Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Curci, Pasquale L ^a   De Paola, Domenico ^a   Danzi, Donatella ^a   Vendramin, Giovanni G ^b   Sonnante, Gabriella ^a  

^a Institute of Biosciences and Bioresources   (Italy)

^b Institute of Biosciences and BioResources   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AGERATINA ADENOPHORA; ARTEMISIA FRIGIDA; ARTICHOKE; ARTICLE; ASTERACEAE; BACTERIAL ARTIFICIAL CHROMOSOME; CHLOROPLAST GENOME; CHRYSANTHEMUM MORIFOLIUM; CONTROLLED STUDY; DNA BARCODING; DNA CONTENT; GENE LOCATION; GENUS; GUIZOTIA ABYSSINICA; HELIANTHUS ANNUUS; HIGH THROUGHPUT SEQUENCING; INVERTED REPEAT; JACOBAEA VULGARIS; LETTUCE; NDHF GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PARTHENIUM ARGENTATUM; PHYLOGENY; PLANT GENE; PSEUDOGENE; SEQUENCE ANALYSIS; SIMPLE SEQUENCE REPEAT; SPECIES COMPARISON; YCF1 GENE; BIOLOGY; CLASSIFICATION; EXON; GENE ORDER; GENE STRUCTURE; GENETICS; GENOMICS; INTRON; MOLECULAR EVOLUTION; MOLECULAR GENETICS;

ASTERACEAE; CYNARA; CYNARA SCOLYMUS;

ASTERACEAE; COMPUTATIONAL BIOLOGY; CYNARA SCOLYMUS; DNA BARCODING, TAXONOMIC; EVOLUTION, MOLECULAR; EXONS; GENE ORDER; GENES, PLANT; GENETIC STRUCTURES; GENOME, CHLOROPLAST; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTRONS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 84925002917     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0120589     Document Type: Article

References (67)

1. Bremer K. Asteraceae: cladistics and classification. Portland, Oregon, USA: Timber Press; 1994.
2. Rottenberg A, Zohary D. The wild ancestry of the cultivated artichoke. Genet Resour Crop Evol. 1996;43:53-58.
3. Sonnante G, Pignone D, Hammer K. The domestication of artichoke and cardoon: from Roman times to the genomic age. Ann Bot. 2007;100:1095-1100. PMID: 17611191
4. Gebhardt R. Antioxidative and protective properties of extracts from leaves of the artichoke (Cynara scolymus L.) against hydroperoxide-induced oxidative stress in cultured rat hepatocytes. Toxicol Appl Pharmacol. 1997;144:279-286. PMID: 9194411
5. Sonnante G, D'Amore R, Blanco E, Pierri CL, De Palma M, Luo J, et al. Novel hydroxycinnamoyl-CoenzymeAquinate transferase genes from artichoke are involved in the synthesis of chlorogenic acid. Plant Physiol. 2010;153:1-15.
6. Negro D, Montesano V, Grieco S, Crupi P, Sarli G, De Lisi A, et al. Polyphenol compounds in artichoke plant tissues and varieties. J Food Sci. 2012;77:C244-252. doi: 10.1111/j.1750-3841.2011.02531.x PMID: 22251096
7. Kraft K. Artichoke leaf extract: recent findings reflecting effects on lipid metabolism, liver and gastrointestinal tracts. Phytomedicine 1997;4:369-378. doi: 10.1016/S0944-7113 (97) 80049-9 PMID: 23195590
8. Gatto A, De Paola D, De Bagnoli F, Vendramin GG, Sonnante G. Population structure of Cynara cardunculus complex and the origin of the conspecific crops artichoke and cardoon. Ann Bot. 2013;112:855-865. doi: 10.1093/aob/mct150 PMID: 23877076
9. Calabrese N, Carito A, Boari F, Cantore V, De Palma E, Damato G. Agronomical evaluation of artichoke cultivar propagated by seed. Acta Hortic. 2011;942:153-158.
10. Panero JL, Funk VA. The value of sampling anomalous taxa in phylogenetic studies: Major clades of the Asteraceae revealed. Mol Phylogenet Evol. 2008;47:757-782. doi: 10.1016/j.ympev. 2008.02.011 PMID: 18375151
11. Barres L, Sanmartín I, Anderson CL, Susanna A, Buerki S, Galbany-Casals M, et al. Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae). Am J Bot. 2013;100:867-882. doi: 10.3732/ajb.1200058 PMID: 23624927
12. Dyall SD, Brown MT, Johnson PJ. Ancient invasions: from endosymbionts to organelles. Science 2004;304:253-257. PMID: 15073369
13. Odintsova MS, Yurina NP. Chloroplast genomics of land plants and algae. In: Giardi MT, Piletska EV, editors. Biotechnological applications of photosynthetic proteins: biochips, biosensors and biodevices. Georgetown, TX, USA: Landes Bioscience/Eurekah; 2006.
14. Olmstead RG, Palmer JD. Chloroplast DNA systematic: a review of methods and data analysis. Am J Bot. 1994;81:1205-1224.
15. Jansen RK, Raubeson LA, Boore JL, De Pamphilis CW, Chumley TW, Haberle RC, et al. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol. 2005;395:348-384. PMID: 15865976
16. Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA. 1987;84:9054-9058. PMID: 3480529
17. Provan J, Powell W, Hollingsworth PM. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol. 2001;16:142-147. PMID: 11179578
18. Ravi V, Khurana JP, Tyagi AK, Khurana P. An update on chloroplast genome. Plant Syst Evol. 2008;271:101-122.
19. Ahmed I, Matthews PJ, Biggs PJ, Naeem M, McLenachan PA, Lockhart PJ. Identification of chloroplast genome loci suitable for high resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa. Mol Ecol Resour. 2013;13:929-937. doi: 10.1111/1755-0998. 12128 PMID: 23718317
20. Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. Plant DNA barcoding: from gene to genome. Biol Rev. 2015;90:157-166. doi: 10.1111/brv. 12104 PMID: 24666563
21. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986;5:2043-2049. PMID: 16453699
22. Sonnante G, De Paolis A, Lattanzio V, Perrino P. Genetic variation in wild and cultivated artichoke revealed by RAPD markers. Genet Resour Crop Evol. 2002;49:247-252.
23. Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004;20:3252-3255. PMID: 15180927
24. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955-964. PMID: 9023104
25. Umashankar V, Arunkumar V, Dorairaj S. ACUA: A software tool for automated codon usage analysis. Bioinformation. 2007;2:62-63. PMID: 18188422
26. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-580. PMID: 9862982
27. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R, et al. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001;29:4633-4642. PMID: 11713313
28. Mudunuri SB, Nagarajaram HA. IMEx: imperfect microsatellite extractor. Bioinformatics. 2007;23:1181-7. PMID: 17379689
29. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32:W273-W279. PMID: 15215394
30. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013;30:2725-2729. doi: 10.1093/molbev/mst197 PMID: 24132122
31. ∗and other methods), Version 4. Sunderland, MA: Sinauer Associates; 2003.
32. Untergrasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012;40:e115. PMID: 22730293
33. Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, et al. Fast statistical alignment. PLoS Comput Biol. 2009;5:e1000392. doi: 10.1371/journal.pcbi.1000392 PMID: 19478997
34. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993;10:512-526. PMID: 8336541
35. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008;57:758-771. doi: 10.1080/10635150802429642 PMID: 18853362
36. Yi D, Kim K. Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS ONE. 2012;7:e35872. doi: 10.1371/journal.pone.0035872 PMID: 22606240
37. Yang JB, Yang SX, Li HT, Yang J, Li DZ. Comparative chloroplast genomes of Camellia species. PLoS ONE. 2013;8:e73053. doi: 10.1371/journal.pone.0073053 PMID: 24009730
38. Palmer JD, Thompson WF. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell. 1982;29:537-550. PMID: 6288261
39. Sasaki T, Yukawa Y, Miyamoto T, Obokata J, Sugiura M. Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing. Mol Biol Evol. 2003;20:1028-1035. PMID: 12716996
40. Rohde W, Gramstat A, Schmitz J, Tacke E, Prûfer D. Plant viruses as model systems for the study of non-canonical translation mechanisms in higher plants. J Gen Virol. 1994;75:2141-2149. PMID: 8077913
41. Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, et al. The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res. 2010;17:1-22. doi: 10. 1093/dnares/dsp024 PMID: 19934175
42. Qian J, Song J, Gao H, Zhu Y, Xu J, Pang X, et al. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS ONE. 2013;8:e57607. doi: 10.1371/journal.pone.0057607 PMID: 23460883
43. Ogihara Y, Terachi T, Sasakuma T. Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Natl Acad Sci USA. 1988;85:8573-8577. PMID: 3186748
44. Milligan BG, Hampton JN, Palmer JD. Dispersed repeats and structural reorganization in subclover chloroplast DNA. Mol Biol Evol. 1989;6:355-368. PMID: 2615639
45. Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'ridge pineapple': organization and phylogenetic relationships to other angiosperms. BMC Plant Biol. 2006;6:21. PMID: 17010212
46. Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, et al. 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. 2006;6:32. PMID: 16603088
47. Li R, Ma PF, Wen J, Yi TS. Complete Sequencing of Five Araliaceae Chloroplast Genomes and the Phylogenetic Implications. PLoS ONE. 2013;8:e78568. doi: 10.1371/journal.pone.0078568 PMID: 24205264
48. Grassi F, Labra M, Scienza A, Imazio S. Chloroplast SSR markers to assess DNA diversity in wild and cultivated grapevines. Vitis. 2002;41:157-158.
49. Timme RE, Kuehl JV, Boore JL, Jansen RK. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot. 2007;94:302-312. doi: 10.3732/ajb.94.3.302 PMID: 21636403
50. Melotto-Passarin D, Tambarussi E, Dressano K, De Martin V, Carrer H. Characterization of chloroplast DNA microsatellites from Saccharum spp and related species. Genet Mol Res. 2011;10:2024-2033. doi: 10.4238/vol10-3gmr1019 PMID: 21948764
51. Kumar S, Hahn FM, McMahan CM, Cornish K, Whalen MC. Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines. BMC Plant Biol. 2009;9:131. doi: 10.1186/1471-2229-9-131 PMID: 19917140
52. Nie X, Lv S, Zhang Y, Du X, Wang L, Biradar SS et al. Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLoS ONE. 2012;7:e36869. doi: 10. 1371/journal.pone.0036869 PMID: 22606302
53. Martin G, Baurens FC, Cardi C, Aury JM, D'Hont A. The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution. PLoS ONE. 2013;8:e67350. doi: 10.1371/journal.pone.0067350 PMID: 23840670
54. Dempewolf H, Kane NC, Ostevik KL, Geleta M, Barker MS, Lai Z, et al. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol Ecol Resour. 2010;10:1048-1058. doi: 10.1111/j.1755-0998.2010.02859.x PMID: 21565115
55. Dong W, Liu J, Yu J, Wang L, Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE. 2012;7(4):e35071. doi: 10.1371/journal.pone.0035071 PMID: 22511980
56. Martin GE, Rousseau-Gueutin M, Cordonnier S, Lima O, Michon-Coudouel S, Naquin D, et al. The first complete chloroplast genome of the genistoid legume Lupinus Luteus: evidence for a novel major lineagespecific rearrangement and new insights regarding plastome evolution in the legume family. Ann Bot. 2014;113:1197-1210. doi: 10.1093/aob/mcu050 PMID: 24769537
57. Liu Y, Huo N, Dong L, Wang Y, Zhang S, Young HA, et al. Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants. PLoS ONE. 2013;8:e57533. doi: 10.1371/journal.pone.0057533 PMID: 23460871
58. Chung HJ, Jong DJ, Park HW. The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. Plant Cell Rep. 2006;25:1369-1379. PMID: 16835751
59. Wolf PG, Roper JM, Duffy AM. The evolution of chloroplast genome structure in ferns. Genome. 2010;53:731-738. doi: 10.1139/g10-061 PMID: 20924422
60. Doorduin L, Gravendeel B, Lammers Y, Ariyurek Y, Chin-A-Woeng T, Vrieling K. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res. 2011;18:93-105. doi: 10.1093/dnares/dsr002 PMID: 21444340
61. Drescher A, Ruf S, Calsa TJ, Carrer H, Bock R. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J. 2000;22:97-104. PMID: 10792825
62. Kuroda H, Maliga P. The plastid clpP1 protease gene is essential for plant development. Nature. 2003;425:86-89. PMID: 12955146
63. Kode V, Mudd EA, Iamtham S, Day A. The tobacco plastid accD gene is essential and is required for leaf development. Plant J. 2005;44:237-244. PMID: 16212603
64. Ueda M, Nishikawa T, Fujimoto M, Takanashi H, Arimura S, Tsutsumi N, et al. Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal. Mol Biol Evol. 2008;25:1566-1575. doi: 10.1093/molbev/msn102 PMID: 18453549
65. Martínez-Alberola F, Del Campo EM, Lázaro-Gimeno D, Mezquita-Claramonte S, Molins A, Mateu-Andrés I, et al. Balanced gene losses, duplications and intensive rearrangements led to an unusual regularly sized genome in Arbutus unedo chloroplasts. PLoS ONE. 2013;8:e79685. doi: 10.1371/journal. pone.0079685 PMID: 24260278
66. Kress WJ, Erickson DL. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE. 2007;2:e508. PMID: 17551588
67. Ortiz S, Bonifacino JM, Crisci JV, Funk VA, Hansen HV, Hind DJN, et al. The basal grade of the Compositae: Mutisieae (sensu Cabrera) and Carduoideae. In: Funk VA, Susanna A, Stuessy TF, Bayer RJ, editors. Systematics, evolution, and biogeography of Compositae. Vienna, Austria: International Association for Plant Taxonomy; 2009. pp. 193-213.