Complete chloroplast genome sequence of pineapple (Ananas comosus)

Tree Genetics and Genomes

Volumn 11, Issue 3, 2015, Pages 1-11

  Nashima, K ^a   Terakami, S ^a   Nishitani, C ^a   Kunihisa, M ^a   Shoda, M ^b   Takeuchi, M ^b   Urasaki, N ^b   Tarora, K ^b   Yamamoto, T ^a   Katayama, H ^c  

^a NATIONAL INSTITUTE OF FRUIT TREE SCIENCE   (Japan)

^b OKINAWA PREFECTURAL AGRICULTURAL RESEARCH CENTER   (Japan)

^c KOBE UNIVERSITY   (Japan)

Author keywords

Ananas comosus; Chloroplast DNA; Complete sequences; Phylogeny

Indexed keywords

EID: 84958240166     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-015-0892-8     Document Type: Article

References (41)

1. Asano T, Tsudzuki T, Takahashi S, Shimada H, Kadowaki K (2004) Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res 11:93–99
2. Bausher MG, Singh ND, Mozoru J, Lee SB, Jansen RK, Daniell H (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var. ‘Ridge Pineapple’: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol 6:21
3. Bremer K (2000) Early cretaceous lineages of monocot flowering plants. Proc Natl Acad Sci U S A 97:4707–4711
4. Cato SA, Richardson TE (1996) Inter- and intraspecific polymorphism at chloroplast SSR loci and the inheritance of plastids in Pinus radiata D. Don. Theor Appl Genet 93:587–592
5. Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chaw SM (2006) The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol 23:279–291
6. Conant GC, Wolfe KH (2008) GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24:861–862
7. Coppens d’Eeckenbrugge G, Leal F (2002) Morphology, anatomy and taxonomy. In: Bartholomew DP, Paull RE, Rohrbach KG (eds) The pineapple: botany, production and uses. CAB International, Wallingford, pp 13–32
8. Coppens d’Eeckenbrugge G, Leal F, Duval MF (1997) Germplasm resources of pineapple. In: Janick J (ed) Horticultural reviews, vol 21. John Wiley and Sons, Hoboken, pp 133–175
9. Duval MF, Noyer JL, Perrier X, Coppens d’Eeckenbrugge G, Hamon P (2001) Molecular diversity in pineapple assessed by RFLP markers. Theor Appl Genet 102:83–90
10. Duval MF, Buso GS, Ferreira FR, Noyer JL, Coppens d’Eeckenbrugge G, Hamon P, Ferreira ME (2003) Relationships in Ananas and other related genera using chloroplast DNA restriction site variation. Genome 46:990–1004
11. Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin JF (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12:245
12. Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH (2005) Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Biol Evol 22:1813–1822
13. Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK (2010) Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genome evolution in Poaceae. J Mol Evol 70:149–166
14. Hamdan N, Samad AA, Hidyat T, Salleh FM (2013) Phylogenetic analysis of eight Malaysian pineapple cultivars using a chloroplast marker (rcbL gene). J Teknol 64:29–33
15. Hepton A (2002) Culture system. In: Bartholomew DP, Paull RE, Rohrbach KG (eds) The pineapple: botany, production and uses. CAB International, Wallingford, pp 109–142
16. Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY 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. Mol Gen Genet 217:185–194
17. Ishii T, Xu Y, McCouch SR (2001) Nuclear and chloroplast microsatellite variation in a genome species of rice. Genome 44:658–666
18. Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6:32
19. Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, Leebens-Mack J, Muller KF, Guisinger-Bellian M, Haberle RC, Hansen AK et al (2007) 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 104:19369–19374
20. Katayama H, Ogihara Y (1996) Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Curr Genet 29:572–581
21. Kim KJ, Lee HL (2004) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11:247–261
22. Kim JS, Jung JD, Lee JA, Park HW, Oh KH, Jeong WJ, Choi DW, Liu JR, Cho KY (2006) Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome. Plant Cell Rep 25:334–340
23. Leebens-Mack J, Raubeson LA, Cui L, Kuehl J, Fourcade M, Chumley T, Boore JL, Jansen RK, dePamphilis CW (2005) Identifying the basal angiosperms in chloroplast genome phylogenies: sampling one’s way out of the Felsenstein zone. Mol Biol Evol 22:1948–1963
24. Maier RM, Neckermann K, Igloi GL, Kossel 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 251:614–628
25. Malézieux E, Côte F, Bartholomew DP (2002) Crop environment, plant growth and physiology. In: Bartholomew DP, Paull RE, Rohrbach KG (eds) The pineapple: botany, production and uses. CAB International, Wallingford, pp 69–108
26. Martin G, Baurens FC, Cardi C, Aury JM, D’Hont A (2013) The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution. PLoS One 8:e67350
27. Naito K, Kaga A, Tomooka N, Kawase M (2013) De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers. Breed Sci 63:176–182
28. Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N et al (2000) Chinese spring wheat (Triticum aestivum L.) chloroplast genome: complete sequence and contig clones. Plant Mol Biol Rep 18:243–253
29. Paz EY, Gil K, Rebolledo L, Rebolledo A, Uriza D, Martinez O, Isidron M, Simpson J (2005) AFLP characterization of the Mexican pineapple germplasm collection. J Am Soc Hort Sci 130:575–579
30. Paz EY, Gil K, Rebolledo L, Rebolledo A, Uriza D, Martinez O, Isidron M, Diaz L, Lorenzo JC, Simpson J (2012) Genetic diversity of Cuban pineapple germplasm assessed by AFLP markers. Crop Breed Appl Biotech 12:104–110
31. Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA (1995) Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci U S A 92:7759–7763
32. Raubeson LA, Peery R, Chumley T, Dziubek C, Fourcade HM, Boore JL, Jansen RK (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8:174
33. Ravi V, Khurana JP, Tyagi AK, Khurana P (2006) The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genet Genomes 3:49–59
34. Rohrbach KG, Leal F, Coppens d’Eeckenbrugge G (2002) History, distribution and world production. In: Bartholomew DP, Paull RE, Rohrbach KG (eds) The pineapple: botany, production and uses. CAB International, Wallingford, pp 1–12
35. Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell D (2006) Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7:224
36. Schwartz S, Zhang Z, Frazer K, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMaker: a web server for aligning two genomic DNA sequences. Genome Res 10:577–586
37. Stamatakis A (2014) RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
38. Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S (2010) The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res 17:11–22
39. Terakami S, Matsumura Y, Kurita K, Kanamori H, Katayose Y, Yamamoto T, Katayama H (2012) Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis. Tree Genet Genomes 8:841–854
40. West-Eberhard MJ, Smith JA, Winter K (2011) Photosynthesis, reorganized. Science 332:311–312
41. Wyman SK, Boore JL, Jansen RK (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255