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: 227.

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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.
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BMC Genomics
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12
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227
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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: 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, 227. doi:10.1186/1471-2164-12-227
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: 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 (2011): 227.
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73 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

TIR1 auxin receptors are implicated in the differential response to 4-Cl-IAA and IAA in developing pea fruit.
Jayasinghege CPA, Ozga JA, Nadeau CD, Kaur H, Reinecke DM., J Exp Bot 70(4), 2019
PMID: 30715391
Identification of Stipules reduced, a leaf morphology gene in pea (Pisum sativum).
Moreau C, Hofer JMI, Eléouët M, Sinjushin A, Ambrose M, Skøt K, Blackmore T, Swain M, Hegarty M, Balanzà V, Ferrándiz C, Ellis THN., New Phytol 220(1), 2018
PMID: 29974468
Proteomics offers insight to the mechanism behind Pisum sativum L. response to pea seed-borne mosaic virus (PSbMV).
Cerna H, Černý M, Habánová H, Šafářová D, Abushamsiya K, Navrátil M, Brzobohatý B., J Proteomics 153(), 2017
PMID: 27235724
Reconstruction of a composite comparative map composed of ten legume genomes.
Lee C, Yu D, Choi HK, Kim RW., Genes Genomics 39(1), 2017
PMID: 28090266
A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.).
Hradilová I, Trněný O, Válková M, Cechová M, Janská A, Prokešová L, Aamir K, Krezdorn N, Rotter B, Winter P, Varshney RK, Soukup A, Bednář P, Hanáček P, Smýkal P., Front Plant Sci 8(), 2017
PMID: 28487704
Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers.
Kulaeva OA, Zhernakov AI, Afonin AM, Boikov SS, Sulima AS, Tikhonovich IA, Zhukov VA., PLoS One 12(10), 2017
PMID: 29073280
Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare.
Brilhaus D, Bräutigam A, Mettler-Altmann T, Winter K, Weber AP., Plant Physiol 170(1), 2016
PMID: 26530316
SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population.
Boutet G, Alves Carvalho S, Falque M, Peterlongo P, Peterlongo P, Lhuillier E, Bouchez O, Lavaud C, Pilet-Nayel ML, Rivière N, Baranger A., BMC Genomics 17(), 2016
PMID: 26892170
OEP40, a Regulated Glucose-permeable β-Barrel Solute Channel in the Chloroplast Outer Envelope Membrane.
Harsman A, Schock A, Hemmis B, Wahl V, Jeshen I, Bartsch P, Schlereth A, Pertl-Obermeyer H, Goetze TA, Soll J, Philippar K, Wagner R., J Biol Chem 291(34), 2016
PMID: 27339897
Identification of LATE BLOOMER2 as a CYCLING DOF FACTOR Homolog Reveals Conserved and Divergent Features of the Flowering Response to Photoperiod in Pea.
Ridge S, Sussmilch FC, Hecht V, Vander Schoor JK, Lee R, Aubert G, Burstin J, Macknight RC, Macknight RC, Weller JL., Plant Cell 28(10), 2016
PMID: 27670672
Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.).
Sudheesh S, Verma P, Forster JW, Cogan NO, Kaur S., Int J Mol Sci 17(11), 2016
PMID: 27845747
Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).
Kim S, Kim MS, Kim YM, Yeom SI, Cheong K, Kim KT, Jeon J, Kim S, Kim DS, Sohn SH, Lee YH, Choi D., DNA Res 22(1), 2015
PMID: 25362073
FAX1, a novel membrane protein mediating plastid fatty acid export.
Li N, Gügel IL, Giavalisco P, Zeisler V, Schreiber L, Soll J, Philippar K., PLoS Biol 13(2), 2015
PMID: 25646734
Next-generation sequencing is a robust strategy for the high-throughput detection of zygosity in transgenic maize.
Fritsch L, Fischer R, Wambach C, Dudek M, Schillberg S, Schröper F., Transgenic Res 24(4), 2015
PMID: 25648956
Oep23 forms an ion channel in the chloroplast outer envelope.
Goetze TA, Patil M, Jeshen I, Bölter B, Grahl S, Soll J., BMC Plant Biol 15(), 2015
PMID: 25849634
Pea VEGETATIVE2 Is an FD Homolog That Is Essential for Flowering and Compound Inflorescence Development.
Sussmilch FC, Berbel A, Hecht V, Vander Schoor JK, Ferrándiz C, Madueño F, Weller JL., Plant Cell 27(4), 2015
PMID: 25804541
The structure of plant photosystem I super-complex at 2.8 Å resolution.
Mazor Y, Borovikova A, Nelson N., Elife 4(), 2015
PMID: 26076232
The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.
O'Rourke JA, Fu F, Bucciarelli B, Yang SS, Samac DA, Lamb JF, Monteros MJ, Graham MA, Gronwald JW, Krom N, Li J, Dai X, Zhao PX, Vance CP., BMC Genomics 16(), 2015
PMID: 26149169
Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids.
Ibarra-Laclette E, Méndez-Bravo A, Pérez-Torres CA, Albert VA, Mockaitis K, Kilaru A, López-Gómez R, Cervantes-Luevano JI, Herrera-Estrella L., BMC Genomics 16(), 2015
PMID: 26268848
De novo assembly and characterisation of the field pea transcriptome using RNA-Seq.
Sudheesh S, Sawbridge TI, Cogan NO, Kennedy P, Forster JW, Kaur S., BMC Genomics 16(), 2015
PMID: 26275991
KNOTTED1-LIKE HOMEOBOX 3: a new regulator of symbiotic nodule development.
Azarakhsh M, Kirienko AN, Zhukov VA, Lebedeva MA, Dolgikh EA, Lutova LA., J Exp Bot 66(22), 2015
PMID: 26351356
Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species.
Alves-Carvalho S, Aubert G, Carrère S, Cruaud C, Brochot AL, Jacquin F, Klein A, Martin C, Boucherot K, Kreplak J, da Silva C, Moreau S, Gamas P, Wincker P, Gouzy J, Burstin J., Plant J 84(1), 2015
PMID: 26296678
De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway.
Miao Z, Xu W, Li D, Hu X, Liu J, Zhang R, Tong Z, Dong J, Su Z, Zhang L, Sun M, Li W, Du Z, Hu S, Wang T., BMC Genomics 16(), 2015
PMID: 26481731
Pre-fractionation strategies to resolve pea (Pisum sativum) sub-proteomes.
Meisrimler CN, Menckhoff L, Kukavica BM, Lüthje S., Front Plant Sci 6(), 2015
PMID: 26539198
De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome.
Zhukov VA, Zhernakov AI, Kulaeva OA, Ershov NI, Borisov AY, Tikhonovich IA., Int J Genomics 2015(), 2015
PMID: 26688806
Comparative Transcriptomic Analyses of Vegetable and Grain Pea (Pisum sativum L.) Seed Development.
Liu N, Zhang G, Xu S, Mao W, Hu Q, Gong Y., Front Plant Sci 6(), 2015
PMID: 26635856
Genomic Tools in Pea Breeding Programs: Status and Perspectives.
Tayeh N, Aubert G, Pilet-Nayel ML, Lejeune-Hénaut I, Warkentin TD, Burstin J., Front Plant Sci 6(), 2015
PMID: 26640470
SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance.
Kaur S, Kimber RB, Cogan NO, Materne M, Forster JW, Paull JG., Plant Sci 217-218(), 2014
PMID: 24467895
RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.
Chow KS, Ghazali AK, Hoh CC, Mohd-Zainuddin Z., BMC Res Notes 7(), 2014
PMID: 24484543
Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir.
Giordano A, Cogan NO, Kaur S, Drayton M, Mouradov A, Panter S, Schrauf GE, Mason JG, Spangenberg GC., PLoS One 9(2), 2014
PMID: 24520314
Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea.
Duarte J, Rivière N, Baranger A, Aubert G, Burstin J, Cornet L, Lavaud C, Lejeune-Hénaut I, Martinant JP, Pichon JP, Pilet-Nayel ML, Boutet G., BMC Genomics 15(), 2014
PMID: 24521263
Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types.
Franssen SU, Gu J, Winters G, Huylmans AK, Wienpahl I, Sparwel M, Coyer JA, Olsen JL, Reusch TB, Bornberg-Bauer E., Mar Genomics 15(), 2014
PMID: 24703884
Diversity in guanosine 3',5'-bisdiphosphate (ppGpp) sensitivity among guanylate kinases of bacteria and plants.
Nomura Y, Izumi A, Fukunaga Y, Kusumi K, Iba K, Watanabe S, Nakahira Y, Weber AP, Nozawa A, Tozawa Y., J Biol Chem 289(22), 2014
PMID: 24722991
Unique and conserved features of floral evocation in legumes.
Liew LC, Singh MB, Bhalla PL., J Integr Plant Biol 56(8), 2014
PMID: 24930396
The selective biotin tagging and thermolysin proteolysis of chloroplast outer envelope proteins reveals information on protein topology and association into complexes.
Hardré H, Kuhn L, Albrieux C, Jouhet J, Michaud M, Seigneurin-Berny D, Falconet D, Block MA, Maréchal E., Front Plant Sci 5(), 2014
PMID: 24999344
Gene-based SNP discovery and genetic mapping in pea.
Sindhu A, Ramsay L, Sanderson LA, Stonehouse R, Li R, Condie J, Shunmugam AS, Liu Y, Jha AB, Diapari M, Burstin J, Aubert G, Tar'an B, Bett KE, Warkentin TD, Sharpe AG., Theor Appl Genet 127(10), 2014
PMID: 25119872
Characterization of proanthocyanidin metabolism in pea (Pisum sativum) seeds.
Ferraro K, Jin AL, Nguyen TD, Reinecke DM, Ozga JA, Ro DK., BMC Plant Biol 14(), 2014
PMID: 25928382
Plastidic type I signal peptidase 1 is a redox-dependent thylakoidal processing peptidase.
Midorikawa T, Endow JK, Dufour J, Zhu J, Inoue K., Plant J 80(4), 2014
PMID: 25182596
Evolution and targeting of Omp85 homologs in the chloroplast outer envelope membrane.
Day PM, Potter D, Inoue K., Front Plant Sci 5(), 2014
PMID: 25352854
Next generation sequencing and de novo transcriptomics to study gene evolution.
Jayasena AS, Secco D, Bernath-Levin K, Berkowitz O, Whelan J, Mylne JS., Plant Methods 10(1), 2014
PMID: 25364374
Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).
Ferreira de Carvalho J, Poulain J, Da Silva C, Wincker P, Michon-Coudouel S, Dheilly A, Naquin D, Boutte J, Salmon A, Ainouche M., Heredity (Edinb) 110(2), 2013
PMID: 23149455
An RNA-Seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants.
O'Rourke JA, Yang SS, Miller SS, Bucciarelli B, Liu J, Rydeen A, Bozsoki Z, Uhde-Stone C, Tu ZJ, Allan D, Gronwald JW, Vance CP., Plant Physiol 161(2), 2013
PMID: 23197803
De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.
Muñoz-Mérida A, González-Plaza JJ, Cañada A, Blanco AM, García-López Mdel C, Rodríguez JM, Pedrola L, Sicardo MD, Hernández ML, De la Rosa R, Belaj A, Gil-Borja M, Luque F, Martínez-Rivas JM, Pisano DG, Trelles O, Valpuesta V, Beuzón CR., DNA Res 20(1), 2013
PMID: 23297299
Defining the core proteome of the chloroplast envelope membranes.
Simm S, Papasotiriou DG, Ibrahim M, Leisegang MS, Müller B, Schorge T, Karas M, Mirus O, Sommer MS, Schleiff E., Front Plant Sci 4(), 2013
PMID: 23390424
Catalyzing plant science research with RNA-seq.
Martin LB, Fei Z, Giovannoni JJ, Rose JK., Front Plant Sci 4(), 2013
PMID: 23554602
Combining gene expression and genetic analyses to identify candidate genes involved in cold responses in pea.
Legrand S, Marque G, Blassiau C, Bluteau A, Canoy AS, Fontaine V, Jaminon O, Bahrman N, Mautord J, Morin J, Petit A, Baranger A, Rivière N, Wilmer J, Delbreil B, Lejeune-Hénaut I., J Plant Physiol 170(13), 2013
PMID: 23632303
Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon.
Vidotto M, Grapputo A, Boscari E, Barbisan F, Coppe A, Grandi G, Kumar A, Congiu L., BMC Genomics 14(), 2013
PMID: 23773438
Putative genes involved in saikosaponin biosynthesis in Bupleurum species.
Lin TY, Chiou CY, Chiou SJ., Int J Mol Sci 14(6), 2013
PMID: 23783277
Transcriptome analysis of Litopenaeus vannamei in response to white spot syndrome virus infection.
Chen X, Zeng D, Chen X, Xie D, Zhao Y, Yang C, Li Y, Ma N, Li M, Yang Q, Liao Z, Wang H., PLoS One 8(8), 2013
PMID: 23991181
Transcriptome sequences resolve deep relationships of the grape family.
Wen J, Xiong Z, Nie ZL, Mao L, Zhu Y, Kan XZ, Ickert-Bond SM, Gerrath J, Zimmer EA, Fang XD., PLoS One 8(9), 2013
PMID: 24069307
SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.).
Leonforte A, Sudheesh S, Cogan NO, Salisbury PA, Nicolas ME, Materne M, Forster JW, Kaur S., BMC Plant Biol 13(), 2013
PMID: 24134188
Current state-of-art of sequencing technologies for plant genomics research.
Thudi M, Li Y, Jackson SA, May GD, Varshney RK., Brief Funct Genomics 11(1), 2012
PMID: 22345601
SNP markers retrieval for a non-model species: a practical approach.
Shahin A, van Gurp T, Peters SA, Visser RG, van Tuyl JM, Arens P., BMC Res Notes 5(), 2012
PMID: 22284269
Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.
Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PG., PLoS One 7(2), 2012
PMID: 22384018
Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers.
Kaur S, Pembleton LW, Cogan NO, Savin KW, Leonforte T, Paull J, Materne M, Forster JW., BMC Genomics 13(), 2012
PMID: 22433453
Using nuclear gene data for plant phylogenetics: progress and prospects.
Zimmer EA, Wen J., Mol Phylogenet Evol 65(2), 2012
PMID: 22842093
RNA-Seq Assembly - Are We There Yet?
Schliesky S, Gowik U, Weber AP, Bräutigam A., Front Plant Sci 3(), 2012
PMID: 23056003
Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species.
Franssen SU, Gu J, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer E, Reusch TB., Proc Natl Acad Sci U S A 108(48), 2011
PMID: 22084086

67 References

Daten bereitgestellt von Europe PubMed Central.

Legume comparative genomics: progress in phylogenetics and phylogenomics.
Cronk Q, Ojeda I, Pennington RT., Curr. Opin. Plant Biol. 9(2), 2006
PMID: 16480916
Kew Royal Botanical Gardens
AUTHOR UNKNOWN, 0
Comparative mapping between Medicago sativa and Pisum sativum.
Kalo P, Seres A, Taylor SA, Jakab J, Kevei Z, Kereszt A, Endre G, Ellis TH, Kiss GB., Mol. Genet. Genomics 272(3), 2004
PMID: 15340836
Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula
AUTHOR UNKNOWN, 2007
Leaf starch degradation comes out of the shadows.
Lloyd JR, Kossmann J, Ritte G., Trends Plant Sci. 10(3), 2005
PMID: 15749471
Starch degradation.
Smith AM, Zeeman SC, Smith SM., Annu Rev Plant Biol 56(), 2005
PMID: 15862090
The importance of maltose in transitory starch breakdown.
Lu Y, Sharkey TD., Plant Cell Environ. 29(3), 2006
PMID: 17080591
A high-conductance solute channel in the chloroplastic outer envelope from Pea.
Pohlmeyer K, Soll J, Grimm R, Hill K, Wagner R., Plant Cell 10(7), 1998
PMID: 9668138
Nitrate regulation of metabolism and growth.
Stitt M., Curr. Opin. Plant Biol. 2(3), 1999
PMID: 10375569
Nitrogen and carbon metabolism in plastids: Evolution, integration, and coordination with reactions in the cytosol
AUTHOR UNKNOWN, 2005
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
National center for biotechnology information
AUTHOR UNKNOWN, 0
DFCI Plant Gene Indices
AUTHOR UNKNOWN, 0
Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells.
Majeran W, Zybailov B, Ytterberg AJ, Dunsmore J, Sun Q, van Wijk KJ., Mol. Cell Proteomics 7(9), 2008
PMID: 18453340
Shedding light on an extremophile lifestyle through transcriptomics.
Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM., New Phytol. 183(3), 2009
PMID: 19549131
Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein.
D'Auria G, Jimenez N, Peris-Bondia F, Pelaz C, Latorre A, Moya A., BMC Genomics 9(), 2008
PMID: 18194518
Expression of genes associated with carbohydrate metabolism in cotton stems and roots.
Taliercio EW, Romano G, Scheffler J, Ayre BG., BMC Plant Biol. 9(), 2009
PMID: 19161628
A gene expression signature shared by human mature oocytes and embryonic stem cells.
Assou S, Cerecedo D, Tondeur S, Pantesco V, Hovatta O, Klein B, Hamamah S, De Vos J., BMC Genomics 10(), 2009
PMID: 19128516
Sequencing technologies - the next generation.
Metzker ML., Nat. Rev. Genet. 11(1), 2009
PMID: 19997069
RNA-Seq: a revolutionary tool for transcriptomics.
Wang Z, Gerstein M, Snyder M., Nat. Rev. Genet. 10(1), 2009
PMID: 19015660
454 Life Sciences - A Roche company
AUTHOR UNKNOWN, 0
Website of Chevreux
AUTHOR UNKNOWN, 0
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
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
AUTHOR UNKNOWN, 2011
Phred, Phrap and Consed
AUTHOR UNKNOWN, 0
PhD Thesis: MIRA: An Automated Genome and EST Assembler
AUTHOR UNKNOWN, 2006
Gene discovery and annotation using LCM-454 transcriptome sequencing.
Emrich SJ, Barbazuk WB, Li L, Schnable PS., Genome Res. 17(1), 2006
PMID: 17095711
CAP3: A DNA sequence assembly program.
Huang X, Madan A., Genome Res. 9(9), 1999
PMID: 10508846
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J., Bioinformatics 19(5), 2003
PMID: 12651724
SOAP::Short Oligonucleotide Assembly Package
AUTHOR UNKNOWN, 0
Gene-based sequence diversity analysis of field pea (Pisum).
Jing R, Johnson R, Seres A, Kiss G, Ambrose MJ, Knox MR, Ellis TH, Flavell AJ., Genetics 177(4), 2007
PMID: 18073431
The pea gene LH encodes ent-kaurene oxidase.
Davidson SE, Smith JJ, Helliwell CA, Poole AT, Reid JB., Plant Physiol. 134(3), 2004
PMID: 14988475
Plastocyanin Is Encoded By A Single-Copy Gene In The Pea Haploid Genome
AUTHOR UNKNOWN, 1989
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
PMID: 2535518
Starch branching enzymes belonging to distinct enzyme families are differentially expressed during pea embryo development.
Burton RA, Bewley JD, Smith AM, Bhattacharyya MK, Tatge H, Ring S, Bull V, Hamilton WD, Martin C., Plant J. 7(1), 1995
PMID: 7894509
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
PMID: 9238076
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
PMID: 9286112
Identification of Mendel's White Flower Character
AUTHOR UNKNOWN, 2010
SCRI living technology: tablet
AUTHOR UNKNOWN, 0
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
AUTHOR UNKNOWN, 2011
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
PMID: 17986450
A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU., Nat. Genet. 37(5), 2005
PMID: 15806101
Rosid radiation and the rapid rise of angiosperm-dominated forests.
Wang H, Moore MJ, Soltis PS, Bell CD, Brockington SF, Alexandre R, Davis CC, Latvis M, Manchester SR, Soltis DE., Proc. Natl. Acad. Sci. U.S.A. 106(10), 2009
PMID: 19223592
Medicago truncatula
AUTHOR UNKNOWN, 0
Glycine max
AUTHOR UNKNOWN, 0
Comparison of next generation sequencing technologies for transcriptome characterization
AUTHOR UNKNOWN, 2009
Approximation properties of haplotype tagging.
Vinterbo SA, Dreiseitl S, Ohno-Machado L., BMC Bioinformatics 7(), 2006
PMID: 16401341
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M., Plant J. 37(6), 2004
PMID: 14996223
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.
Lister R, Gregory BD, Ecker JR., Curr. Opin. Plant Biol. 12(2), 2009
PMID: 19157957
Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling
AUTHOR UNKNOWN, 2009
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure.
Alexa A, Rahnenfuhrer J, Lengauer T., Bioinformatics 22(13), 2006
PMID: 16606683
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
LIGHT CONTROL OF SEEDLING DEVELOPMENT.
Von Arnim A, Deng XW., Annu. Rev. Plant Physiol. Plant Mol. Biol. 47(), 1996
PMID: 15012288
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
PMID: 11752374
Proteases and proteolytic cleavage of storage proteins in developing and germinating dicotyledonous seeds
AUTHOR UNKNOWN, 1996
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species.
Brautigam A, Kajala K, Wullenweber J, Sommer M, Gagneul D, Weber KL, Carr KM, Gowik U, Mass J, Lercher MJ, Westhoff P, Hibberd JM, Weber AP., Plant Physiol. 155(1), 2010
PMID: 20543093
Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing.
Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB., Plant Physiol. 144(1), 2007
PMID: 17351049
Arabidopsis thaliana
AUTHOR UNKNOWN, 0
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 26(5), 2010
PMID: 20080505
The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943

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