Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Duan, Jialei ^a,b   Xia, Chuan ^a   Zhao, Guangyao ^a   Jia, Jizeng ^a   Kong, Xiuying ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENETIC TRANSCRIPTION; INTERMETHOD COMPARISON; NONHUMAN; PERFORMANCE; PROTEIN ASSEMBLY; RNA SEQUENCE; WHEAT;

COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; MOLECULAR SEQUENCE DATA; RNA, PLANT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME; TRITICUM;

TRITICUM AESTIVUM;

EID: 84864930888     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-392     Document Type: Article

References (28)

1. Feng C, Chen M, Xu CJ, Bai L, Yin XR, Li X, Allan AC, Ferguson IB, Chen KS. Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. BMC Genomics 2012, 13:19. 10.1186/1471-2164-13-19, 3398333, 22244270.
2. Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 2010, 20(5):646-654. 10.1101/gr.100677.109, 2860166, 20305017.
3. Ness RW, Siol M, Barrett SC. De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. BMC Genomics 2011, 12:298. 10.1186/1471-2164-12-298, 3128866, 21649902.
4. Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ. Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol J 2009, 7(4):347-354. 10.1111/j.1467-7652.2009.00401.x, 19386042.
5. Trick M, Adamski NM, Mugford SG, Jiang CC, Febrer M, Uauy C. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol 2012, 12:14. 10.1186/1471-2229-12-14, 3296661, 22280551.
6. Pellny TK, Lovegrove A, Freeman J, Tosi P, Love CG, Knox JP, Shewry PR, Mitchell RA. Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome. Plant Physiol 2012, 158(2):612-627. 10.1104/pp.111.189191, 3271754, 22123899.
7. Pont C, Murat F, Confolent C, Balzergue S, Salse J. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol 2011, 12(12):R119. 10.1186/gb-2011-12-12-r119, 3334614, 22136458.
8. Li A, Zhang R, Pan L, Tang L, Zhao G, Zhu M, Chu J, Sun X, Wei B, Zhang X, et al. Transcriptome analysis of H2O2-treated wheat seedlings reveals a H2O2-responsive fatty acid desaturase gene participating in powdery mildew resistance. PLoS One 2011, 6(12):e28810. 10.1371/journal.pone.0028810, 3236209, 22174904.
9. Zhang J, Liang S, Duan J, Wang J, Chen S, Cheng Z, Zhang Q, Liang X, Li Y. De novoassembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 2012, 13(1):90. 10.1186/1471-2164-13-90, 3350410, 22409576.
10. Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012, 28(8):1086-1092. 10.1093/bioinformatics/bts094, 3324515, 22368243.
11. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652. 10.1038/nbt.1883, 21572440.
12. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, et al. De novo assembly and analysis of RNA-seq data. Nat Methods 2010, 7(11):909-912. 10.1038/nmeth.1517, 20935650.
13. Cantu D, Pearce SP, Distelfeld A, Christiansen MW, Uauy C, Akhunov E, Fahima T, Dubcovsky J. Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence. BMC Genomics 2011, 12:492. 10.1186/1471-2164-12-492, 3209470, 21981858.
14. Surget-Groba Y, Montoya-Burgos JI. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 2010, 20(10):1432-1440. 10.1101/gr.103846.109, 2945192, 20693479.
15. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658-1659. 10.1093/bioinformatics/btl158, 16731699.
16. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, et al. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 2003, 19(5):651-652. 10.1093/bioinformatics/btg034, 12651724.
17. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011, 27(4):578-579. 10.1093/bioinformatics/btq683, 21149342.
18. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
19. Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol 2009, 150(3):1135-1146. 10.1104/pp.109.138214, 2705016, 19448038.
20. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595. 10.1093/bioinformatics/btp698, 2828108, 20080505.
21. Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, et al. De novo transcriptome assembly with ABySS. Bioinformatics 2009, 25(21):2872-2877. 10.1093/bioinformatics/btp367, 19528083.
22. Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP. The TIGR Plant Transcript Assemblies database. Nucleic Acids Res 2007, 35(Database issue):D846-D851. 1669722, 17088284.
23. Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 2008, 36(Database issue):D959-D965. 2238959, 18063570.
24. Cox MP, Peterson DA, Biggs PJ. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010, 11:485. 10.1186/1471-2105-11-485, 2956736, 20875133.
25. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families database. Nucleic Acids Res 2012, 40(Database issue):D290-301. 3245129, 22127870.
26. Birney E, Clamp M, Durbin R. Genewise and genomewise. Genome Res 2004, 14(5):988-995. 10.1101/gr.1865504, 479130, 15123596.
27. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
28. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 1000 Genome Project Data Processing Subgroup: the sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.