Genome sequence of the date palm Phoenix dactylifera L

Nature Communications

Volumn 4, Issue , 2013, Pages

  Al Mssallem, Ibrahim S ^a,b   Hu, Songnian ^a,c   Zhang, Xiaowei ^a,c   Lin, Qiang ^a,c   Liu, Wanfei ^a,c   Tan, Jun ^a   Yu, Xiaoguang ^a,c   Liu, Jiucheng ^a,c   Pan, Linlin ^a,c   Zhang, Tongwu ^a,c   Yin, Yuxin ^a,c   Xin, Chengqi ^a,c   Wu, Hao ^a,c   Zhang, Guangyu ^a,c   Ba Abdullah, Mohammed M ^a,c   Huang, Dawei ^a   Fang, Yongjun ^a,c   Alnakhli, Yasser O ^a,c   Jia, Shangang ^a   Yin, An ^a,c   Alhuzimi, Eman M ^a   Alsaihati, Burair A ^a   Al Owayyed, Saad A ^a   Zhao, Duojun ^a,c   Zhang, Sun ^a,c   Al Otaibi, Noha A ^a   Sun, Gaoyuan ^a,c   Majrashi, Majed A ^a   Li, Fusen ^a,c   Wang, Jixiang ^a,c   Yun, Quanzheng ^a,c   Alnassar, Nafla A ^a   Wang, Lei ^a,c   Yang, Meng ^a,c   Al Jelaify, Rasha F ^a   Liu, Kan ^a,c   Gao, Shenghan ^a,c   Chen, Kaifu ^a,c   Alkhaldi, Samiyah R ^a   Liu, Guiming ^a,c   Zhang, Meng ^a,c   Guo, Haiyan ^a,c   Yu, Jun ^a,c   more..

^a KING ABDULAZIZ CITY FOR SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b KING FAISAL UNIVERSITY   (Saudi Arabia)

^c Chinese Academy of Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

SUGAR;

COMMERCIAL SPECIES; CULTIVATION; ECONOMIC ACTIVITY; FRUIT; GENETIC VARIATION; GENOME; METABOLISM; MONOCOTYLEDON; POLYMORPHISM; RIPENING; SUGAR;

ARECACEAE; ARTICLE; CONTROLLED STUDY; DATE (FRUIT); FRUIT DEVELOPMENT; GENE DUPLICATION; GENETIC VARIABILITY; NONHUMAN; PLANT GENOME; PLANT STRESS; PYROSEQUENCING; SEGMENTAL DUPLICATION; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS; WOODY PLANT;

EID: 84882301829     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3274     Document Type: Article

References (51)

1. Balick, M. J. &Beck, H. T. Useful Palms of the World: a Synoptic Bibliography (Columbia University Press, 1990).
2. Mahmoudi, H., Hosseininia, G., Azadi, H. &Fatemi, M. Enhancing date palm processing, marketing and pest control through organic culture. J. Org. Sys. 3, 29-39 (2008).
3. Munier, P. Le palmier-dattier Vol. 24 (G P Maisonneuve and Larose, 1973).
4. El-Juhany, L Degradation of date palm trees and date production in arab countries: causes and potential rehabilitation. Aust. J. Basic. Appl. Sci. 4, 3998-4010 (2010).
5. Al-Maasllem, I. S. Date Palm (Phoenix dactylifera L.) Vol. 7 (Encyclopedia Works Publishing &Distribution, 1996).
6. Al-Dous, E. K. et al. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat. Biotechnol. 29, 521-527 (2011).
7. Bourgis, F. et al. Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning. Proc. Natl Acad. Sci. USA 108, 12527-12532 (2011).
8. Yang, M. et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS ONE 5, e12762 (2010).
9. Fang, Y. J. et al. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS ONE 7, e37164 (2012).
10. Yin, Y. X. et al. High-throughput sequencing-based gene profiling on multistaged fruit development of date palm (Phoenix dactylifera, L.). Plant Mol. Biol. 78, 617-626 (2012).
11. Zhang, G. Y. et al. Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.). Plant Mol. Biol. 79, 521-536 (2012).
12. Solovyev, V., Kosarev, P., Seledsov, I. &Vorobyev, D. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome. Biol. 7 Suppl 1, S10 11-S10 12 (2006).
13. Yu, J. et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).
14. Yu, J. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92 (2002).
15. Noma, K., Nakajima, R., Ohtsubo, H. &Ohtsubo, E. RIRE1, a retrotransposon from wild rice Oryza australiensis. Genes Genet. Syst. 72, 131-140 (1997).
16. De Bodt, S., Maere, S. &Van de Peer, Y. Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-597 (2005).
17. Friis, E. M., Pedersen, K. R. &Crane, P. R. Cretaceous angiosperm flowers: Innovation and evolution in plant reproduction. Palaeogeogr. Palaeoclimatol. Palaeoecol. 232, 251-293 (2006).
18. Freeling, M. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60, 433-453 (2009).
19. Wilson, M. A., Gaut, B. &Clegg, M. T. Chloroplast DNA evolves slowly in the palm family (Arecaceae). Mol. Biol. Evol. 7, 303-314 (1990).
20. Harley, M. M. A summary of fossil records for Arecaceae. Bot. J. Linn. Soc. 151, 39-67 (2006).
21. Abrouk, M. et al. Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends. Plant. Sci. 15, 479-487 (2010).
22. Shao, H. B., Liang, Z. S. &Shao, M. A. LEA proteins in higher plants: structure, function, gene expression and regulation. Colloids Surf. B Biointerfaces 45, 131-135 (2005).
23. Hesse, H. &Willmitzer, L. Expression analysis of a sucrose synthase gene from sugar beet (Beta vulgaris L). Plant Mol. Biol. 30, 863-872 (1996).
24. Huber, S. C. &Huber, J. L. Role and regulation of sucrose-phosphate synthase in higher plants. Annu. Rev. Plant Phys. 47, 431-444 (1996).
25. Myhara, R. M., Karkalas, J. &Taylor, M. S. The composition of maturing Omani dates. J. Sci. Food Agr. 79, 1345-1350 (1999).
26. Komatsu, A., Takanokura, Y., Moriguchi, T., Omura, M. &Akihama, T. Differential expression of three sucrose-phosphate synthase isoforms during sucrose accumulation in citrus fruits (Citrus unshiu Marc.). Plant Sci. 140, 169-178 (1999).
27. Verma, A. K., Upadhyay, S. K., Verma, P. C., Solomon, S. &Singh, S. B. Functional analysis of sucrose phosphate synthase (SPS) and sucrose synthase (SS) in sugarcane (Saccharum) cultivars. Plant Biol. 13, 325-332 (2011).
28. Choudhury, S. R., Roy, S. &Sengupta, D. N. A comparative study of cultivar differences in sucrose phosphate synthase gene expression and sucrose formation during banana fruit ripening. Postharvest Biol. Technol. 54, 15-24 (2009).
29. Kaplan, N. L., Hudson, R. R. &Langley, C. H. The hitchhiking effect revisited. Genetics 123, 887-899 (1989).
30. Cervino, A. C. L. et al. A comprehensive mouse IBD database for the efficient localization of quantitative trait loci. Mamm. Genome 17, 565-574 (2006).
31. Thomas, G. et al. A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat. Genet. 41, 579-584 (2009).
32. Yu, J., Wong, G. K. S., Liu, S. Q., Wang, J. A. &Yang, H. M. A comprehensive crop genome research project: the superhybrid rice genome project in China. Phil. Trans. R. Soc. B 362, 1023-1034 (2007).
33. Wang, L. et al. SNP deserts of Asian cultivated rice: genomic regions under domestication. J. Evol. Biol. 22, 751-761 (2009).
34. He, Z. W. et al. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet. 7, e1002100 (2011).
35. Xu, X. et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30, 105-U157 (2012).
36. Austin, R. S. et al. Next-generation mapping of Arabidopsis genes. Plant J. 67, 715-725 (2011).
37. Yu, J., Wong, G. K.-S., Wang, J. &Yang, H. in Encyclopedia of Molecular Cell Biology and Molecular Medicine Vol. 13 (ed. Meyers, Robert A.) 71-114 (Wiley-VCH Verlag GmbH &Co. KGaA, 2005).
38. Zhang, H. B., Zhao, X. P., Ding, X. L., Paterson, A. H. &Wing, R. A. Preparation of megabase-size DNA from plant nuclei. Plant J. 7, 175-184 (1995).
39. Porebski, S., Bailey, L. G. &Baum, B. R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol. Biol. Rep. 15, 8-15 (1997).
40. Chang, S. J., Puryear, J. &Cairney, J. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11, 113-116 (1993).
41. Birnboim, H. &Doly, J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7, 1513-1523 (1979).
42. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. &Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).
43. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. &Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007).
44. Robinson, M. D., McCarthy, D. J. &Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
45. Du, Z., Zhou, X., Ling, Y., Zhang, Z. H. &Su, Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, W64-W70 (2010).
46. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
47. Gaut, B. S., Morton, B. R., McCaig, B. C. &Clegg, M. T. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl Acad. Sci. USA 93, 10274-10279 (1996).
48. Koch, M. A., Haubold, B. &Mitchell-Olds, T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Genome Biol. Evol. 17, 1483-1498 (2000).
49. Wang, X. Y., Tang, H. B. &Paterson, A. H. Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell 23, 27-37 (2011).
50. Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112-1115 (2009).
51. Young, N. D. et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520-524 (2011).