Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber APM (2011)
BMC Genomics 12(1): 227.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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URN
urn:nbn:de:0070-pub-29151603
Autor*in
Franssen, Susanne U.; Shrestha, Roshan P.; Bräutigam, AndreaUniBi ; Bornberg-Bauer, Erich; Weber, Andreas P. M.
Einrichtung
Fakultät für Biologie > Computational Biology
Abstract / Bemerkung
Background: The garden pea, Pisum sativum, is among the best-investigated legume plants and of significant agro-commercial relevance. Pisum sativum has a large and complex genome and accordingly few comprehensive genomic resources exist. Results: We analyzed the pea transcriptome at the highest possible amount of accuracy by current technology. We used next generation sequencing with the Roche/454 platform and evaluated and compared a variety of approaches, including diverse tissue libraries, normalization, alternative sequencing technologies, saturation estimation and diverse assembly strategies. We generated libraries from flowers, leaves, cotyledons, epi- and hypocotyl, and etiolated and light treated etiolated seedlings, comprising a total of 450 megabases. Libraries were assembled into 324,428 unigenes in a first pass assembly. A second pass assembly reduced the amount to 81,449 unigenes but caused a significant number of chimeras. Analyses of the assemblies identified the assembly step as a major possibility for improvement. By recording frequencies of Arabidopsis orthologs hit by randomly drawn reads and fitting parameters of the saturation curve we concluded that sequencing was exhaustive. For leaf libraries we found normalization allows partial recovery of expression strength aside the desired effect of increased coverage. Based on theoretical and biological considerations we concluded that the sequence reads in the database tagged the vast majority of transcripts in the aerial tissues. A pathway representation analysis showed the merits of sampling multiple aerial tissues to increase the number of tagged genes. All results have been made available as a fully annotated database in fasta format. Conclusions: We conclude that the approach taken resulted in a high quality - dataset which serves well as a first comprehensive reference set for the model legume pea. We suggest future deep sequencing transcriptome projects of species lacking a genomics backbone will need to concentrate mainly on resolving the issues of redundancy and paralogy during transcriptome assembly.
Erscheinungsjahr
2011
Zeitschriftentitel
BMC Genomics
Band
12
Ausgabe
1
Art.-Nr.
227
ISSN
1471-2164
Page URI
https://pub.uni-bielefeld.de/record/2915160

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Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber APM. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics. 2011;12(1): 227.
Franssen, S. U., Shrestha, R. P., Bräutigam, A., Bornberg-Bauer, E., & Weber, A. P. M. (2011). Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics, 12(1), 227. doi:10.1186/1471-2164-12-227
Franssen, Susanne U., Shrestha, Roshan P., Bräutigam, Andrea, Bornberg-Bauer, Erich, and Weber, Andreas P. M. 2011. “Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing”. BMC Genomics 12 (1): 227.
Franssen, S. U., Shrestha, R. P., Bräutigam, 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.
Franssen, S.U., et al., 2011. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics, 12(1): 227.
S.U. Franssen, et al., “Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing”, BMC Genomics, vol. 12, 2011, : 227.
Franssen, S.U., Shrestha, R.P., Bräutigam, A., Bornberg-Bauer, E., Weber, A.P.M.: Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics. 12, : 227 (2011).
Franssen, Susanne U., Shrestha, Roshan P., Bräutigam, Andrea, Bornberg-Bauer, Erich, and Weber, Andreas P. M. “Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing”. BMC Genomics 12.1 (2011): 227.
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Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes.
Brautigam A, Shrestha RP, Whitten D, Wilkerson CG, Carr KM, Froehlich JE, Weber AP., J. Biotechnol. 136(1-2), 2008
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Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
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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
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Phred, Phrap and Consed
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PhD Thesis: MIRA: An Automated Genome and EST Assembler
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Gene discovery and annotation using LCM-454 transcriptome sequencing.
Emrich SJ, Barbazuk WB, Li L, Schnable PS., Genome Res. 17(1), 2006
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CAP3: A DNA sequence assembly program.
Huang X, Madan A., Genome Res. 9(9), 1999
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TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
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SOAP::Short Oligonucleotide Assembly Package
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Gene-based sequence diversity analysis of field pea (Pisum).
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Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes.
Blanc G, Wolfe KH., Plant Cell 16(7), 2004
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The pea gene LH encodes ent-kaurene oxidase.
Davidson SE, Smith JJ, Helliwell CA, Poole AT, Reid JB., Plant Physiol. 134(3), 2004
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The single-copy gene encoding high-mobility-group protein HMG-I/Y from pea contains a single intron and is expressed in all organs.
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Plastocyanin Is Encoded By A Single-Copy Gene In The Pea Haploid Genome
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Characterization of a single copy gene encoding ferredoxin I from pea.
Elliott RC, Pedersen TJ, Fristensky B, White MJ, Dickey LF, Thompson WF., Plant Cell 1(7), 1989
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Molecular cloning and characterization of a gene encoding pea cytosolic ascorbate peroxidase.
Mittler R, Zilinskas BA., J. Biol. Chem. 267(30), 1992
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Starch branching enzymes belonging to distinct enzyme families are differentially expressed during pea embryo development.
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Mendel's dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins.
Martin DN, Proebsting WM, Hedden P., Proc. Natl. Acad. Sci. U.S.A. 94(16), 1997
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Mendel's stem length gene (Le) encodes a gibberellin 3 beta-hydroxylase.
Lester DR, Ross JJ, Davies PJ, Reid JB., Plant Cell 9(8), 1997
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Identification of Mendel's White Flower Character
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SCRI living technology: tablet
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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
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The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E., Nucleic Acids Res. 36(Database issue), 2007
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A gene expression map of Arabidopsis thaliana development.
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Rosid radiation and the rapid rise of angiosperm-dominated forests.
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Medicago truncatula
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Glycine max
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Comparison of next generation sequencing technologies for transcriptome characterization
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Approximation properties of haplotype tagging.
Vinterbo SA, Dreiseitl S, Ohno-Machado L., BMC Bioinformatics 7(), 2006
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MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
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Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes.
Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK., Plant J. 38(2), 2004
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Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.
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Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling
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Improved scoring of functional groups from gene expression data by decorrelating GO graph structure.
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Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
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LIGHT CONTROL OF SEEDLING DEVELOPMENT.
Von Arnim A, Deng XW., Annu. Rev. Plant Physiol. Plant Mol. Biol. 47(), 1996
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Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways.
Ma L, Li J, Qu L, Hager J, Chen Z, Zhao H, Deng XW., Plant Cell 13(12), 2001
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Proteases and proteolytic cleavage of storage proteins in developing and germinating dicotyledonous seeds
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An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species.
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Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing.
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Arabidopsis thaliana
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Fast and accurate long-read alignment with Burrows-Wheeler transform.
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The Sequence Alignment/Map format and SAMtools.
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