RNA-seq assembly - Are we there yet?

Frontiers in Plant Science

Volumn 3, Issue SEP, 2012, Pages

  Schliesky, Simon ^a   Gowik, Udo ^a   Weber, Andreas P M ^a   Bräutigam, Andrea ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Assembly; Next generation sequencing; NGS; Plant; RNA seq; Transcriptome

Indexed keywords

EID: 84873130027     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2012.00220     Document Type: Review

References (74)

1. Alagna, F., D'Agostino, N., Torchia, L., Servili, M., Rao, R., Pietrella, M., Giuliano, G., Chiusano, M. L., Baldoni, L., and Perrotta, G. (2009). Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 10, 399. doi:10.1186/1471-2164-10-399
2. Angeloni, F., Wagemaker, C. A. M., Jetten, M. S. M., Den Camp, H., Janssen-Megens, E. M., Francoijs, K. J., Stunnenberg, H. G., and Ouborg, N. J. (2011). De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques. Mol. Ecol. Resour. 11, 662-674.
3. Aury, J.-M., Cruaud, C., Barbe, V., Rogier, O., Mangenot, S., Samson, G., Poulain, J., Anthouard, V., Scarpelli, C., Artiguenave, F., and Wincker, P. (2008). High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9, 603. doi:10.1186/1471-2164-9-603
4. Barakat, A., Diloreto, D. S., Zhang, Y., Smith, C., Baier, K., Powell, W. A., Wheeler, N., Sederoff, R., and Carlson, J. E. (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. doi:10.1186/1471-2229-9-51
5. Barrero, R. A., Chapman, B., Yang, Y. F., Moolhuijzen, P., Keeble-Gagnere, G., Zhang, N., Tang, Q., Bellgard, M. I., and Qiu, D. Y. (2011). De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes. BMC Genomics 12, 600. doi:10.1186/1471-2164-12-600
6. Bergero, R., and Charlesworth, D. (2011). Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system. Curr. Biol. 21, 1470-1474.
7. Blavet, N., Charif, D., Oger-Desfeux, C., Marais, G. A. B., and Widmer, A. (2011). Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database. BMC Genomics 12, 376. doi:10.1186/1471-2164-12-376
8. Bleeker, P. M., Spyropoulou, E. A., Diergaarde, P. J., Volpin, H., De Both, M. T. J., Zerbe, P., Bohlmann, J., Falara, V., Matsuba, Y., Pichersky, E., Haring, M. A., and Schuurink, R. C. (2011). RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes. Plant Mol. Biol. 77, 323-336.
9. Bräutigam, A., Kajala, K., Wullenweber, J., Sommer, M., Gagneul, D., Weber, K. L., Carr, K. M., Gowik, U., Mass, J., Lercher, M. J., Westhoff, P., Hibberd, J. M., and Weber, A. P. M. (2011a). An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. Plant Physiol. 155, 142-156.
10. Bräutigam, A., Mullick, T., Schliesky, S., and Weber, A. P. M. (2011b). Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species. J. Exp. Bot. 62, 3093-3102.
11. Bräutigam, A., Shrestha, R. P., Whitten, D., Wilkerson, C. G., Carr, K. M., Froehlich, J. E., and Weber, A. P. M. (2008). Comparison of the use of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. J. Biotechnol. 136, 44-53.
12. Cantu, D., Pearce, S., Distelfeld, A., Christiansen, M., Uauy, C., Akhunov, E., Fahima, T., and Dubcovsky, J. (2011). Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence. BMC Genomics 12, 492. doi: 10.1186/1471-2164-12-492
13. Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A. J., Muller, W. E. G., Wetter, T., and Suhai, S. (2004). Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147-1159.
14. Chibalina, M. V., and Filatov, D. A. (2011). Plant Y chromosome degeneration is retarded by haploid purifying selection. Curr. Biol. 21, 1475-1479.
15. Christodoulou, D. C., Gorham, J. M., Herman, D. S., and Seidman, J. G. (2001). Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr. Protoc. Mol. Biol. 94, 4.12.1-4.12.11.
16. Czechowski, T., Bari, R. P., Stitt, M., Scheible, W. R., and Udvardi, M. K. (2004). Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root-and shoot-specific genes. Plant J. 38, 366-379.
17. Dai, N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G. F., Diber, A., Pollock, S., Karchi, H., Yeselson, Y., Petreikov, M., Shen, S., Sahar, U., Hovav, R., Lewinsohn, E., Tadmor, Y., Granot, D., Ophir, R., Sherman, A., Fei, Z. J., Giovannoni, J., Burger, Y., Katzir, N., and Schaffer, A. A. (2011). Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol. Biol. 76, 1-18.
18. Dassanayake, M., Haas, J. S., Bohnert, H. J., and Cheeseman, J. M. (2009). Shedding light on an extremophile lifestyle through transcriptomics. New Phytol. 183, 764-775.
19. Der, J., Barker, M., Wickett, N., Depamphilis, C., and Wolf, P. (2011). De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 12, 99. doi: 10.1186/1471-2164-12-99
20. Desgagne-Penix, I., Farrow, S. C., Cram, D., Nowak, J., and Facchini, P. J. (2012). Integration of deep transcript and targeted metabolite profiles for eight cultivars of opium poppy. Plant Mol. Biol. 79, 295-313.
21. Edwards, C. E., Parchman, T. L., and Weekley, C. W. (2012). Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, florida endemic plant. DNA Res. 19, 1-9.
22. Emrich, S. J., Barbazuk, W. B., Li, L., and Schnable, P. S. (2007). Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res. 17, 69-73.
23. Flicek, P., and Birney, E. (2009). Sense from sequence reads: methods for alignment and assembly. Nat. Methods 6, S6-S12.
24. Fluhr, R., Moses, P., Morelli, G., Coruzzi, G., and Chua, N. H. (1986). Expression dynamics of the pea rbcS multigene family and organ distribution of the transcripts. EMBO J. 5, 2063-2071.
25. Franssen, S.U., Shrestha, R.P., Brautigam, A., Bornberg-Bauer, E., and Weber, A.P.M. (2011). Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics 12, 227. doi:10.1186/1471-2164-12-227
26. Furumoto, T., Yamaguchi, T., Ohshima-Ichie, Y., Nakamura, M., Tsuchida-Iwata, Y., Shimamura, M., Ohnishi, J., Hata, S., Gowik, U., Westhoff, P., Brautigam, A., Weber, A. P. M., and Izui, K. (2011). A plastidial sodium-dependent pyruvate transporter. Nature 476, 472-475.
27. Gahlan, P., Singh, H. R., Shankar, R., Sharma, N., Kumari, A., Chawla, V., Ahuja, P. S., and Kumar, S. (2012). De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genomics 13, 126. doi:10.1186/1471-2164-13-126
28. Garg, R., Patel, R. K., Jhanwar, S., Priya, P., Bhattacharjee, A., Yadav, G., Bhatia, S., Chattopadhyay, D., Tyagi, A. K., and Jain, M. (2011). Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol. 156, 1661-1678.
29. Glenn, T. C. (2011). Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11, 759-769.
30. Gowik, U., Brautigam, A., Weber, K. L., Weber, A. P. M., and Westhoff, P. (2011). Evolution of C4 Photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? Plant Cell 23, 2087-2105.
31. Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q. D., Chen, Z. H., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., Di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., and Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652.
32. Gruenheit, N., Deusch, O., Esser, C., Becker, M., Voelckel, C., and Lockhart, P. (2012). Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics 13, 92. doi: 10.1186/1471-2164-13-92
33. Guo, S. G., Zheng, Y., Joung, J. G., Liu, S. Q., Zhang, Z. H., Crasta, O. R., Sobral, B. W., Xu, Y., Huang, S. W., and Fei, Z. J. (2010). Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11, 384. doi:10.1186/1471-2164-11-384
34. Hao, D. C., Ge, G. B., Xiao, P. G., Zhang, Y. Y., and Yang, L. (2011). The first insight into the tissue specific taxus transcriptome via illumina second generation sequencing. PLoS ONE 6, e21220. doi:10.1371/journal.pone.0021220
35. Hao, D. C., Ma, P., Mu, J., Chen, S. L., Xiao, P. G., Peng, Y., Huo, L., Xu, L. J., and Sun, C. (2012). De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. Sci. China Life Sci. 55, 452-466.
36. Hiremath, P. J., Farmer, A., Cannon, S. B., Woodward, J., Kudapa, H., Tuteja, R., Kumar, A., Bhanuprakash, A., Mulaosmanovic, B., Gujaria, N., Krishnamurthy, L., Gaur, P. M., Kavikishor, P. B., Shah, T., Srinivasan, R., Lohse, M., Xiao, Y. L., Town, C. D., Cook, D. R., May, G. D., and Varshney, R. K. (2011). Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol. J. 9, 922-931.
37. Huang, J., Lu, X., Yan, H., Chen, S., Zhang, W., Huang, R., and Zheng, Y. (2012). Transcriptome characterization and sequencing-based identification of salt-responsive genes in Millettia pinnata, a semi-mangrove plant. DNA Res. 19, 195-207.
38. Huang, X. Q., and Madan, A. (1999). CAP3: a DNA sequence assembly program. Genome Res. 9, 868-877.
39. Hyun, T. K., Rim, Y., Jang, H. J., Kim, C. H., Park, J., Kumar, R., Lee, S., Kim, B. C., Bhak, J., Binh, Q., Kim, S. W., Lee, S. Y., and Kim, J. Y. (2012). De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis. Plant Mol. Biol. 79, 413-427.
40. Ibarra-Laclette, E., Albert, V. A., Perez-Torres, C. A., Zamudio-Hernandez, F., Ortega-Estrada, M. D., Herrera-Estrella, A., and Herrera-Estrella, L. (2011). Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome. BMC Plant Biol. 11, 101. doi:10.1186/1471-2229-11-101
41. Kalavacharla, V., Liu, Z., Meyers, B., Thimmapuram, J., and Melmaiee, K. (2011). Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biol. 11, 135. doi: 10.1186/1471-2229-11-135
42. Kaur, S., Cogan, N. O. I., Pembleton, L. W., Shinozuka, M., Savin, K. W., Materne, M., and Forster, J. W. (2011). Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics 12, 265. doi:10.1186/1471-2164-12-265
43. Kent, W. J. (2002). BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664.
44. King, A. J., Li, Y., and Graham, I. A. (2011). Profiling the developing Jatropha curcas L. Seed transcriptome by pyrosequencing. Bioenergy Res. 4, 211-221. doi:10.1007/s12155-011-9114-x
45. Krishnan, N. M., Pattnaik, S., Deepak, S. A., Hariharan, A. K., Gaur, P., Chaudhary, R., Jain, P., Vaidyanathan, S., Krishna, P. G. B., and Panda, B. (2011). De novo sequencing and assembly of Azadirachta indica fruit transcriptome. Curr. Sci. 101, 1553-1561.
46. Li, P. H., Ponnala, L., Gandotra, N., Wang, L., Si, Y. Q., Tausta, S. L., Kebrom, T. H., Provart, N., Patel, R., Myers, C. R., Reidel, E. J., Turgeon, R., Liu, P., Sun, Q., Nelson, T., and Brutnell, T. P. (2011). The developmental dynamics of the maize leaf transcriptome. Nat. Genet. 42, 1060-1067.
47. Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., and Usadel, B. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 40, W622-W627.
48. Lu, F.-H., Cho, M.-C., and Park, Y.-J. (2012). Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Mol. Biol. Rep. 39, 3327-3335.
49. McKain, M. R., Wickett, N., Zhang, Y., Ayyampalayam, S., McCombie, W. R., Chase, M. W., Pires, J. C., Depamphilis, C. W., and Leebens-Mack, J. (2012). Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in agavoideae (Asparagaceae). Am. J. Bot. 99, 397-406.
50. Metzker, M. L. (2010). Applications of next-generation sequencing sequencing technologies-the next generation. Nat. Rev. Genet. 11, 31-46.
51. Meyer, E., Logan, T. L., and Juenger, T. E. (2012). Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research. Plant J. 70, 879-890.
52. Mizrachi, E., Hefer, C. A., Ranik, M., Joubert, F., and Myburg, A. A. (2010). De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by illumina mRNA-seq. BMC Genomics 11, 681. doi:10.1186/1471-2164-11-681
53. Mutasa-Göttgens, E. S., Joshi, A., Holmes, H. F., Hedden, P., and Gottgens, B. (2012). A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. BMC Genomics 13, 99. doi:10.1186/1471-2164-13-99
54. Novaes, E., Drost, D. R., Farmerie, W. G., Pappas, G. J., Grattapaglia, D., Sederoff, R. R., and Kirst, M. (2008). High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9, 312. doi:10.1186/1471-2164-9-312
55. Pertea, G., Huang, X., Liang, F., Antonescu, V., Sultana, R., Karamycheva, S., Lee, Y. H., White, J., Cheung, F., Parvizi, B., Tsai, J., and Quackenbush, J. (2003). TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651-652.
56. Pevzner, P. A., Tang, H. X., and Waterman, M. S. (2001). An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. U.S.A. 98, 9748-9753.
57. Pont, C., Murat, F., Confolent, C., Balzergue, S., and Salse, J. (2011). RNA-seq in grain unveils fate of neo-and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol. 12, R119.
58. Riggins, C. W., Peng, Y. H., Stewart, C. N., and Tranel, P. J. (2010). Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Manag. Sci. 66, 1042-1052.
59. Shi, C. Y., Yang, H., Wei, C. L., Yu, O., Zhang, Z. Z., Jiang, C. J., Sun, J., Li, Y. Y., Chen, Q., Xia, T., and Wan, X. C. (2011). Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12, 131. doi:10.1186/1471-2164-12-131
60. Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., and Birol, I. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117-1123.
61. Sommer, M., Bräutigam, A., and Weber, A. P. M. (2012). The dicotyledonous NAD malic enzyme C4 plant Cleome gynandra displays age-dependent plasticity of C4 decarboxylation biochemistry. Plant Biol. 14, 621-629.
62. Su, C. L., Chao, Y. T., Chang, Y. C. A., Chen, W. C., Chen, C. Y., Lee, A. Y., Hwa, K. T., and Shih, M. C. (2011). De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. Plant Cell Physiol. 52, 1501-1514.
63. Sun, H., Paulin, L., Alatalo, E., and Asiegbu, F. O. (2011). Response of living tissues of Pinus sylvestris to the saprotrophic biocontrol fungus Phlebiopsis gigantea. Tree Physiol. 31, 438-451.
64. Swarbreck, S. M., Sudderth, E. A., St. Clair, S. B., Salve, R., Castanha, C., Torn, M. S., Ackerly, D. D., and Andersen, G. L. (2011). Linking leaf transcript levels to whole plant analyses provides mechanistic insights to the impact of warming and altered water availability in an annual grass. Glob. Change Biol. 17, 1577-1594.
65. Tang, Q., Ma, X. J., Mo, C. M., Wilson, I. W., Song, C., Zhao, H., Yang, Y. F., Fu, W., and Qiu, D. Y. (2011). An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics 12, 343. doi:10.1186/1471-2164-12-343
66. Troncoso-Ponce, M. A., Kilaru, A., Cao, X., Durrett, T. P., Fan, J. L., Jensen, J. K., Thrower, N. A., Pauly, M., Wilkerson, C., and Ohlrogge, J. B. (2011). Comparative deep transcriptional profiling of four developing oilseeds. Plant J. 68, 1014-1027.
67. Vega-Arreguin, J. C., Ibarra-Laclette, E., Jimenez-Moraila, B., Martinez, O., Vielle-Calzada, J. P., Herrera-Estrella, L., and Herrera-Estrella, A. (2009). Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing. BMC Genomics 10, 299. doi:10.1186/1471-2164-10-299
68. Villar, E., Klopp, C., Noirot, C., Novaes, E., Kirst, M., Plomion, C., and Gion, J. M. (2011). RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus. BMC Genomics 12, 538. doi:10.1186/1471-2164-12-538
69. Wang, W., Wang, Y. J., Zhang, Q., Qi, Y., and Guo, D. J. (2009). Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics 10, 465. doi:10.1186/1471-2164-10-465
70. Weber, A. P. M., Weber, K. L., Carr, K., Wilkerson, C., and Ohlrogge, J. B. (2007). Sampling the arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol. 144, 32-42.
71. Wong, M., Cannon, C., and Wickneswari, R. (2011). Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing. BMC Genomics 12, 342. doi:10.1186/1471-2164-12-342
72. Xia, Z. H., Xu, H. M., Zhai, J. L., Li, D. J., Luo, H. L., He, C. Z., and Huang, X. (2011). RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol. Biol. 77, 299-308.
73. Zerbino, D. R., and Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829.
74. Zhang, J. A., Liang, S., Duan, J. L., Wang, J., Chen, S. L., Cheng, Z. S., Zhang, Q., Liang, X. Q., and Li, Y. R. (2012). 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