Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome

Frontiers in Plant Science

Volumn 6, Issue APR, 2015, Pages

  Wu, Gang ^a   Zhang, Libin ^a   Yin, Yongtai ^a   Wu, Jiangsheng ^b   Yu, Longjiang ^a   Zhou, Yanhong ^a   Li, Maoteng ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Raphanus sativus; RNA sequencing; Simple sequence repeats; Transcription factor; Transcriptome

Indexed keywords

BRASSICACEAE; RAPHANUS SATIVUS;

EID: 84928125354     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00198     Document Type: Article

References (45)

1. Bouché, N., Scharlat, A., Snedden, W., Bouchez, D., and Fromm, H. (2002). A novel family of calmodulin-binding transcription activators in multicel-lular organisms. J. Biol. Chem. 277, 21851–21861. doi: 10.1074/jbc.M200268200
2. Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., and Rob-les, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis of functional genomics research. Bioinformatics 21, 3674–3676. doi: 10.1093/bioinformatics/bti610
3. Deisenroth, C., and Zhang, Y. (2011). The ribosomal protein-Mdm2-p53 pathway and energy metabolism: bridging the gap between feast and famine. Genes Cancer 2, 392–403. doi: 10.1177/1947601911409737
4. Gangappa, S. N., Prasad, V. B., and Chattopadhyay, S. (2010). Functional interconnection of MYC2 and SPA1 in the photomorphogenic seedling development of Arabidopsis. Plant Physiol. 154, 1210–1219. doi: 10.1104/pp.110.163717
5. Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., et al. (2011). Full length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652. doi: 10.1038/nbt.1883
6. Heim, M. A., Jakoby, M., Werber, M., Martin, C., Weisshaar, B., and Bailey, P. C. (2003). The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20, 735–747. doi: 10.1093/molbev/msg088
7. Herrig, V., Ferrarese-Mde, L., Suzuki, L. S., Rodrigues, J. D., and Ferrarese-Filho, O. (2002). Peroxidase and phenylalanine ammonia-lyase activities, phenolic acid contents, and allelochemicals-inhibited root growth of soybean. Biol. Res. 35, 59–66. doi: 10.4067/S0716-97602002000100009
8. Jiao, Y., Yang, H., Ma, L., and Sun, N. (2003). A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol. 133, 1480–1493. doi: 10.1104/pp.103.029439
9. Jin, H., and Martin, C. (1999). Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41, 577–585.
10. Kalra, S., Puniya, B. L., Kulshreshtha, D., Kumar, S., Kaur, J., Ramachandran, S., et al. (2013). De novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant, Chlorophytum borivilianum. PloS ONE 8:e83336. doi: 10.1371/journal.pone.0083336
11. Kamei, A., Tsuro, M., Kubo, N., Hayashi, T., Wang, N., Fujimura, T., et al. (2010). QTL mapping of clubroot resistance in radish (Raphanus sativus L.). Theor. Appl. Genet. 120, 1021–1027. doi: 10.1007/s00122-009-1230-z
12. Kappen, C. (2000). The homeodomain: an ancient evolutionary motif in animals and plants. Comput. Chem. 24, 95–103. doi: 10.1016/S0097-8485(99)00049-2
13. Kim, H. A., Lim, C. J., Kim, S., Choe, J. K., Jo, S. H., Baek, N., et al. (2014). High-throughput sequencing and de novo assembly of Brassica oleracea var. capitata L. for transcriptome analysis. PLoS ONE 9:e92087. doi: 10.1371/jour-nal.pone.0092087
14. Knowles, D. G., and McLysaght, A. (2009). Recent de novo origin of human protein coding genes. Genome Res. 19, 1752–1759. doi: 10.1101/gr.095026.109
15. Li, D. J., Deng, Z., Qin, B., Liu, X. H., and Men, Z. H. (2012). De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13:192 doi: 10.1186/1471-2164-13-192
16. Li, Y. C., Korol, A. B., Fahima, T., Beiles, A., and Nevo, E. (2002). Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 11, 2453–2465. doi: 10.1046/j.1365-294X.2002.01643.x
17. Li, Y. C., Korol, A. B., Fahima, T., and Nevo, E. (2004). Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 21, 991–1007. doi: 10.1093/molbev/msh073
18. Mitsuda, N., and Ohme-Takagi, M. (2009). Functional analysis of transcription factors in Arabidopsis. Plant Cell Physiol. 50, 1232–1248. doi: 10.1093/pcp/pcp075
19. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628. doi: 10.1038/nmeth.1226
20. Mudalkar, S., Golla, R., Ghatty, S., and Reddy, A. R. (2014). De novo transcrip-tome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers. Plant Mol. Biol. 84, 159–171. doi: 10.1007/s11103-013-0125-1
21. Mumby, M. C., and Walter, G. (1993). Protein serine/threonine phosphatases: structure, regulation, and functions in cell growth. Physiol. Rev. 73, 673–699.
22. Ohsako, T., Hirai, M., and Yamabuki, M. (2010). Spatial structure of microsatellite variability within and among populations of wild radish Raphanus sativus L. var. hortensis Backer f. raphanistroides Makino (Brassicaceae) in Japan. Breed. Sci. 60, 195–202. doi: 10.1270/jsbbs.60.195
23. Paritosh, K., Yadava, S. K., Gupta, V., Panjabi-Massand, P., Sodhi, Y. S., Pradhan, A. K., et al. (2013). RNA-seq based SNPs in some agronomically important oleifer-ous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping. BMC Genomics 14:463. doi: 10.1186/1471-2164-14-463
24. Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., et al. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 2, 225–238. doi: 10.1007/BF00564200
25. Qiu, L., Yang, C., Tian, B., Yang, J. B., and Liu, A. (2010). Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol. 10:278. doi: 10.1186/1471-2229-10-278
26. Riechmann, J. L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., et al. (2000). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290, 2105–2110. doi: 10.1126/science.290.5499.2105
27. Schulz, M., and Zerbino, D. (2010). Oases – De Novo Transcriptome Assembler for Very Short Reads. Technical Report, MPI for Molecular Genomics, European Bioinformatics Institute (EMBL-EBI), UC Santa Cruz.
28. Schuster, S. C. (2008). Next-generation sequencing transforms today’s biology. Nat. Methods 5, 16–18. doi: 10.1038/nmeth1156
29. Sharopova, N., McMullen, M. D., Schultz, L., Schroeder, S., Sanchez-Villeda, H., Gardiner, J., et al. (2002). Development and mapping of SSR markers for maize. Plant Mol. Biol. 48, 463–481. doi: 10.1023/A:1014868625533
30. Shendure, J., and Ji, H. (2008). Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135–1145. doi: 10.1038/nbt1486
31. Shi, Y. (2009). Serine/threonine phosphatases: mechanism through structure. Cell 139, 468–484. doi: 10.1016/j.cell.2009.10.006
32. Wang, L., Wei, L., Wang, L., and Xu, C. (2002). Effects of peroxidase on hyperlipi-demia in mice. J. Agric. Food. Chem. 50, 868–870. doi: 10.1021/jf011130+
33. Wang, N., Hu, J., Ohsawa, R., Ohta, M., and Fujimura, T. (2007). Identification and characterization of microsatellite markers derived from expressed sequence tags (ESTs) of radish (Raphanus sativus L.). Mol. Ecol. Notes 7, 503–506. doi: 10.1111/j.1471-8286.2006.01635.x
34. Wang, Y., Pan, Y., Liu, Z., Zhu, X., Zhai, L., Xu, L., et al. (2013b). De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. BMC Genomics 14:836. doi: 10.1186/1471-2164-14-836
35. Wang, Y., Xu, L., Chen, Y., Shen, H., Gong, Y., Limera, C., et al. (2013a). Tran-scriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to lead (Pb) stress with next generation sequencing. PLoS ONE 8:e66539. doi: 10.1371/journal.pone.0066539
36. Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63. doi: 10.1038/nrg2484
37. Watt, J., and Breyer-Brandwijk, M. (1962). The Medicinal and Poisonous Plants of Southern and Eastern Africa, 2nd Edn. Edinburgh; London: E. and S. Livingstone.
38. Xu, L., Wang, Y., Xu, Y., Wang, L., Zhai, L., Zhu, X., et al. (2013). Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing. Plant Sci. 201, 108–114. doi: 10.1016/j.plantsci.2012.11.010
39. Xu, P., Wu, X., Wang, B., Liu, Y., Ehlers, J. D., Close, T. J., et al. (2011). A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. sesqui-pedialis) and comparison with the broader species. PLoS ONE 6:15952. doi: 10.1371/journal.pone.0015952
40. Yamane, K., Lü, N., and Ohnishi, O. (2009). Multiple origins and high genetic diversity of cultivated radish inferred from polymorphism in chloroplast simple sequence repeats. Breed. Sci. 59, 55–65. doi: 10.1270/jsbbs.59.55
41. Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., et al. (2006). WEGO: a web tool for plotting GO annotations. Nucleic. Acids Res. 34, 293–297. doi: 10.1093/nar/gkl031
42. Yu, Y., Yuan, D., Liang, S., Li, X., Wang, X., Lin, Z., et al. (2011). Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. Barbadense. BMC Genomics 12:15. doi: 10.1186/1471-2164-12-15
43. Zhang, H. Y., Wei, L. B., Miao, H. M., Zhang, T. D., and Wang, C. Y. (2012a). Development and validation ofgenic-SSR markers in sesameby RNA-seq. BMC Genomics 13:316. doi: 10.1186/1471-2164-13-316
44. Zhang, J., Liang, S., Duan, J., Wang, J., Chen, S., Cheng, Z., et al. (2012b). De novo assembly and characterisation of the transcriptome during seed development and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 13:90. doi: 10.1186/1471-2164-13-90
45. Zhang, L., Jia, H., Yin, Y., Wu, G., Xia, H., Wang, X., et al. (2013). Transcrip-tome analysis of leaf tissue of Raphanus sativus by RNA sequencing. PLoS ONE 8:e80350. doi: 10.1371/journal.pone.0080350