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International Journal of Genomics
Volume 2015, Article ID 528395, 12 pages
http://dx.doi.org/10.1155/2015/528395
Research Article

Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease in Lagerstroemia indica

1USDA-ARS, Crop Germplasm Research, College Station, TX 77845, USA
2Texas A&M AgriLife Research and Extension Center, Dallas, TX 75252, USA
3Department of Plant Pathology, Texas A&M University, College Station, TX 77843, USA
4USDA-ARS, Thad Cochran Southern Horticultural Laboratory, Poplarville, MS 39470, USA

Received 30 November 2014; Accepted 6 May 2015

Academic Editor: Giuliana Napolitano

Copyright © 2015 Xinwang Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. R. Pooler, “Crapemyrtle,” in Flower Breeding and Genetics, N. O. Anderson, Ed., pp. 439–457, Springer, Dordrecht, The Netherlands, 2006. View at Google Scholar
  2. D. R. Egolf and A. O. Andrick, The Lagerstroemia Handbook/Checklist, American Association of Botanical Gardens and Arboreta, 1978.
  3. U.S. Department of Agricultural, Census of Horticultural Specialties, vol. 3, special studies, part 3. AC-07-SS-3, U.S. Department of Agricultural, 2009, http://www.agcensus.usda.gov/Publications/2007/Online_Highlights/Census_of_Horticulture_Specialties/hortic_1_020_021.pdf.
  4. C. X. Furtado and M. Srisuko, A Revision of Lagerstroemia L. (Lythraceae), 1969.
  5. R. I. Cabrera, “Evaluating and promoting the cosmopolitan and multipurpose lagerstroemia,” Acta Horticulturae, vol. 630, pp. 177–184, 2004. View at Google Scholar · View at Scopus
  6. R. L. Dix, Cultivars and Names of Lagerstroemia, 1999, http://www.usna.usda.gov/Research/Herbarium/Lagerstroemia/index.html.
  7. E. West, “Powdery mildew of crape myrtle caused by Erysiphe lagerstroemiae, n.sp.,” Phytopathology, vol. 23, pp. 814–819, 1933. View at Google Scholar
  8. A. K. Hagan, G. J. Keever, C. H. Gilliam, J. D. Williams, and G. Creech, “Susceptibility of crape myrtle cultivars to powdery mildew and Cercospora leaf spot in Alabama,” Journal of Environmental Horticulture, vol. 16, pp. 143–147, 1998. View at Google Scholar
  9. M. Beck, W. Heard, M. Mbengue, and S. Robatzek, “The INs and OUTs of pattern recognition receptors at the cell surface,” Current Opinion in Plant Biology, vol. 15, no. 4, pp. 367–374, 2012. View at Publisher · View at Google Scholar · View at Scopus
  10. J. Łaźniewska, V. K. Macioszek, and A. K. Kononowicz, “Plant-fungus interface: the role of surface structures in plant resistance and susceptibility to pathogenic fungi,” Physiological and Molecular Plant Pathology, vol. 78, pp. 24–30, 2012. View at Publisher · View at Google Scholar · View at Scopus
  11. K. Weng, Z.-Q. Li, R.-Q. Liu, L. Wang, Y.-J. Wang, and Y. Xu, “Transcriptome of Erysiphe necator-infected Vitis pseudoreticulata leaves provides insight into grapevine resistance to powdery mildew,” Horticulture Research, vol. 1, article 14049, 2014. View at Publisher · View at Google Scholar
  12. S. van Nocker and S. E. Gardiner, “Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops,” Horticulture Research, vol. 1, Article ID 14022, 2014. View at Publisher · View at Google Scholar
  13. J. C. Marioni, C. E. Mason, S. M. Mane, M. Stephens, and Y. Gilad, “RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays,” Genome Research, vol. 18, no. 9, pp. 1509–1517, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. J. A. Ward, L. Ponnala, and C. A. Weber, “Strategies for transcriptome analysis in nonmodel plants,” American Journal of Botany, vol. 99, no. 2, pp. 267–276, 2012. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Li, H. Zhu, J. Ruan et al., “De novo assembly of human genomes with massively parallel short read sequencing,” Genome Research, vol. 20, no. 2, pp. 265–272, 2010. View at Publisher · View at Google Scholar · View at Scopus
  16. J. W. Davey, P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen, and M. L. Blaxter, “Genome-wide genetic marker discovery and genotyping using next-generation sequencing,” Nature Reviews Genetics, vol. 12, no. 7, pp. 499–510, 2011. View at Publisher · View at Google Scholar · View at Scopus
  17. M. R. Pooler, “Molecular genetic diversity among 12 clones of Lagerstroemia fauriei revealed by AFLP and RAPD markers,” HortScience, vol. 38, no. 2, pp. 256–259, 2003. View at Google Scholar · View at Scopus
  18. T. A. Rinehart, B. E. Scheffler, and S. M. Reed, “Genetic diversity estimates for the genus Hydrangea and development of a molecular key based on SSR,” Journal of the American Society for Horticultural Science, vol. 131, no. 6, pp. 787–797, 2006. View at Google Scholar · View at Scopus
  19. C. Pounders, T. Rinehart, N. Edwards, and P. Knight, “An analysis of combining ability for height, leaf out, bloom date, and flower color for crapemyrtle,” HortScience, vol. 42, no. 6, pp. 1496–1499, 2007. View at Google Scholar · View at Scopus
  20. X. Wang, D. Dean, P. Wadl et al., “Development of microsatellite markers from crape myrtle (Lagerstroemia L.),” HortScience, vol. 45, no. 5, pp. 842–844, 2010. View at Google Scholar · View at Scopus
  21. X. Wang, P. A. Wadl, C. Pounders et al., “Evaluation of genetic diversity and pedigree within crapemyrtle cultivars using simple sequence repeat markers,” Journal of the American Society for Horticultural Science, vol. 136, no. 2, pp. 116–128, 2011. View at Google Scholar · View at Scopus
  22. A. Shi and M. T. Mmbaga, “Perpetuation of powdery mildew infection and identification of Erysiphe australiana as the crape myrtle pathogen in mid-Tennessee,” Plant Disease, vol. 90, no. 8, pp. 1098–1101, 2006. View at Publisher · View at Google Scholar · View at Scopus
  23. E. Pruesse, C. Quast, K. Knittel et al., “SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB,” Nucleic Acids Research, vol. 35, no. 21, pp. 7188–7196, 2007. View at Publisher · View at Google Scholar
  24. J. Martin, V. M. Bruno, Z. Fang et al., “Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads,” BMC Genomics, vol. 11, no. 1, article 663, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. P. Rice, I. Longden, and A. Bleasby, “EMBOSS: the European molecular biology open software suite,” Trends in Genetics, vol. 16, no. 6, pp. 276–277, 2000. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Kanehisa and S. Goto, “KEGG: kyoto encyclopedia of genes and genomes,” Nucleic Acids Research, vol. 28, no. 1, pp. 27–30, 2000. View at Publisher · View at Google Scholar · View at Scopus
  27. W. Shi, C. D. Moon, S. C. Leahy et al., “Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome,” Genome Research, vol. 24, no. 9, pp. 1517–1525, 2014. View at Publisher · View at Google Scholar
  28. Z. Fang, J. Martin, and Z. Wang, “Statistical methods for identifying differentially expressed genes in RNA-Seq experiments,” Cell & Bioscience, vol. 2, no. 1, p. 26, 2012. View at Publisher · View at Google Scholar
  29. Y. Benjamini and Y. Hochberg, “Controlling the false discovery rate: a practical and powerful approach to multiple testing,” Journal of the Royal Statistical Society Series B: Methodological, vol. 57, pp. 289–300, 1995. View at Google Scholar
  30. J. H. Schefe, K. E. Lehmann, I. R. Buschmann, T. Unger, and H. Funke-Kaiser, “Quantitative real-time RT-PCR data analysis: current concepts and the novel ‘gene expression's CT difference’ formula,” Journal of Molecular Medicine, vol. 84, no. 11, pp. 901–910, 2006. View at Publisher · View at Google Scholar · View at Scopus
  31. K. J. Livak and T. D. Schmittgen, “Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method,” Methods, vol. 25, no. 4, pp. 402–408, 2001. View at Publisher · View at Google Scholar · View at Scopus
  32. V. Cambier, T. Hance, and E. de Hoffmann, “Variation of DIMBOA and related compounds content in relation to the age and plant organ in maize,” Phytochemistry, vol. 53, no. 2, pp. 223–229, 2000. View at Publisher · View at Google Scholar · View at Scopus
  33. H. M. Niemeyer, “Hydroxamic acids derived from 2-hydroxy-2h-1,4-benzoxazin-3(4h)-one: key defense chemicals of cereals,” Journal of Agricultural and Food Chemistry, vol. 57, no. 5, pp. 1677–1696, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. D. Treutter, “Significance of flavonoids in plant resistance: a review,” Environmental Chemistry Letters, vol. 4, no. 3, pp. 147–157, 2006. View at Publisher · View at Google Scholar
  35. F. Galeotti, E. Barile, P. Curir, M. Dolci, and V. Lanzotti, “Flavonoids from carnation (Dianthus caryophyllus) and their antifungal activity,” Phytochemistry Letters, vol. 1, no. 1, pp. 44–48, 2008. View at Publisher · View at Google Scholar · View at Scopus
  36. X.-M. Zhang, L. Zhao, Z. Larson-Rabin, D.-Z. Li, and Z.-H. Guo, “De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae),” PLoS ONE, vol. 7, no. 8, Article ID e42082, 2012. View at Publisher · View at Google Scholar · View at Scopus
  37. L. F. Castillo, N. Galeano, G. A. Isaza, and A. Gaitán, “Construction of coffee transcriptome networks based on gene annotation semantics,” Journal of Integrative Bioinformatics, vol. 9, no. 3, article 205, 2012. View at Google Scholar · View at Scopus
  38. M. Ranik, N. M. Creux, and A. A. Myburg, “Within-tree transcriptome profiling in wood-forming tissues of a fast-growing Eucalyptus tree,” Tree Physiology, vol. 26, no. 3, pp. 365–375, 2006. View at Publisher · View at Google Scholar · View at Scopus
  39. E. Mizrachi, C. A. Hefer, M. Ranik, F. Joubert, and A. A. Myburg, “De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq,” BMC Genomics, vol. 11, no. 1, article 681, 2010. View at Publisher · View at Google Scholar · View at Scopus
  40. J. Derory, P. Léger, V. Garcia et al., “Transcriptome analysis of bud burst in sessile oak (Quercus petraea),” New Phytologist, vol. 170, no. 4, pp. 723–738, 2006. View at Publisher · View at Google Scholar · View at Scopus
  41. T. L. Parchman, K. S. Geist, J. A. Grahnen, C. W. Benkman, and C. A. Buerkle, “Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery,” BMC Genomics, vol. 11, no. 1, article 180, 2010. View at Publisher · View at Google Scholar · View at Scopus
  42. D. Janz, K. Behnke, J.-P. Schnitzler, B. Kanawati, P. Schmitt-Kopplin, and A. Polle, “Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms,” BMC Plant Biology, vol. 10, article 150, 2010. View at Publisher · View at Google Scholar · View at Scopus
  43. S. Hacquard, C. Delaruelle, P. Frey, E. Tisserant, A. Kohler, and S. Duplessis, “Transcriptome analysis of poplar rust telia reveals overwintering adaptation and tightly coordinated karyogamy and meiosis processes,” Frontiers in Plant Science, vol. 4, article 456, 2013. View at Publisher · View at Google Scholar · View at Scopus
  44. S. M. Huse, J. A. Huber, H. G. Morrison, M. L. Sogin, and D. M. Welch, “Accuracy and quality of massively parallel DNA pyrosequencing,” Genome Biology, vol. 8, no. 7, article R143, 2007. View at Publisher · View at Google Scholar · View at Scopus
  45. M. Pop and S. L. Salzberg, “Bioinformatics challenges of new sequencing technology,” Trends in Genetics, vol. 24, no. 3, pp. 142–149, 2008. View at Publisher · View at Google Scholar · View at Scopus
  46. A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008. View at Publisher · View at Google Scholar · View at Scopus