De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Mizrachi, Eshchar ^a   Hefer, Charles A ^a   Ranik, Martin ^a   Joubert, Fourie ^a   Myburg, Alexander A ^a  

^a UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PLANT RNA; TRANSCRIPTOME; VEGETABLE PROTEIN;

ARTICLE; BIOMASS PRODUCTION; CONTIG MAPPING; CONTROLLED STUDY; EUCALYPTUS; EUCALYPTUS GRANDIS; EUCALYPTUS UROPHYLLA; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC DATABASE; GENETIC SCREENING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; MOLECULAR CLONING; NONHUMAN; PLANT DEVELOPMENT; PLANT GENE; PLANT GROWTH; PLANT TISSUE; PROTEIN ASSEMBLY; PROTEIN DATABASE; RNA SEQUENCE; TECHNOLOGY; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT LEAF; REPRODUCIBILITY; SEQUENCE ANALYSIS; TREE; XYLEM;

EUCALYPTUS; EUCALYPTUS GRANDIS; EUCALYPTUS UROPHYLLA;

BASE SEQUENCE; DATABASES, GENETIC; EUCALYPTUS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MOLECULAR SEQUENCE ANNOTATION; PLANT LEAVES; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TREES; XYLEM;

EID: 78649501801     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-681     Document Type: Article

References (54)

1. Cloonan N, Forrest ARR, Kolle G, Gardiner BBA, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 2008, 5(7):613-619. 10.1038/nmeth.1223, 18516046.
2. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
3. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320(5881):1344-1349. 10.1126/science.1158441, 2951732, 18451266.
4. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009, 6(5):377-382. 10.1038/nmeth.1315, 19349980.
5. Wilhelm BT, Landry JR. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 2009, 48(3):249-257. 10.1016/j.ymeth.2009.03.016, 19336255.
6. Farrer RA, Kemen E, Jones JDG, Studholme DJ. De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads: RESEARCH LETTER. FEMS Microbiol Lett 2009, 291(1):103-111. 10.1111/j.1574-6968.2008.01441.x, 19077061.
7. Hernandez D, François P, Farinelli L, Østerås M, Schrenzel J. De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Res 2008, 18(5):802-809. 10.1101/gr.072033.107, 2336802, 18332092.
8. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009, 6(4):291-295. 10.1038/nmeth.1311, 2664327, 19287394.
9. DiGuistini S, Liao N, Platt D, Robertson G, Seidel M, Chan S, Docking TR, Birol I, Holt R, Hirst M. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology 2009, 10(9). 10.1186/gb-2009-10-9-r94, 2768983, 19747388.
10. Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC. De novo Assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet 2010, (6):e1000891. 10.1371/journal.pgen.1000891, 2851567, 20386741.
11. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010, 463(7279):311-317. 10.1038/nature08696, 20010809.
12. Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM. Shedding light on an extremophile lifestyle through transcriptomics. New Phytol 2009, 183(3):764-775. 10.1111/j.1469-8137.2009.02913.x, 19549131.
13. Hahn DA, Ragland GJ, Shoemaker DD, Denlinger DL. Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. BMC Genomics 2009, 10(234).
14. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10(219). 2689275, 19435504.
15. Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9(312). 2483731, 18590545.
16. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008, 17(7):1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
17. 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.
18. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 2009, 26(12):2731-2744. 10.1093/molbev/msp188, 19706727.
19. Wu T, Qin Z, Zhou X, Feng Z, Du Y. Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol 2010, 167(11):905-913. 10.1016/j.jplph.2010.02.004, 20303197.
20. Eldridge K, Davidson J, Harwood C, van Wyk G. Eucalypt domestication and breeding 1993, Oxford: Clarendon Press.
21. FAO Forests and Energy. FAO Forestry Paper No 2008, 154. (Rome):(ISBN 978-992-975-105985-105982), FAO.
22. Hinchee M, Rottmann W, Mullinax L, Zhang C, Chang S, Cunningham M, Pearson L, Nehra N. Short-rotation woody crops for bioenergy and biofuels applications. In Vitro Cell Dev Biol - Plant 2009, 45(6):619-629. 10.1007/s11627-009-9235-5, 2778772, 19936031.
23. Myburg AA, Grattapaglia D, Tuskan GA, Schmutz J, Barry K, Bristow J, . The Eucalyptus Genome Network Sequencing the Eucalyptus genome: Genomic resources for renewable energy and fiber production. Plant & Animal Genome XVI Conference: January 12-16, 2008; San Diego, CA 2008, The Eucalyptus Genome Network.
24. Hibino T. "Post-genomics" research in Eucalyptus in the near future. Plant Biotechnol 2009, 26(1):109-113.
25. Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, Feldblyum T, Nierman W, Benito MI, Lin X, et al. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408(6814):796-815. 10.1038/35048692, 11130711.
26. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam M, Ralph S, Rombauts S, Salamov A, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313(5793):1596-1604. 10.1126/science.1128691, 16973872.
27. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007, 449(7161):463-467. 10.1038/nature06148, 17721507.
28. Sjödin A, Street NR, Sandberg G, Gustafsson P, Jansson S. The Populus Genome Integrative Explorer (PopGenIE): A new resource for exploring the Populus genome. New Phytol 2009, 182(4):1013-1025.
29. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829. 10.1101/gr.074492.107, 2336801, 18349386.
30. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268(1):78-94. 10.1006/jmbi.1997.0951, 9149143.
31. Pinheiro M, Afreixo V, Moura G, Freitas A, Santos MAS, Oliveira JL. Statistical, computational and visualization methodologies to unveil gene primary structure features. Methods Inf Med 2006, 45(2):163-168.
32. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
33. Rengel D, Clemente HS, Servant F, Ladouce N, Paux E, Wincker P, Couloux A, Sivadon P, Grima-Pettenati J. A new genomic resource dedicated to wood formation in Eucalyptus. BMC Plant Biol 2009, 9(36). 2670833, 19327132.
34. Geisler-Lee J, Geisler M, Coutinho PM, Segerman B, Nishikubo N, Takahashi J, Aspeborg H, Djerbi S, Master E, Andersson-Gunneras S, et al. Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Plant Physiol 2006, 140(3):946-962. 10.1104/pp.105.072652, 1400564, 16415215.
35. Pavy N, Laroche J, Bousquet J, Mackay J. Large-scale statistical analysis of secondary xylem ESTs in pine. Plant Mol Biol 2005, 57(2):203-224. 10.1007/s11103-004-6969-7, 15821878.
36. Hale MC, McCormick CR, Jackson JR, DeWoody JA. 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 2009, 10(203). 2688523, 19402907.
37. Kristiansson E, Asker N, Förlin L, Joakim DGJ. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics 2009, 10(345).
38. Schwarz D, Robertson HM, Feder JL, Varala K, Hudson ME, Ragland GJ, Hahn DA, Berlocher SH. Sympatric ecological speciation meets pyrosequencing: Sampling the transcriptome of the apple maggot Rhagoletis pomonella. BMC Genomics 2009, 10(633). 2807884, 20035631.
39. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 2007, 144(1):32-42. 10.1104/pp.107.096677, 1913805, 17351049.
40. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10(3).
41. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515. 10.1038/nbt.1621, 20436464.
42. Ko JH, Beers EP, Han KH. Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana. Mol Genet Genomics 2006, 276(6):517-531. 10.1007/s00438-006-0157-1, 16969662.
43. Dharmawardhana P, Brunner AM, Strauss SH. Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. BMC Genomics 2010, 11(1):150. 10.1186/1471-2164-11-150, 2846914, 20199690.
44. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 2007, 104(49):19428-19433. 10.1073/pnas.0709013104, 2148306, 18040051.
45. Dinger ME, Pang KC, Mercer TR, Mattick JS. Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLoS Comput Biol 2008, 4(11):1-5.
46. Pavy N, Boyle B, Nelson C, Paule C, Giguère I, Caron S, Parsons LS, Dallaire N, Bedon F, Bérubé H, et al. Identification of conserved core xylem gene sets: Conifer cDNA microarray development, transcript profiling and computational analyses. New Phytol 2008, 180(4):766-786. 10.1111/j.1469-8137.2008.02615.x, 18811621.
47. Betancur L, Singh B, Rapp RA, Wendel JF, Marks MD, Roberts AW, Haigler CH. Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber. J Integr Plant Biol 2010, 52(2):205-220. 10.1111/j.1744-7909.2010.00934.x, 20377682.
48. Ranik M, Myburg AA. Six new cellulose synthase genes from Eucalyptus are associated with primary and secondary cell wall biosynthesis. Tree Physiol 2006, 26(5):545-556.
49. Chang S, Puryear J, Cairney J. A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Report 1993, 11(2):113-116.
50. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133(3):523-536. 10.1016/j.cell.2008.03.029, 2723732, 18423832.
51. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754. 10.1093/bioinformatics/btp324, 2705234, 19451168.
52. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
53. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003, 19(SUPPL 2):ii215-ii225.
54. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676. 10.1093/bioinformatics/bti610, 16081474.