The Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L. cv. ‘Aseel-

详细信息    查看全文

• 作者：Asifullah Khan (1)
  Ishtiaq A. Khan (1)
  Berthold Heinze (2)
  M. Kamran Azim (1) kamran.azim@iccs.edu
• 关键词：Intervarietal polymorphism – Plastid – Next ; generation sequencing – Genetic diversity
• 刊名：Plant Molecular Biology Reporter
• 出版年：2012
• 出版时间：June 2012
• 年：2012
• 卷：30
• 期：3
• 页码：666-678
• 全文大小：550.4 KB
• 参考文献：1. Abdulla M, Gamal O (2010) Investigation on molecular phylogeny of some date palm (Phoenix dactylifra L.) cultivars by protein, RAPD and ISSR markers in Saudi Arabia. Aust J Crop Sci 4:23–28
  2. Al-Farsi M, Alasalvar C, Morris A, Baron M, Shahidi F (2005) Compositional and sensory characteristics of three native sun-dried date (Phoenix dactylifera L.) varieties grown in Oman. J Agric Food Chem 53:7586–7591
  3. Al-Farsi MA, Lee CY (2008) Nutritional and functional properties of dates: a review. Crit Rev Food Sci Nutr 48:877–887
  4. Al-Khalifah NS, Askari E (2003) Molecular phylogeny of date palm (Phoenix dactyliferaL.) cultivars from Saudi Arabia by DNA fingerprinting. Theor Appl Genet 107:1266–1270
  5. Al-Shahib W, Marshall RJ (2003) The fruit of the date palm: its possible use as the best food for the future? Int J Food Sci Nutr 54:247–259
  6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
  7. Bendich AJ (1987) Why do chloroplasts and mitochondria contain so many copies of their genome? BioEssays 6:279–282
  8. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S (2003) LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA. Genome Research 13(4):721–731
  9. Celamkoti S, Kundeti S, Purkayastha A, Mazumder R, Buck C, Seto D (2004) GeneOrder 3.0: software for comparing the order of genes in pairs of small bacterial genomes. BMC Bioinforma 5:52
  10. Chang C, Lin H, Lin I 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
  11. Chung HJ, Jung JD, Park HW, Kim JH, Cha HW, Min SR, Jeong WJ, Liu JR (2006) 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 25:1369–1379
  12. Conant GC, Wolfe KH (2008) GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 2:861–862
  13. Dhingra A, Folta KM (2005) ASAP: amplification, sequencing & annotation of plastomes. BMC Genomics 6:176
  14. Elshibli S, Korpelainen H (2008) Microsatellite markers reveal high genetic diversity in date palm (Phoenix dactylifera L.) germplasm from Sudan. Genetica 134:251–260
  15. Elshibli S, Korpelainen H (2009a) Excess heterozygosity and scarce genetic differentiation in the populations of Phoenix dactylifera L.: human impact or ecological determinants. Plant Genet Res 7:95–104
  16. Elshibli S, Korpelainen H (2009b) Biodiversity of date palms (Phoenix dactylifera L.) in Sudan: chemical, morphological and DNA polymorphisms of selected cultivars. Plant Genet Res 7:194–203
  17. Fitter JT, Thomas MR, Rose RJ, Steelescott N (1996) Heteroplasmy of the chloroplast genome of Medicago sativa L cv 'Regen S' confirmed by sequence analysis. Theor Appl Genet 93:685–690
  18. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273–W279
  19. Gao L, Su Y-J, Wang T (2010) Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects. J Syst Evol 48:77–93
  20. GoremykinVV HB, Hirsch-Ernst KI, Hellwig FH (2005) Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Biol Evol 22:1813–1822
  21. 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
  22. Haberle R, Fourcade H, Boore J, Jansen R (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol 66:350–361
  23. Hansen DR, Dastidar SG, Cai Z 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). Mol Phylogenet Evol 45:547–563
  24. He Q, Li XW, Liang GL, Ji K, Guo QG, Yuan WM, Zhou GZ, Chen KS, Van de Weg WE, Gao ZS (2011) Genetic diversity and identity of Chinese loquat cultivars/accessions (Eriobotrya japonica) using apple SSR markers. Plant Mol Biol Rep 29:197–208
  25. Hirai A, Nakazon M (1993) Six percent of the mitochondrial genome in rice came from chloroplast DNA. Plant Mol Biol Rep 11(2):98–100
  26. Johnson L, Palmer J (1989) Heteroplasmy of chloroplast DNA in Medicago. Plant Mol Biol 12:3–11
  27. Khan A, Khan IA, Asif H, Azim MK (2010) Current trends in chloroplast genomics. Afric J Biotech 9:3494–3500
  28. 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
  29. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29:4633–4642
  30. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
  31. 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
  32. Mardanov AV, Ravin NV, Kuznetsov BB 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
  33. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402
  34. Marqués J, Fadda ZG, Duran-Vila N, Flores R, Bové JM, Daròs JA (2008) A set of novel RNAs transcribed from the chloroplast genome accumulates in date palm leaflets affected by brittle leaf disease. Phytopathol 98:337–344
  35. Masood MS, Nishikawa T, Fukuoka S, Njenga PK, Tsudzuki T, Kadowaki K (2004) The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene 340:133–139
  36. 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. Plant Cell 17:665–675
  37. Ogihara Y, Isono K, Kojima T et al (2000) Chinese spring wheat (Triticum aestivum L.) chloroplast genome: complete sequence and contig clones. Plant Mol Biol Rep 18:243–253
  38. Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15:8–15
  39. Ravi V, Khurana J, Tyagi A, Khurana P (2006) The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genet Genomes 3:49–59
  40. Ravi V, Khurana JP, Tyagi AK, Khurana P (2008) An update on chloroplast genomes. Plant Syst Evol 271:101–102
  41. Sedra MyH, Lashermes P, Trouslot P, Combes M-C (1998) Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers. Euphytica 103:75–82
  42. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599
  43. Tang J, Xia H, Cao M, Zhang X, Zeng W, Hu S, Tong W, Wang J, Wang J, Yu J, Yang H, Zhu L (2004) A comparison of rice chloroplast genomes. Plant Physiol 135:412–420
  44. Tanya P, Taeprayoon P, Hadkam Y, Srinives P (2011) Genetic diversity among Jatropha and Jatropha-related species based on ISSR markers. Plant Mol Biol Rep 29:252–264
  45. Triboush SO, Danilenko NG, Davydenko OG (1998) A method for isolation of chloroplast DNA and mitochondrial DNA from sunflower. Plant Mol Biol Rep 16:183–189
  46. Tuskan GA, DiFazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604
  47. Vayalil PK (2002) Antioxidant and antimutagenic properties of aqueous extract of date fruit (Phoenix dactylifera L. Arecaceae). J Agric Food Chem 50:610–617
  48. Wolfe AD, Randle CP (2004) Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics. Syst Bot 29:1011–1020
  49. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci 84:9054–9058
  50. Wu F, Kan D, Lee SB et al (2009) Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree Physiol 29:847–856
  51. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255
  52. Xie R-J, Zhou J, Wang G-Y, Zhang S-M, Chen L, Gao Z-S (2011) Cultivar identification and genetic diversity of Chinese bayberry (Myrica rubra) accessions based on fluorescent SSR markers. Plant Mol Biol Rep 29:554–562
  53. Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, Al-Mssallem IS, Yu J (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5:e12762
  54. Younis RAA, Ismail OM, Soliman SS (2008) Identification of sex-specific DNA markers for date palm (Phoenix dactylifera L.) using RAPD and ISSR techniques. Res J Agric Biol Sci 4:278–284
  55. Zhang Q, Li J, Zhao Y, Schuyler SK, Han Y (2011) Evaluation of genetic diversity in Chinese wild apple species along with apple cultivars using SSR markers. Plant Mol Biol Rep Early online. doi:10.1007/s11105-011-0366-6
  56. Zohary D, Hopf M (2000) Domestication of plants in the old world: the origin and spread of cultivated plants in West Asia, Europe, and the Nile Valley, 3rd edn. Oxford University Press, Oxon
• 作者单位：1. International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan2. Department of Genetics, Federal Research Centre for Forests, Hauptstra?e 7, 1140 Vienna, Austria
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Plant Sciences
  Plant Physiology
  
• 出版者：Springer Netherlands
• ISSN：1572-9818

文摘

Date palm (Phoenix dactylifera L.) is an economically important and widely cultivated palm of the family Arecaceae. We sequenced the complete date palm chloroplast genome (cpDNA) from Pakistani cv. ‘Aseel’, using a combination of Sanger-based and next-generation sequencing technologies. Being very similar to a sequence from a Saudi Arabian date palm cultivar ‘Khalas’ published recently, the size of the genome was 158,458 bp with a pair of inverted repeat (IR) regions of 27,276 bp that were separated by a large single-copy (LSC) region of 86,195 bp and a small single-copy (SSC) region of 17,711 bp. Genome annotation demonstrated a total of 138 genes, of which 89 were protein coding, 39 were tRNA, and eight were rRNA genes. Comparison of cpDNA sequences of cultivars ‘Aseel’ and ‘Khalas’ showed following intervarietal variations in the LSC region; (a) two SNPs in intergenic spacers and one SNP in the rpoc1 gene, (b) polymorphism in two mono-nucleotide simple sequence repeats (SSR), and (c) a 4-bp indel in the accD-psaI intergenic spacer. The SSC region has a polymorphic site in the mono-nucleotide SSR located at position 120,710. We also compared cv. ‘Aseel’ cpDNA sequence with partial P. dactylifera cpDNA sequence entries deposited in Genbank and identified a number of potentially useful polymorphisms in this species. Analysis of date palm cpDNA sequences revealed a close relationship with Typha latifolia. Occurrence of small numbers of forward and inverted repeats in date palm cpDNA indicated conserved genome arrangement.