Genomic limitations to RNA sequencing expression profiling

Plant Journal

Volumn 84, Issue 3, 2015, Pages 491-503

  Hirsch, Cory D ^a   Springer, Nathan M ^a   Hirsch, Candice N ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Arabidopsis; expression profile; maize; RNAseq; structural annotation

Indexed keywords

PLANTS (BOTANY); RNA;

ARABIDOPSIS; EXPRESSION PROFILE; MAIZE; RNASEQ; STRUCTURAL ANNOTATION;

GENES;

ARABIDOPSIS; BRACHYPODIUM; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; MAIZE; MOLECULAR GENETICS; ORYZA; PLANT GENOME; POTATO; PROCEDURES; SEQUENCE ANALYSIS; SOYBEAN; TOMATO;

ARABIDOPSIS; BRACHYPODIUM; GENE EXPRESSION PROFILING; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LYCOPERSICON ESCULENTUM; MOLECULAR SEQUENCE ANNOTATION; ORYZA; SEQUENCE ANALYSIS, RNA; SOLANUM TUBEROSUM; SOYBEANS; ZEA MAYS;

EID: 84944876337     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.13014     Document Type: Article

References (74)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and, Lipman, D.J., (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Anders, S., and, Huber, W., (2010) Differential expression analysis for sequence count data. Genome Biol. 11, R106.
3. Anders, S., Pyl, P.T., and, Huber, W., (2015) HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169.
4. Anderson, J.E., Kantar, M.B., Kono, T.Y., et al. (2014) A roadmap for functional structural variants in the soybean genome. G3: Genes-Genomes-Genetics, 4, 1307-1318.
5. Arabidopsis Genome I (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
6. Beck, A.H., Weng, Z., Witten, D.M., et al. (2010) 3′-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS ONE, 5, e8768.
7. Cao, J., Schneeberger, K., Ossowski, S., et al. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43, 956-963.
8. Chandramohan, R., Wu, P.Y., Phan, J.H., and, Wang, M.D., (2013) Benchmarking RNA-Seq quantification tools. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2013, 647-650.
9. Chen, F., Mackey, A.J., Vermunt, J.K., and, Roos, D.S., (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE, 2, e383.
10. Chen, J., Zeng, B., Zhang, M., Xie, S., Wang, G., Hauck, A., and, Lai, J., (2014) Dynamic transcriptome landscape of maize embryo and endosperm development. Plant Physiol. 166, 252-264.
11. Chia, J.M., Song, C., Bradbury, P.J., et al. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44, 803-807.
12. Davidson, R.M., Gowda, M., Moghe, G., Lin, H., Vaillancourt, B., Shiu, S.H., Jiang, N., and, Robin Buell, C., (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J. 71, 492-502.
13. Du, Z., Zhou, X., Ling, Y., Zhang, Z., and, Su, Z., (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, W64-W70.
14. Emrich, S.J., Li, L., Wen, T.J., Yandeau-Nelson, M.D., Fu, Y., Guo, L., Chou, H.H., Aluru, S., Ashlock, D.A., and, Schnable, P.S., (2007) Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution. Genetics, 175, 429-439.
15. Engstrom, P.G., Steijger, T., Sipos, B., et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat. Methods, 10, 1185-1191.
16. Flagel, L.E., and, Wendel, J.F., (2009) Gene duplication and evolutionary novelty in plants. New Phytol. 183, 557-564.
17. Frazee, A.C., Jaffe, A.E., Langmead, B., and, Leek, J., (2015) Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics, 31, 2778-2784.
18. Freeling, M., (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60, 433-453.
19. Gan, X., Stegle, O., Behr, J., et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature, 477, 419-423.
20. Gao, L., Tu, Z.J., Millett, B.P., and, Bradeen, J.M., (2013) Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions. BMC Genom. 14, 340.
21. Gelli, M., Duo, Y., Konda, A.R., Zhang, C., Holding, D., and, Dweikat, I., (2014) Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. BMC Genom. 15, 179.
22. Gentleman, R.C., Carey, V.J., Bates, D.M., et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80.
23. Gordon, S.P., Priest, H., Des Marais, D.L., et al. (2014) Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J. 79, 361-374.
24. Grant, G.R., Farkas, M.H., Pizarro, A.D., Lahens, N.F., Schug, J., Brunk, B.P., Stoeckert, C.J., Hogenesch, J.B., and, Pierce, E.A., (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics, 27, 2518-2528.
25. Griebel, T., Zacher, B., Ribeca, P., Raineri, E., Lacroix, V., Guigo, R., and, Sammeth, M., (2012) Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res. 40, 10073-10083.
26. Guo, Y., Li, C.I., Ye, F., and, Shyr, Y., (2013) Evaluation of read count based RNAseq analysis methods. BMC Genom. 14 (Suppl 8), S2.
27. Hansey, C.N., Vaillancourt, B., Sekhon, R.S., de Leon, N., Kaeppler, S.M., and, Buell, C.R., (2012) Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PLoS ONE, 7, e33071.
28. Hirsch, C.N., Foerster, J.M., Johnson, J.M., et al. (2014) Insights into the maize pan-genome and pan-transcriptome. Plant Cell, 26, 121-135.
29. Huan, Q., Mao, Z., Zhang, J., Xu, Y., and, Chong, K., (2013) Transcriptome-wide analysis of vernalization reveals conserved and species-specific mechanisms in Brachypodium. J. Integr. Plant Biol. 55, 696-709.
30. International Brachypodium I (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763-768.
31. International Rice Genome Sequencing P (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
32. Kang, C., Darwish, O., Geretz, A., Shahan, R., Alkharouf, N., and, Liu, Z., (2013) Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. Plant Cell, 25, 1960-1978.
33. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and, Salzberg, S.L., (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36.
34. Koenig, D., Jimenez-Gomez, J.M., Kimura, S., et al. (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc. Natl Acad. Sci. USA, 110, E2655-E2662.
35. Langmead, B., and, Salzberg, S.L., (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
36. Lee, J., Mun, S., Meyer, T.J., and, Han, K., (2012) High levels of sequence diversity in the 5′ UTRs of human-specific L1 elements. Comp. Funct. Genomics, 2012, 1-8.
37. Lee, T.H., Tang, H., Wang, X., and, Paterson, A.H., (2013) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res. 41, D1152-D1158.
38. Leisner, C.P., Ming, R., and, Ainsworth, E.A., (2014) Distinct transcriptional profiles of ozone stress in soybean (Glycine max) flowers and pods. BMC Plant Biol. 14, 335.
39. Li, L., Stoeckert, C.J. Jr, and, Roos, D.S., (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189.
40. Li, L., Petsch, K., Shimizu, R., et al. (2013) Mendelian and non-Mendelian regulation of gene expression in maize. PLoS Genet. 9, e1003202.
41. Li, G., Wang, D., Yang, R., et al. (2014) Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing. Proc. Natl Acad. Sci. USA, 111, 7582-7587.
42. Lindner, R., and, Friedel, C.C., (2012) A comprehensive evaluation of alignment algorithms in the context of RNA-seq. PLoS ONE, 7, e52403.
43. Makarevitch, I., Waters, A.J., West, P.T., Stitzer, M., Hirsch, C.N., Ross-Ibarra, J., and, Springer, N.M., (2015) Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet. 11, e1004915.
44. Martin, M., (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10-12.
45. Martin, J.A., Johnson, N.V., Gross, S.M., et al. (2014) A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci. Rep. 4, 4519.
46. Massa, A.N., Childs, K.L., Lin, H., Bryan, G.J., Giuliano, G., and, Buell, C.R., (2011) The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. PLoS ONE, 6, e26801.
47. Moll, P., Ante, M., Seitz, A., and, Reda, T., (2014) QuantSeq 3′ mRNA sequencing for RNA quantification. Nat. Methods, 11, i-iii.
48. Nguyen, C.V., Vrebalov, J.T., Gapper, N.E., Zheng, Y., Zhong, S., Fei, Z., and, Giovannoni, J.J., (2014) Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. Plant Cell, 26, 585-601.
49. Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlen, M., and, Nielsen, J., (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 40, 10084-10097.
50. Paschold, A., Jia, Y., Marcon, C., et al. (2012) Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genome Res. 22, 2445-2454.
51. Potato Genome Sequencing C, Xu, X., Pan, S., et al. (2011) Genome sequence and analysis of the tuber crop potato. Nature, 475, 189-195.
52. Quinlan, A.R., and, Hall, I.M., (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
53. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
54. Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C.E., Socci, N.D., and, Betel, D., (2013) Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol. 14, R95.
55. Schatz, M.C., Maron, L.G., Stein, J.C., et al. (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 15, 506.
56. Schmutz, J., Cannon, S.B., Schlueter, J., et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature, 463, 178-183.
57. Schnable, P.S., Ware, D., Fulton, R.S., et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326, 1112-1115.
58. Schnable, J.C., Springer, N.M., and, Freeling, M., (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl Acad. Sci. USA, 108, 4069-4074.
59. Schnable, J.C., Freeling, M., and, Lyons, E., (2012) Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol. Evol. 4, 265-277.
60. Sekhon, R.S., Hirsch, C.N., Childs, K.L., Breitzman, M.W., Kell, P., Duvick, S., Spalding, E.P., Buell, C.R., de Leon, N., and, Kaeppler, S.M., (2014) Phenotypic and transcriptional analysis of divergently selected maize populations reveals the role of developmental timing in seed size determination. Plant Physiol. 165, 658-669.
61. Severin, A.J., Woody, J.L., Bolon, Y.T., et al. (2010) RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 10, 160.
62. Seyednasrollah, F., Laiho, A., and, Elo, L.L., (2015) Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform. 16, 59-70.
63. Song, G., Guo, Z., Liu, Z., et al. (2013) Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids. BMC Plant Biol. 13, 221.
64. Stelpflug, S., Sekhon, R.S., Vaillancourt, B., Hirsch, C.N., Buell, C.R., de Leon, N., and, Kaeppler, S., (2015) An expanded maize gene expression atlas based on RNA-sequenceing and its use to explore root development. The Plant Genome, doi: 10.3835/plantgenome2015.3804.0025.
65. Tao, P., Peng, L., Huang, X., and, Wang, J., (2012) Comparative analysis of the variable 3′ UTR and gene expression of the KIN and KIN-homologous LEA genes in Capsella bursa-pastoris. Plant Cell Rep. 31, 1769-1777.
66. Tomato Genome C (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635-641.
67. Trapnell, C., Pachter, L., and, Salzberg, S.L., (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
68. Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and, Pachter, L., (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515.
69. Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and, Pachter, L., (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578.
70. Wakasa, Y., Oono, Y., Yazawa, T., Hayashi, S., Ozawa, K., Handa, H., Matsumoto, T., and, Takaiwa, F., (2014) RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions. BMC Plant Biol. 14, 101.
71. Wang, Z., Gerstein, M., and, Snyder, M., (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63.
72. Yazawa, T., Kawahigashi, H., Matsumoto, T., and, Mizuno, H., (2013) Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PLoS ONE, 8, e62460.
73. Zhai, R., Feng, Y., Wang, H., et al. (2013) Transcriptome analysis of rice root heterosis by RNA-Seq. BMC Genom. 14, 19.
74. Zhang, Z.H., Jhaveri, D.J., Marshall, V.M., et al. (2014) A comparative study of techniques for differential expression analysis on RNA-Seq data. PLoS ONE, 9, e103207.