carreel F, Horry J-P, Bakry F, et al. (1994) Maternal inheritance of chloroplast genome and paternal inheritance of mitochondrial genome in bananas (Musa acuminata). Curr Genet 25: 265-269 doi:10.1007/BF00357172.
13. Simmonds NW (1962) The evolution of the bananas. London: Longmans.
14. De Langhe E, Hřibová E, Carpentier S, Doležel J, Swennen R, (2010) Did backcrossing contribute to the origin of hybrid edible bananas? Annals of Botany 106: 849-857 doi:10.1093/aob/mcq187.
15. Perrier X, De Langhe E, Donohue M, Lentfer C, Vrydaghs L, et al. (2011) Multidisciplinary perspectives on banana (Musa spp.) domestication. Proceedings of the National Academy of Sciences 108: 11311-11318 doi:10.1073/pnas.1102001108.
16. Carreel F, de Leon DG, Lagoda P, Lanaud C, Jenny C, et al. (2002) Ascertaining maternal and paternal lineage within Musa by chloroplast and mitochondrial DNA RFLP analyses. Genome 45: 679-692.
17. Boonruangrod R, Desai D, Fluch S, Berenyi M, Burg K, (2008) Identification of cytoplasmic ancestor gene-pools of Musa acuminata Colla and Musa balbisiana Colla and their hybrids by chloroplast and mitochondrial haplotyping. Theor Appl Genet 118: 43-55 doi:10.1007/s00122-008-0875-3.
18. Lescot T, (2011) The genetic diversity of the banana in figures. FruiTrop 189: 58-62.
19. Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, et al. (2009) Circos: An information aesthetic for comparative genomics. Genome Research 19: 1639-1645 doi:10.1101/gr.092759.109.
20. Wyman SK, Jansen RK, Boore JL, (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255 doi:10.1093/bioinformatics/bth352.
21. Yang M, Zhang X, Liu G, Yin Y, Chen K, et al. (2010) The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.). PLoS ONE 5: e12762 doi:10.1371/journal.pone.0012762.
22. Uthaipaisanwong P, Chanprasert J, Shearman JR, Sangsrakru D, Yoocha T, et al. (2012) Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.). Gene 500: 172-180 doi:10.1016/j.gene.2012.03.061.
23. Lowe TM, Eddy SR, (1997) tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 0955-0964 doi:10.1093/nar/25.5.0955.
24. Charif D, Lobry J (2007) SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis. In: Bastolla U, Porto M, Roman HE, Vendruscolo M, editors. Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer Berlin Heidelberg. 207-232. Available: http://dx.doi.org/10.1007/978-3-540-35306-5_10.
25. The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641 doi:10.1038/nature11119.
26. Katoh K, Misawa K, Kuma K, Miyata T, (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066 doi:10.1093/nar/gkf436.
27. Posada D, (2008) jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256 doi:10.1093/molbev/msn083.
28. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, et al. (2010) New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology 59: 307-321 doi:10.1093/sysbio/syq010.
29. Goremykin VV, Hirsch-Ernst KI, Wölfl S, Hellwig FH, (2003) Analysis of the Amborella trichopoda Chloroplast Genome Sequence Suggests That Amborella Is Not a Basal Angiosperm. Molecular Biology and Evolution 20: 1499-1505 doi:10.1093/molbev/msg159.
30. Thiel T, Michalek W, Varshney R, 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 doi:10.1007/s00122-002-1031-0.
31. Krumsiek J, Arnold R, Rattei T, (2007) Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23: 1026-1028 doi:10.1093/bioinformatics/btm039.
32. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S, editors. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Totowa: Humana Press. 365-386.
33. Clegg MT, Gaut BS, Learn GH, Morton BR, (1994) Rates and patterns of chloroplast DNA evolution. Proceedings of the National Academy of Sciences 91: 6795-6801.
34. Palmer JD, (1983) Chloroplast DNA exists in two orientations. Nature 301: 92-93 doi:10.1038/301092a0.
35. Oldenburg DJ, Bendich AJ, (2004) Most Chloroplast DNA of Maize Seedlings in Linear Molecules with Defined Ends and Branched Forms. Journal of Molecular Biology 335: 953-970 doi:10.1016/j.jmb.2003.11.020.
36. Shahmuradov I, Akbarova Y, Solovyev V, Aliyev J, (2003) Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Plant Mol Biol 52: 923-934 doi:10.1023/A:1025472709537.
37. Cullis CA, Vorster BJ, Van Der Vyver C, Kunert KJ, (2009) Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants? Annals of Botany 103: 625-633 doi:10.1093/aob/mcn173.
38. Matsuo M, Ito Y, Yamauchi R, Obokata J, (2005) The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast-Nuclear DNA Flux. The Plant Cell Online 17: 665-675 doi:10.1105/tpc.104.027706.
39. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, et al. (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43: 109-116 doi:10.1038/ng.740.
40. Degnan JH, Rosenberg NA, (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution 24: 332-340 doi:10.1016/j.tree.2009.01.009.
41. Hendy MD, Penny D, (1989) A Framework for the Quantitative Study of Evolutionary Trees. Systematic Biology 38: 297-309 doi:10.2307/2992396.
42. Bergsten J, (2005) A review of long-branch attraction. Cladistics 21: 163-193 doi:10.1111/j.1096-0031.2005.00059.x.
43. Renoult J, Kjellberg F, Grout C, Santoni S, Khadari B, (2009) Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associations. BMC Evolutionary Biology 9: 248.
44. Mardanov A, Ravin N, Kuznetsov B, Samigullin T, Antonov A, et al. (2008) Complete Sequence of the Duckweed (Lemna minor) Chloroplast Genome: Structural Organization and Phylogenetic Relationships to Other Angiosperms. J Mol Evol 66: 555-564 doi:10.1007/s00239-008-9091-7.
45. Morris LM, Duvall MR, (2010) The chloroplast genome of Anomochloa marantoidea (Anomochlooideae; Poaceae) comprises a mixture of grass-like and unique features. American Journal of Botany 97: 620-627 doi:10.3732/ajb.0900226.
46. Chang C-C, Lin H-C, Lin I-P, Chow T-Y, Chen H-H, et al. (2006) The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with that of Grasses and Its Phylogenetic Implications. Molecular Biology and Evolution 23: 279-291 doi:10.1093/molbev/msj029.
47. Wu F-H, Chan M-T, Liao D-C, Hsu C-T, Lee Y-W, et al. (2010) Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biol 10: 1-12 doi:10.1186/1471-2229-10-68.
48. Jheng C-F, Chen T-C, Lin J-Y, Chen T-C, Wu W-L, et al. (2012) The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. Plant Science 190: 62-73 doi:10.1016/j.plantsci.2012.04.001.
49. Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, et al. (2007) Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Molecular Phylogenetics and Evolution 45: 547-563 doi:10.1016/j.ympev.2007.06.004.
50. Doyle JJ, Davis JI, Soreng RJ, Garvin D, Anderson MJ, (1992) Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proceedings of the National Academy of Sciences 89: 7722-7726 doi:10.1073/pnas.89.16.7722.
51. Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, et al. (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Molec Gen Genet 217: 185-194 doi:10.1007/BF02464880.
52. Howe C, Barker R, Bowman C, Dyer T, (1988) Common features of three inversions in wheat chloroplast DNA. Curr Genet 13: 343-349 doi:10.1007/BF00424430.
53. Katayama H, Ogihara Y, (1993) Structural alterations of the chloroplast genome found in grasses are not common in monocots. Curr Genet 23: 160-165 doi:10.1007/BF00352016.
54. Wang R-J, Cheng C-L, Chang C-C, Wu C-L, Su T-M, et al. (2008) Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol 8: 1-14 doi:10.1186/1471-2148-8-36.
55. Terrab A, Paun O, Talavera S, Tremetsberger K, Arista M, et al. (2006) Genetic diversity and population structure in natural populations of Moroccan Atlas cedar (Cedrus atlantica; Pinaceae) determined with cpSSR markers. American Journal of Botany 93: 1274-1280 doi:10.3732/ajb.93.9.1274.
56. Grassi F, Labra M, Scienza A, Imazio S (2002) Chloroplast SSR markers to assess DNA diversity in wild and cultivated grapevines. Vitis.
57. Melotto-Passarin D, Tambarussi E, Dressano K, De Martin V, Carrer H, (2011) Characterization of chloroplast DNA microsatellites from Saccharum spp and related species. Genet Mol Res 10: 2024-2033.
58. 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 Research 11: 247-261 doi:10.1093/dnares/11.4.247.
59. Kim J-S, Jung J, Lee J-A, Park H-W, Oh K-H, et al. (2006) Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome. Plant Cell Rep 25: 334-340 doi:10.1007/s00299-005-0097-y.
60. Kuang D-Y, Wu H, Wang Y-L, Gao L-M, Zhang S-Z, et al. (2011) Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome 54: 663-673.
61. Kim Y-K, Park C, Kim K-J, (2009) Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications. Mol Cells 27: 365-381 doi:10.1007/s10059-009-0047-6.
62. Yi D-K, Kim K-J, (2012) Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L. PLoS ONE. 7: e35872 doi:10.1371/journal.pone.0035872.
63. Raboin LM, Carreel F, Noyer J-L, Baurens F-C, Horry JP, et al. (2005) Diploid ancestors of triploid export banana cultivars: molecular identification of 2n restitution gamete donors and n gamete donors. Molecular Breeding 16: 333-341.