Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical oncidium breeding

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Pan, I Chun ^a,b,c   Liao, Der Chih ^b   Wu, Fu Huei ^b   Daniell, Henry ^d   Singh, Nameirakpam Dolendro ^d   Chang, Chen ^e   Shih, Ming Che ^b   Chan, Ming Tsair ^a,b,c   Lin, Choun Sea ^b  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^b AGRICULTURAL BIOTECHNOLOGY RESEARCH CENTER   (Taiwan)

^c Academia Sinica Biotechnology Center in Southern Taiwan   (Taiwan)

^d UNIVERSITY OF CENTRAL FLORIDA   (United States)

^e NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHLOROPLAST; CONTROLLED STUDY; DNA PURIFICATION; ERYCINA PUSILLA; GENE DELETION; GENE SEQUENCE; GENETIC IDENTIFICATION; HYBRIDIZATION; IN VITRO STUDY; LIFE CYCLE; NONHUMAN; NUCLEOTIDE SEQUENCE; ORCHIDACEAE; PHYLOGENY; PLANT BREEDING; TAIWAN; CHLOROPLAST GENOME; DNA SEQUENCE; GENETICS; GENOME SIZE; METHODOLOGY; MOLECULAR GENETICS;

APHRODITA; BACTERIA (MICROORGANISMS); CYMBIDIEAE; EPIDENDROIDEAE; ERYCINA PUSILLA; ONCIDIINAE; ONCIDIUM; ONCIDIUM GOWER RAMSEY; ORCHIDACEAE; RODRIGUEZIA; TOLUMNIA;

BASE SEQUENCE; GENOME SIZE; GENOME, CHLOROPLAST; MOLECULAR SEQUENCE DATA; ORCHIDACEAE; SEQUENCE ANALYSIS, DNA;

EID: 84859367618     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034738     Document Type: Article

References (63)

1. Chase MW, Cameron KM, Barrett RL, Freudenstein JV, (2003) DNA data and Orchidaceae systematics: a new phylogenetic classification. In: Dixon KWKS, Barrett RL, Cribb PJ, editors. Orchid conservation Kota Kinabalu Natural History Publications (Borneo) pp. 69-89.
2. Kerbauy GB, (1984) In vitro flowering of Oncidium varicosum mericlones (Orchidaceae). Plant Sci Lett 35: 73-75.
3. Chen CC, Hsu YM, (2003) Effect of accumulation temperature on the flower quality of Oncidium. J Agric For 52: 33-48 (in Chinese).
4. Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, et al. (2011) Research on orchid biology and biotechnology. Plant Cell Physiol 52: 1467-1486.
5. Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, et al. (2011) OrchidBase: a collection of sequences of the transcriptome derived from orchids. Plant Cell Physiol 52: 238-243.
6. Su C, Chao YT, Chang YCA, Chen WC, Chen CY, et al. (2011) De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. Plant Cell Physiol 52: 1501-1514.
7. Chang YY, Chu YW, Chen CW, Leu WM, Hsu HF, et al. (2011) Characterization of Oncidium 'Gower Ramsey' transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time. Plant Cell Physiol 52: 1532-1545.
8. Chang CC, Lin HC, Lin I, Chow TY, Chen HH, et al. (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.
9. Wu FH, Chan MT, Liao DC, Hsu CT, Lee YW, 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: 68-80.
10. Hsu CT, Liao DC, Wu FH, Liu NT, Shen SC, et al. (2011) Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey. BMC Plant Biol 11: 60-74.
11. Liau CH, You SJ, Prasad V, Hsiao HH, Lu JC, et al. (2003) Agrobacterium tumefaciens-mediated transformation of an Oncidium orchid. Plant Cell Rep 21: 993-998.
12. Sanjaya, Chan MT, (2007) Genetic transformation as a tool for improvement of orchids. In: Chen WH, Chen HH, editors. Orchid Biotechnology World Scientific pp. 225-253.
13. You SJ, Liau CH, Huang HE, Feng TY, Prasad V, et al. (2003) Sweet pepper ferredoxin-like protein (pflp) gene as a novel selection marker for orchid transformation. Planta 217: 60-65.
14. Liao LJ, Pan IC, Chan YL, Hsu YH, Chen WH, et al. (2004) Transgene silencing in Phalaenopsis expressing the coat protein of Cymbidium Mosaic Virus is a manifestation of RNA-mediated resistance. Mol Breeding 13: 229-242.
15. Chase MW, (1986) A reappraisal of the oncidioid orchids. Syst Bot 11: 477-491.
16. Pellegrino G, Bellusci F, Musacchio A, (2009) Genetic integrity of sympatric hybridising plant species: the case of Orchis italica and O. anthropophora. Plant Biol 11: 434-441.
17. Pinheiro F, De Barros F, Palma-Silva C, Meyer D, Fay MF, et al. (2010) Hybridization and introgression across different ploidy levels in the neotropical orchids Epidendrum fulgens and E. puniceoluteum (Orchidaceae). Mol Ecol 19: 3981-3994.
18. Russell A, Samuel R, Klejna V, Barfuss MHJ, Rupp B, et al. (2010) Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Ann Bot 106: 37-56.
19. Thiruvengadam M, Yang CH, (2009) Ectopic expression of two MADS box genes from orchid (Oncidium Gower Ramsey) and lily (Lilium longiflorum) alters flower transition and formation in Eustoma grandiflorum. Plant Cell Rep 28: 1463-1473.
20. Hsu HF, Yang CH, (2002) An orchid (Oncidium Gower Ramsey) AP3-like MADS gene regulates floral formation and initiation. Plant Cell Physiol 43: 1198.
21. Chiou CY, Yeh KW, (2008) Differential expression of MYB gene (OgMYB1) determines color patterning in floral tissue of Oncidium Gower Ramsey. Plant Mol Biol 66: 379-388.
22. Felix PL, Guerra M, (1999) Chromosome analysis in Psygmorchis pusilla (L.) Dodson & Dressler: the smallest chromosome number known in Orchidaceae. Carylogia 52: 165-168.
23. Chase MW, Hanson L, Albert VA, Whitten W, Williams NH, (2005) Life history evolution and genome size in subtribe Oncidiinae (Orchidaceae). Ann Bot 95: 191-199.
24. Damon A, Salas-Roblero P, (2007) A survey of pollination in remnant orchid populations in Soconusco, Chiapas, Mexico. Trop Ecol 48: 1-14.
25. Chen YC, Chang C, Chang W, (2000) A reliable protocol for plant regeneration from callus culture of Phalaenopsis. In Vitro Cell Dev-Pl 36: 420-423.
26. Chiu YT, Lin CS, Chang C, (2011) In vitro fruiting and seed production in Erycina Pusilla (L.) N. H. Williams and M. W. Chase. Propag Ornam Plants 11: 131-136.
27. Lin CS, Chiu YT, Chang C, (2011) Intergeneric cross between Erycina pusilla and Oncidiinae species and cultuivars. Seed Nursery 13: 31-39 (in Chinese).
28. Tien X, Li DZ, (2002) Application of DNA sequences in plant phylogenetic study. Acta Bot Yunnan 24: 170-184.
29. Cameron KM, Carmen Molina M, (2006) Photosystem II gene sequences of psbB and psbC clarify the phylogenetic position of Vanilla (Vanilloideae, Orchidaceae). Cladistics 22: 239-248.
30. Cameron KM, (2004) Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae. Mol Phylogenet Evol 31: 1157-1180.
31. Daniell H, Wurdack KJ, Kanagaraj A, Lee SB, Saski C, et al. (2008) The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron. Theor Appl Genet 116: 723-737.
32. Jansen RK, Wojciechowski MF, Sanniyasi E, Lee SB, Daniell H, (2008) Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Mol Phylogenet Evol 48: 1204-1217.
33. Verma D, Daniell H, (2007) Chloroplast vector systems for biotechnology applications. Plant Physiol 145: 1129-1143.
34. Daniell H, Kumar S, Dufourmantel N, (2005) Breakthrough in chloroplast genetic engineering of agronomically important crops. Trends Biotechnol 23: 238-245.
35. Zhang Y, Zhang X, Scheuring CF, Zhang HB, Huan P, et al. (2008) Construction and characterization of two bacterial artificial chromosome libraries of Zhikong scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system. Mar Biotechnol 10: 358-365.
36. Wyman SK, Jansen RK, Boore JL, (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255.
37. Sheu JJ, Yu TS, Tong WF, Yu SM, (1996) Carbohydrate starvation stimulates differential expression of rice α-amylase genes that is modulated through complicated transcriptional and posttranscriptional processes. J Biol Chem 271: 26998-27004.
38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
39. Kumar S, Tamura K, Nei M, (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5: 150-163.
40. Nock CJ, Waters DLE, Edwards MA, Bowen SG, Rice N, et al. (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol J 9: 328-333.
41. Bausher MG, Singh ND, 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.
42. Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H, (2007) The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms. Plant Biotechnol J 5: 339-353.
43. Mach JM, Castillo AR, Hoogstraten R, Greenberg JT, (2001) The Arabidopsis-accelerated cell death gene ACD2 encodes red chlorophyll catabolite reductase and suppresses the spread of disease symptoms. Proc Natl Acad Sci U S A 98: 771-776.
44. Stern DB, Palmer JD, (1984) Extensive and widespread homologies between mitochondrial DNA and chloroplast DNA in plants. Proc Natl Acad Sci U S A 81: 1946-1950.
45. Nakazono M, Hira A, (1993) Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice. Mol Gen Genet 236: 341-346.
46. Ayliffe M, Timmis J, (1992) Tobacco nuclear DNA contains long tracts of homology to chloroplast DNA. Theor Appl Genet 85: 229-238.
47. Timmis JN, Ayliffe MA, Huang CY, Martin W, (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5: 123-135.
48. Stern DB, Lonsdale DM, (1982) Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common. Nature 299: 698.
49. Hirai A, Nakazono M, (1993) Six percent of the mitochondrial genome in rice came from chloroplast DNA. Plant Mol Biol Rep 11: 98-100.
50. Goremykin VV, Salamini F, Velasco R, Viola R, (2009) Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol 26: 99-110.
51. Wu FH, Kan DP, Lee SB, Daniell H, Lee YW, et al. (2009) Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree Physiol 29: 847-856.
52. Zhang YJ, Ma PF, Li DZ, (2011) High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PloS One 6: e20596.
53. Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, et al. (2005) Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol Biol 59: 309-322.
54. Martin M, Sabater B, (2010) Plastid ndh genes in plant evolution. Plant Physiol Biochem 48: 636-645.
55. Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, et al. (1994) Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci U S A 91: 9794-9799.
56. Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM, (2009) Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol 52: 115-124.
57. McCoy S, Kuehl J, Boore J, Raubeson L, (2008) The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol 8: 130-146.
58. Chris BJ, Guisinger MM, Jansen RK, (2011) Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae). Plant Mol Biol pp. 1-10.
59. Scarcelli N, Barnaud A, Eiserhardt W, Treier UA, Seveno M, et al. (2011) A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons. PloS One 6: e19954.
60. Chase MW, Williams NH, De Faria AD, Neubig KM, Amaral MCE, et al. (2009) Floral convergence in Oncidiinae (Cymbidieae; Orchidaceae): an expanded concept of Gomesa and a new genus Nohawilliamsia. Ann Bot 104: 387-402.
61. Neubig KM, Whitten WM, Carlsward BS, Blanco MA, Endara L, et al. (2009) Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK. Plant Syst Evol 277: 75-84.
62. Dodson C, Dressler R, (1972) Two undescribed genera in the Orchidaceae-Oncidiinae. Phytologia 24: 285-292.
63. Williams N, Chase M, Fulcher T, Whitten W, (2001) Molecular systematics of the Oncidiinae based on evidence from four DNA sequence regions: expanded circumscriptions of Cyrtochilum, Erycina, Otoglossum, and Trichocentrum and a new genus (Orchidaceae). Lindleyana 16: 113-139.