Complete chloroplast genome sequence of omani lime (Citrus aurantiifolia) and comparative analysis within the rosids

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Su, Huei Jiun ^a   Hogenhout, Saskia A ^b   Al Sadi, Abdullah M ^c   Kuo, Chih Horng ^d,e  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b JOHN INNES CENTRE   (United Kingdom)

^c SULTAN QABOOS UNIVERSITY   (Oman)

^d INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

^e NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHLOROPLAST GENOME; CODON USAGE; COMPARATIVE STUDY; CONTROLLED STUDY; GENE LOSS; GENE SEQUENCE; GENETIC DIFFERENCE; GENETIC MARKER; INTERSPECIFIC RELATIONSHIP; LIME (FRUIT); NONHUMAN; NUCLEOTIDE SEQUENCE; ORF56 GENE; PHYLOGENETIC TREE; PLANT GENE; PLANT LEAF; SIMPLE SEQUENCE REPEAT; START CODON; STOP CODON; SWEET ORANGE; VITIS; VITIS VENIFERA; YCF68 GENE; ANGIOSPERM; CITRUS; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; PHYLOGENY; STATISTICAL MODEL;

CITRUS AURANTIIFOLIA; ROSIDS;

MICROSATELLITE DNA; VEGETABLE PROTEIN;

ANGIOSPERMS; BASE SEQUENCE; CITRUS; COMPARATIVE GENOMIC HYBRIDIZATION; GENOME, CHLOROPLAST; LIKELIHOOD FUNCTIONS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 84911886333     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113049     Document Type: Article

References (62)

1. Mabberley DJ (2004) Citrus (Rutaceae): A review of recent advances in etymology, systematics and medical applications. Blumea 49: 481-198.
2. Tripoli E, Guardia ML, Giammanco S, Majo DD, Giammanco M (2007) Citrus flavonoids: Molecular structure, biological activity and nutritional properties: A review. Food Chem 104: 466-479.
3. Ezeabara CA, Okeke CU, Aziagba BO, Ilodibia CV, Emeka AN (2014) Determination of saponin content of various parts of six Citrus species. Int Res J Pure Appl Chem 4: 137-143.
4. Nicolosi E, Deng ZN, Gentile A, La Malfa S, Continella G, et al. (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100: 1155-66.
5. Hynniewta M, Malik SK, Rao SR (2014) Genetic diversity and phylogenetic analysis of Citrus (L) from north-east India as revealed by meiosis, and molecular analysis of internal transcribed spacer region of rDNA. Meta Gene 2: 237-251.
6. Liu Y, Heying E, Tanumihardjo SA (2012) History, global distribution, and nutritional importance of citrus fruits. Compr Rev Food Sci Food Saf 11: 530-545.
7. Penjor T, Yamamoto M, Uehara M, Ide M, Matsumoto N, et al. (2013) Phylogenetic relationships of Citrus and its relatives based on matK gene sequences. PLoS ONE 8: E62574.
8. Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am J Bot 75: 1443-1458.
9. Zhang Q, Liu Y, Sodmergen (2003) Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species. Plant Cell Physiol 44: 941-951.
10. 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.
11. Davies FS, Albrigo LG (1994). Citrus. CABI International, Wiltshire, UK. 1-2.
12. Vand SH, Abdullah TL (2012) Identification and introduction of Thornless Lime (Citrus aurantifolia) in Hormozgan, Iran. Indian J Sci Technol 5: 3670-3673.
13. Al-Sadi AM, Al-Moqbali HS, Al-Yahyai RA, Al-Said FA (2012) AFLP data suggest a potential role for the low genetic diversity of acid lime (Citrus aurantifolia Swingle) in Oman in the outbreak of witches' broom disease of lime. Euphytica 188: 285-297.
14. Taheri F, Nematzadeh G, Zamharir MG, Nekouei MK, Naghavi M, et al. (2011) Proteomic analysis of the Mexican lime tree response to "Candidatus Phytoplasma aurantifolia" infection. Mol Biosyst 7: 3028-3035.
15. Zamharir MG, Mardi M, Alavi SM, Hasanzadeh N, Nekouei MK, et al. (2011) Identification of genes differentially expressed during interaction of Mexican lime tree infected with "Candidatus Phytoplasma aurantifolia". BMC Microbiol 11: 1.
16. Monavarfeshani A, Mirzaei M, Sarhadi E, Amirkhani A, Khayam Nekouei M, et al. (2013) Shotgun proteomic analysis of the Mexican lime tree infected with "Candidatus Phytoplasma aurantifolia." J Proteome Res 12: 785-795.
17. Faghihi MM, Bagheri AN, Bahrami HR, Hasanzadeh H, Rezazadeh R, et al. (2011) Witches'-broom disease of lime affects seed germination and seedling growth but is not seed transmissible. Plant Disease 95: 419-422.
18. Zafari S, Niknam V, Musetti R, Noorbakhsh SN (2012) Effect of phytoplasma infection on metabolite content and antioxidant enzyme activity in lime (Citrus aurantifolia). Acta Physiol Plant 34: 561-568.
19. Maixner M, Ahrens U, Seemü ller E (1995) Detection of the German grapevine yellows (Vergilbungskrankheit) MLO in grapevine, alternative hosts and a vector by a specific PCR procedure. Eur J Plant Pathol 101: 241-250.
20. Ku C, Hu J-M, Kuo C-H (2013) Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE 8: E62548.
21. Ku C, Chung W-C, Chen L-L, Kuo C-H (2013) The complete plastid genome sequence of Madagascar periwinkle Catharanthus roseus (L.) G. Don: Plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids. PLoS ONE 8: E68518.
22. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
23. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
24. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
25. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24-26.
26. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255.
27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
28. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: Architecture and applications. BMC Bioinformatics 10: 421.
29. Charif D, Lobry JR (2007) SeqinR 1.0-2: A contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In: Bastolla DU, Porto PDM, Roman DHE, Vendruscolo DM, editors. Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer Berlin Heidelberg. 207-232.
30. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52: 267-274.
31. Darling ACE, Mau B, Blattner FR, Perna NT (2004) Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403.
32. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32: 1792-1797.
33. Felsenstein J (1989) PHYLIP -Phylogeny Inference Package (version 3.2). Cladistics 5: 164-166.
34. Kurtz S, Schleiermacher C (1999) REPuter: Fast computation of maximal repeats in complete genomes. Bioinformatics 15: 426-427.
35. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
36. Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
37. Clegg MT, Gaut BS, Learn GH, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci U S A 91: 6795-6801.
38. Kane N, Sveinsson S, Dempewolf H, Yang JY, Zhang D, et al. (2012) Ultrabarcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Am J Bot 99: 320-329.
39. Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, et al. (2006) The complete chloroplast genome sequence of Gossypium hirsutum: Organization and phylogenetic relationships to other angiosperms. BMC Genomics 7: 61.
40. Xu Q, Xiong G, Li P, He F, Huang Y, et al. (2012) Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: Origin and evolution of allotetraploids. PLoS ONE 7: E37128.
41. Bremer B, Bremer K, Chase MW, Fay MF, Reveal JL, et al. (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161: 105-121.
42. Worberg A, Alford MH, Quandt D, Borsch T (2009) Huerteales sister to Brassicales plus Malvales, and newly circumscribed to include Dipentodon, Gerrardina, Huertea, Perrottetia, and Tapiscia. Taxon 58: 468-478.
43. Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG (2014) From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol 14: 23.
44. 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. Plant Cell 13: 645-658.
45. Gantt JS, Baldauf SL, Calie PJ, Weeden NF, Palmer JD (1991) Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J 10: 3073-3078.
46. Jansen RK, Saski C, Lee S-B, Hansen AK, Daniell H (2011) Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): Evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol 28: 835-847.
47. Ueda M, Nishikawa T, Fujimoto M, Takanashi H, Arimura S, et al. (2008) Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal. Mol Biol Evol 25: 1566-1575.
48. Magee AM, Aspinall S, Rice DW, Cusack BP, Sémon M, et al. (2010) Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res 20: 1700-1710.
49. Cusack BP, Wolfe KH (2007) When gene marriages don't work: Divorce by subfunctionalization. Trends Genet 23: 270-272.
50. Ueda M, Fujimoto M, Arimura S, Murata J, Tsutsumi N, et al. (2007) Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. Gene 402: 51-56.
51. Jansen RK, Ruhlman TA (2012) Plastid genomes of seed plants. In: Bock R, Knoop V, editors. Genomics of chloroplasts and mitochondria. Advances in photosynthesis and respiration. Springer Netherlands. 103-126.
52. Wojciechowski MF, Lavin M, Sanderson MJ (2004) A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many wellsupported subclades within the family. Am J Bot 91: 1846-1862.
53. Blazier JC, Guisinger MM, Jansen RK (2011) Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae). Plant Mol Biol 76: 263-272.
54. Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage. Mol Biol Evol 28: 583-600.
55. Njuguna W, Liston A, Cronn R, Ashman TL, Bassil N (2013) Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Mol Phylogenet Evol 66: 17-29.
56. Ohtani K, Yamamoto H, Akimitsu K (2002) Sensitivity to Alternaria alternata toxin in citrus because of altered mitochondrial RNA processing. Proc Natl Acad Sci U S A 99: 2439-2444.
57. Goremykin V, Hirsch-Ernst KI, Wölfl S, Hellwig FH (2003) The chloroplast genome of the "basal" angiosperm Calycanthus fertilis -structural and phylogenetic analyses. Plant Syst Evol 242: 119-135.
58. Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, et al. (2006) The complete chloroplast genome sequence of Pelargonium 6hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol 23: 2175-2190.
59. Richardson AO, Rice DW, Young GJ, Alverson AJ, Palmer JD (2013) The "fossilized" mitochondrial genome of Liriodendron tulipifera: Ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biol 11: 29.
60. Sloan DB, Mü ller K, McCauley DE, Taylor DR, S ? orchová H (2012) Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility. New Phytol 196: 1228-1239.
61. Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, et al. (2007) Comparative chloroplast genomics: Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8: 174.
62. Ahmed I, Biggs PJ, Matthews PJ, Collins LJ, Hendy MD, et al. (2012) Mutational dynamics of aroid chloroplast genomes. Genome Biol Evol 4: 1316-1323.