Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish

详细信息    查看全文

• 作者：Shufen Wang (1)
  Xiufeng Wang (2)
  Qiwei He (1)
  Xianxian Liu (1)
  Wenling Xu (1)
  Libin Li (1)
  Jianwei Gao (1) jianweigao3@yahoo.com
  Fengde Wang (1) wfengde@163.com
• 关键词：EST ; SSR markers &#8211 ; Illumina paired ; end sequencing &#8211 ; Radish &#8211 ; Tuberous root &#8211 ; Transcriptome
• 刊名：Plant Cell Reports
• 出版年：2012
• 出版时间：August 2012
• 年：2012
• 卷：31
• 期：8
• 页码：1437-1447
• 全文大小：601.7 KB
• 参考文献：1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
  2. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995
  3. Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE (2009) Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol 9:51
  4. Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Statist 29:1165–1188
  5. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2011) GenBank. Nucleic Acids Res 39:32–37
  6. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB (2008) ALLPATHS de novo assembly of whole-genome shotgun microreads. Genome Res 18(5):810–820
  7. Cameron M, Williams HE, Cannane A (2004) Improved gapped alignment in BLAST. IEEE/ACM Trans Comput Biol Bioinforma 1:116–129
  8. Collins LJ, Biggs PJ, Voelckel C, Joly S (2008) An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Inform 21:3–14
  9. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676
  10. Curtis IS (2003) The noble radish: past, present and future. Trends Plant Sci 8:305–307
  11. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29:644–652
  12. Gupta AK, Singh J, Kaur N (2001) Sink development, sucrose metabolising enzymes and carbohydrate status in turnip (Brassica rapa L.). Acta Physiol Plant 23:31–36
  13. Hale MC, McCormick CR, Jackson JR, Dewoody JA (2009) Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics 10:203
  14. Hegedus Z, Zakrzewska A, Agoston VC, Ordas A, Racz P, Mink M, Spaink HP, Meijer AH (2009) Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol 46(15):2918–2930
  15. Huang YW, Huang TH, Wang LS (2010) Profiling DNA methylomes from microarray to genome-scale sequencing. Technol Cancer Res Treat 9:139–147
  16. Jakmatakul R, Suttisri R, Tengamnuay P (2009) Evaluation of antityrosinase and antioxidant activities of Raphanus sativus root: comparison between freeze-dried juice and methanolic extract. Thai J Pharm Sci 33:22–30
  17. Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, Price HJ (2005) Evolution of genome size in Brassicaceae. Ann Bot 95(1):229–235
  18. Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510
  19. Kortt AA, Caldwell JB, Lilley GG, Higgins TJV (1991) Amino acid and cDNA sequences of a methionine-rich 2S protein from sunflower seed (Helianthus annuus L.). Eur J Biochem 195(2):329–334
  20. Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48(6):985–998
  21. Li JW, Lu ZH, Wang RY, Lu GY, Ge XG, Zhang Y, Chen JF, Jiang XM (1979) Cultivation of vegetables. Agricultural Press, Beijing (in Chinese)
  22. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y et al (2010a) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317
  23. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K et al (2010b) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20(2):265–272
  24. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCт method. Methods 25:402–408
  25. Lu Z, Liu L, Li X, Gong Y, Hou X, Zhu X, Yang J, Wang L (2008) Analysis and evaluation of nutritional quality in Chinese radish (Raphanus sativus L.). Agri Sci China 7(7):823–830
  26. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10:219
  27. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30(2):194–200
  28. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
  29. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180
  30. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B et al (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19(5):651–652
  31. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222
  32. Prat S, Frommer WB, H枚fgen R, Keil M, Ko脽mann J, K枚ster-T枚pfer M, Liu XJ, M眉ller B, Pe帽a-Cort茅s H, Rocha-Sosa M et al (1990) Gene expression during tuber development in potato plants. FEBS Lett 268(2):334–338
  33. Rouhier H, Usuda H (2001) Spatial and temporal distribution of sucrose synthase in the radish hypocotyl in relation to thickening growth. Plant Cell Physiol 42(6):583–593
  34. Rubatzky VE, Yamaguchi M (1997) World vegetables: principles, production, and nutritive values, 2nd edn. Chapman & Hall, USA
  35. Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M et al (2011) An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res 18:221–232
  36. Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12(6):1339–1348
  37. Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EM, Chen S (2010) De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 11:262
  38. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10(7):967–981
  39. Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J 7(4):334–346
  40. Tsuro M, Suwabe K, Kubo N, Matsumoto S, Hirai M (2008) Mapping of QTLs controlling root shape and red pigmentation in radish, Raphanus sativus L. Breed Sci 58:55–61
  41. Usuda H, Demura T, Shimogawara K, Fukuda H (1999) Development of sink capacity of the “storage root” in a radish cultivar with a high ratio of “storage root” to shoot. Plant Cell Physiol 40(4):369–377
  42. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotech 23(1):48–55
  43. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63
  44. Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L (2010a) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res 38(15):5075–5087
  45. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS (2010b) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11:400
  46. Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010c) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 11:726
  47. Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039
  48. Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:451
  49. Werth E (1937) Abstammung und Heimat des Rettichs. Angew Bot 19:194–205
  50. Wu T, Qin Z, Zhou X, Feng Z, Du Y (2010) Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol 167(11):905–913
  51. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11(1):1–16
  52. Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe B, Wang Y (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics 11(1):94
• 作者单位：1. Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, 250100 China2. College of Horticulture Science and Engineering, Shandong Agricultural University, Tai鈥檃n, 271018 China
• ISSN：1432-203X

文摘

Abstract The tuberous root of radish is an important vegetable, but insufficient transcriptomic and genomic data are currently available to understand the molecular mechanisms underlying tuberous root formation and development. High-throughput transcriptomic sequencing is essential to generate a large transcript sequence data set for gene discovery and molecular marker development. In this study, a total of 107.3 million clean reads were generated using Illumina paired-end sequencing technology. De novo assembly generated 61,554 unigenes with an average length of 820 bp. Based on a sequence similarity search with known proteins or nucleotides, 85.51 % (52,634), 90.18 % (55,507) and 54 % (33,242) consensus sequences showed homology with sequences in the Nr, Nt and Swiss-Prot databases, respectively. Of these annotated unigenes, 21,109 and 17,343 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 27,809 unigenes were assigned to 123 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Analysis of transcript differences between libraries from the early and late seedling developmental stages demonstrated that starch and sucrose metabolism and phenylpropanoid biosynthesis may be the dominant metabolic events during tuberous root formation and plant hormones probably play critical roles in regulation of this developmental process. In total, 14,641 potential EST-SSRs were identified among the unigenes, and 12,733 primer pairs for 2,511 SSR were obtained. Summarily, this study gave us a clue to understand the radish tuberous root formation and development, and also provided us with a valuable sequence resource for novel gene discovery and marker-assisted selective breeding in radish.