Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence
Pucker B, Holtgräwe D, Weisshaar B (2017)
BMC Research Notes 10(1): 667.
Zeitschriftenaufsatz
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Einrichtung
Abstract / Bemerkung
Abstract
Objective
The Arabidopsis thaliana Niederzenz-1 genome sequence was recently published with an ab initio gene prediction. In depth analysis of the predicted gene set revealed some errors involving genes with non-canonical splice sites in their introns. Since non-canonical splice sites are difficult to predict ab initio, we checked for options to improve the annotation by transferring annotation information from the recently released Columbia-0 reference genome sequence annotation Araport11.
Results
Incorporation of hints generated from Araport11 enabled the precise prediction of non-canonical splice sites. Manual inspection of RNA-Seq read mapping and RT-PCR were applied to validate the structural annotations of non-canonical splice sites. Predictions of untranslated regions were also updated by harnessing the potential of Araport11’s information, which was generated by using high coverage RNA-Seq data. The improved gene set of the Nd-1 genome assembly (GeneSet_Nd-1_v1.1) was evaluated via comparison to the initial gene prediction (GeneSet_Nd-1_v1.0) as well as against Araport11 for the Col-0 reference genome sequence. GeneSet_Nd-1_v1.1 contains previously missed non-canonical splice sites in 1256 genes. Reciprocal best hits for 24,527 (89.4%) of all nuclear Col-0 genes against the GeneSet_Nd-1_v1.1 indicate a high gene prediction quality.
Stichworte
Genome annotation;
Splicing;
Araport11;
Gene prediction hints;
Reciprocal best hit
Erscheinungsjahr
2017
Zeitschriftentitel
BMC Research Notes
Band
10
Ausgabe
1
Art.-Nr.
667
ISSN
1756-0500
eISSN
1756-0500
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2915524
Zitieren
Pucker B, Holtgräwe D, Weisshaar B. Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes. 2017;10(1): 667.
Pucker, B., Holtgräwe, D., & Weisshaar, B. (2017). Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes, 10(1), 667. doi:10.1186/s13104-017-2985-y
Pucker, Boas, Holtgräwe, Daniela, and Weisshaar, Bernd. 2017. “Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence”. BMC Research Notes 10 (1): 667.
Pucker, B., Holtgräwe, D., and Weisshaar, B. (2017). Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes 10:667.
Pucker, B., Holtgräwe, D., & Weisshaar, B., 2017. Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes, 10(1): 667.
B. Pucker, D. Holtgräwe, and B. Weisshaar, “Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence”, BMC Research Notes, vol. 10, 2017, : 667.
Pucker, B., Holtgräwe, D., Weisshaar, B.: Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes. 10, : 667 (2017).
Pucker, Boas, Holtgräwe, Daniela, and Weisshaar, Bernd. “Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence”. BMC Research Notes 10.1 (2017): 667.
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Daten bereitgestellt von European Bioinformatics Institute (EBI)
2 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
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PMID: 31112551
Pucker B, Holtgräwe D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B., PLoS One 14(5), 2019
PMID: 31112551
A major QTL on chromosome C05 significantly reduces acid detergent lignin (ADL) content and increases seed oil and protein content in oilseed rape (Brassica napus L.).
Behnke N, Suprianto E, Möllers C., Theor Appl Genet 131(11), 2018
PMID: 30143828
Behnke N, Suprianto E, Möllers C., Theor Appl Genet 131(11), 2018
PMID: 30143828
66 References
Daten bereitgestellt von Europe PubMed Central.
The precursor of mouse beta-globin messenger RNA contains two intervening RNA sequences.
Kinniburgh AJ, Mertz JE, Ross J., Cell 14(3), 1978
PMID: 688388
Kinniburgh AJ, Mertz JE, Ross J., Cell 14(3), 1978
PMID: 688388
Organization and expression of eucaryotic split genes coding for proteins.
Breathnach R, Chambon P., Annu. Rev. Biochem. 50(), 1981
PMID: 6791577
Breathnach R, Chambon P., Annu. Rev. Biochem. 50(), 1981
PMID: 6791577
Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries.
Breathnach R, Benoist C, O'Hare K, Gannon F, Chambon P., Proc. Natl. Acad. Sci. U.S.A. 75(10), 1978
PMID: 283395
Breathnach R, Benoist C, O'Hare K, Gannon F, Chambon P., Proc. Natl. Acad. Sci. U.S.A. 75(10), 1978
PMID: 283395
A reappraisal of non-consensus mRNA splice sites.
Jackson IJ., Nucleic Acids Res. 19(14), 1991
PMID: 1713664
Jackson IJ., Nucleic Acids Res. 19(14), 1991
PMID: 1713664
Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns.
Dietrich RC, Incorvaia R, Padgett RA., Mol. Cell 1(1), 1997
PMID: 9659912
Dietrich RC, Incorvaia R, Padgett RA., Mol. Cell 1(1), 1997
PMID: 9659912
Requirement of U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns.
Hall SL, Padgett RA., Science 271(5256), 1996
PMID: 8596930
Hall SL, Padgett RA., Science 271(5256), 1996
PMID: 8596930
A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro.
Tarn WY, Steitz JA., Cell 84(5), 1996
PMID: 8625417
Tarn WY, Steitz JA., Cell 84(5), 1996
PMID: 8625417
Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns.
Tarn WY, Steitz JA., Science 273(5283), 1996
PMID: 8791582
Tarn WY, Steitz JA., Science 273(5283), 1996
PMID: 8791582
The splicing of U12-type introns can be a rate-limiting step in gene expression.
Patel AA, McCarthy M, Steitz JA., EMBO J. 21(14), 2002
PMID: 12110592
Patel AA, McCarthy M, Steitz JA., EMBO J. 21(14), 2002
PMID: 12110592
Analysis of canonical and non-canonical splice sites in mammalian genomes.
Burset M, Seledtsov IA, Solovyev VV., Nucleic Acids Res. 28(21), 2000
PMID: 11058137
Burset M, Seledtsov IA, Solovyev VV., Nucleic Acids Res. 28(21), 2000
PMID: 11058137
Role of the 3' splice site in U12-dependent intron splicing.
Dietrich RC, Peris MJ, Seyboldt AS, Padgett RA., Mol. Cell. Biol. 21(6), 2001
PMID: 11238930
Dietrich RC, Peris MJ, Seyboldt AS, Padgett RA., Mol. Cell. Biol. 21(6), 2001
PMID: 11238930
Comparison of splice sites in mammals and chicken.
Abril JF, Castelo R, Guigo R., Genome Res. 15(1), 2004
PMID: 15590946
Abril JF, Castelo R, Guigo R., Genome Res. 15(1), 2004
PMID: 15590946
A conserved unusual posttranscriptional processing mediated by short, direct repeated (SDR) sequences in plants.
Niu X, Luo D, Gao S, Ren G, Chang L, Zhou Y, Luo X, Li Y, Hou P, Tang W, Lu BR, Liu Y., J Genet Genomics 37(1), 2010
PMID: 20171581
Niu X, Luo D, Gao S, Ren G, Chang L, Zhou Y, Luo X, Li Y, Hou P, Tang W, Lu BR, Liu Y., J Genet Genomics 37(1), 2010
PMID: 20171581
Lessons from non-canonical splicing.
Sibley CR, Blazquez L, Ule J., Nat. Rev. Genet. 17(7), 2016
PMID: 27240813
Sibley CR, Blazquez L, Ule J., Nat. Rev. Genet. 17(7), 2016
PMID: 27240813
Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants.
Shukla GC, Padgett RA., RNA 5(4), 1999
PMID: 10199569
Shukla GC, Padgett RA., RNA 5(4), 1999
PMID: 10199569
AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes.
Wu Q, Krainer AR., Mol. Cell. Biol. 19(5), 1999
PMID: 10207048
Wu Q, Krainer AR., Mol. Cell. Biol. 19(5), 1999
PMID: 10207048
Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping.
Zhu W, Schlueter SD, Brendel V., Plant Physiol. 132(2), 2003
PMID: 12805580
Zhu W, Schlueter SD, Brendel V., Plant Physiol. 132(2), 2003
PMID: 12805580
Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome.
Zhu W, Brendel V., Nucleic Acids Res. 31(15), 2003
PMID: 12888517
Zhu W, Brendel V., Nucleic Acids Res. 31(15), 2003
PMID: 12888517
Determinants of plant U12-dependent intron splicing efficiency.
Lewandowska D, Simpson CG, Clark GP, Jennings NS, Barciszewska-Pacak M, Lin CF, Makalowski W, Brown JW, Jarmolowski A., Plant Cell 16(5), 2004
PMID: 15100401
Lewandowska D, Simpson CG, Clark GP, Jennings NS, Barciszewska-Pacak M, Lin CF, Makalowski W, Brown JW, Jarmolowski A., Plant Cell 16(5), 2004
PMID: 15100401
ERISdb: a database of plant splice sites and splicing signals.
Szczesniak MW, Kabza M, Pokrzywa R, Gudys A, Makalowska I., Plant Cell Physiol. 54(2), 2013
PMID: 23299413
Szczesniak MW, Kabza M, Pokrzywa R, Gudys A, Makalowska I., Plant Cell Physiol. 54(2), 2013
PMID: 23299413
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
Brendel V, Xing L, Zhu W., Bioinformatics 20(7), 2004
PMID: 14764557
Brendel V, Xing L, Zhu W., Bioinformatics 20(7), 2004
PMID: 14764557
Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants.
Sparks ME, Brendel V., Bioinformatics 21 Suppl 3(), 2005
PMID: 16306388
Sparks ME, Brendel V., Bioinformatics 21 Suppl 3(), 2005
PMID: 16306388
Recent advances in gene structure prediction.
Brent MR, Guigo R., Curr. Opin. Struct. Biol. 14(3), 2004
PMID: 15193305
Brent MR, Guigo R., Curr. Opin. Struct. Biol. 14(3), 2004
PMID: 15193305
A comparative analysis of soft computing techniques for gene prediction.
Goel N, Singh S, Aseri TC., Anal. Biochem. 438(1), 2013
PMID: 23529114
Goel N, Singh S, Aseri TC., Anal. Biochem. 438(1), 2013
PMID: 23529114
Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction.
Huang Y, Chen SY, Deng F., Comput Struct Biotechnol J 14(), 2016
PMID: 27536341
Huang Y, Chen SY, Deng F., Comput Struct Biotechnol J 14(), 2016
PMID: 27536341
Araport: the Arabidopsis information portal.
Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25414324
Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25414324
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD., Plant J. 89(4), 2017
PMID: 27862469
Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD., Plant J. 89(4), 2017
PMID: 27862469
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny.
Pucker B, Holtgrawe D, Rosleff Sorensen T, Stracke R, Viehover P, Weisshaar B., PLoS ONE 11(10), 2016
PMID: 27711162
Pucker B, Holtgrawe D, Rosleff Sorensen T, Stracke R, Viehover P, Weisshaar B., PLoS ONE 11(10), 2016
PMID: 27711162
OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li L, Stoeckert CJ Jr, Roos DS., Genome Res. 13(9), 2003
PMID: 12952885
Li L, Stoeckert CJ Jr, Roos DS., Genome Res. 13(9), 2003
PMID: 12952885
Choosing BLAST options for better detection of orthologs as reciprocal best hits.
Moreno-Hagelsieb G, Latimer K., Bioinformatics 24(3), 2007
PMID: 18042555
Moreno-Hagelsieb G, Latimer K., Bioinformatics 24(3), 2007
PMID: 18042555
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss?
Ward N, Moreno-Hagelsieb G., PLoS ONE 9(7), 2014
PMID: 25013894
Ward N, Moreno-Hagelsieb G., PLoS ONE 9(7), 2014
PMID: 25013894
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.
Emms DM, Kelly S., Genome Biol. 16(), 2015
PMID: 26243257
Emms DM, Kelly S., Genome Biol. 16(), 2015
PMID: 26243257
A genomic perspective on protein families.
Tatusov RL, Koonin EV, Lipman DJ., Science 278(5338), 1997
PMID: 9381173
Tatusov RL, Koonin EV, Lipman DJ., Science 278(5338), 1997
PMID: 9381173
STAR: ultrafast universal RNA-seq aligner.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR., Bioinformatics 29(1), 2012
PMID: 23104886
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR., Bioinformatics 29(1), 2012
PMID: 23104886
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris).
Stracke R, Holtgrawe D, Schneider J, Pucker B, Sorensen TR, Weisshaar B., BMC Plant Biol. 14(), 2014
PMID: 25249410
Stracke R, Holtgrawe D, Schneider J, Pucker B, Sorensen TR, Weisshaar B., BMC Plant Biol. 14(), 2014
PMID: 25249410
Use of mutants from T-DNA insertion populations generated by high-throughput screening
Stracke R, Huep G, Weisshaar B., 2010
Stracke R, Huep G, Weisshaar B., 2010
Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling.
Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, Weisshaar B., Plant J. 50(4), 2007
PMID: 17419845
Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, Weisshaar B., Plant J. 50(4), 2007
PMID: 17419845
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Katoh K, Standley DM., Mol. Biol. Evol. 30(4), 2013
PMID: 23329690
Katoh K, Standley DM., Mol. Biol. Evol. 30(4), 2013
PMID: 23329690
Gene prediction with a hidden Markov model and a new intron submodel.
Stanke M, Waack S., Bioinformatics 19 Suppl 2(), 2003
PMID: 14534192
Stanke M, Waack S., Bioinformatics 19 Suppl 2(), 2003
PMID: 14534192
A novel hybrid gene prediction method employing protein multiple sequence alignments.
Keller O, Kollmar M, Stanke M, Waack S., Bioinformatics 27(6), 2011
PMID: 21216780
Keller O, Kollmar M, Stanke M, Waack S., Bioinformatics 27(6), 2011
PMID: 21216780
ParsEval: parallel comparison and analysis of gene structure annotations.
Standage DS, Brendel VP., BMC Bioinformatics 13(), 2012
PMID: 22852583
Standage DS, Brendel VP., BMC Bioinformatics 13(), 2012
PMID: 22852583
Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
Dal Bosco C, Lezhneva L, Biehl A, Leister D, Strotmann H, Wanner G, Meurer J., J. Biol. Chem. 279(2), 2003
PMID: 14576160
Dal Bosco C, Lezhneva L, Biehl A, Leister D, Strotmann H, Wanner G, Meurer J., J. Biol. Chem. 279(2), 2003
PMID: 14576160
Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
Wang Y, Zhang WZ, Song LF, Zou JJ, Su Z, Wu WH., Plant Physiol. 148(3), 2008
PMID: 18775970
Wang Y, Zhang WZ, Song LF, Zou JJ, Su Z, Wu WH., Plant Physiol. 148(3), 2008
PMID: 18775970
Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling.
Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jahne F, Graf A, Kappel C, Baurle I., Elife 5(), 2016
PMID: 27680998
Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jahne F, Graf A, Kappel C, Baurle I., Elife 5(), 2016
PMID: 27680998
Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
Ascencio-Ibanez JT, Sozzani R, Lee TJ, Chu TM, Wolfinger RD, Cella R, Hanley-Bowdoin L., Plant Physiol. 148(1), 2008
PMID: 18650403
Ascencio-Ibanez JT, Sozzani R, Lee TJ, Chu TM, Wolfinger RD, Cella R, Hanley-Bowdoin L., Plant Physiol. 148(1), 2008
PMID: 18650403
cpSecA, a thylakoid protein translocase subunit, is essential for photosynthetic development in Arabidopsis.
Liu D, Gong Q, Ma Y, Li P, Li J, Yang S, Yuan L, Yu Y, Pan D, Xu F, Wang NN., J. Exp. Bot. 61(6), 2010
PMID: 20194926
Liu D, Gong Q, Ma Y, Li P, Li J, Yang S, Yuan L, Yu Y, Pan D, Xu F, Wang NN., J. Exp. Bot. 61(6), 2010
PMID: 20194926
Plastids contain a second sec translocase system with essential functions.
Skalitzky CA, Martin JR, Harwood JH, Beirne JJ, Adamczyk BJ, Heck GR, Cline K, Fernandez DE., Plant Physiol. 155(1), 2010
PMID: 21051552
Skalitzky CA, Martin JR, Harwood JH, Beirne JJ, Adamczyk BJ, Heck GR, Cline K, Fernandez DE., Plant Physiol. 155(1), 2010
PMID: 21051552
A novel interaction partner for the C-terminus of Arabidopsis thaliana plasma membrane H+-ATPase (AHA1 isoform): site and mechanism of action on H+-ATPase activity differ from those of 14-3-3 proteins.
Morandini P, Valera M, Albumi C, Bonza MC, Giacometti S, Ravera G, Murgia I, Soave C, De Michelis MI., Plant J. 31(4), 2002
PMID: 12182706
Morandini P, Valera M, Albumi C, Bonza MC, Giacometti S, Ravera G, Murgia I, Soave C, De Michelis MI., Plant J. 31(4), 2002
PMID: 12182706
Characterization of the interaction between the plasma membrane H-ATPase of Arabidopsis thaliana and a novel interactor (PPI1).
Viotti C, Luoni L, Morandini P, De Michelis MI., FEBS J. 272(22), 2005
PMID: 16279950
Viotti C, Luoni L, Morandini P, De Michelis MI., FEBS J. 272(22), 2005
PMID: 16279950
The proton pump interactor (Ppi) gene family of Arabidopsis thaliana: expression pattern of Ppi1 and characterisation of knockout mutants for Ppi1 and 2.
Anzi C, Pelucchi P, Vazzola V, Murgia I, Gomarasca S, Piccoli MB, Morandini P., Plant Biol (Stuttg) 10(2), 2008
PMID: 18304198
Anzi C, Pelucchi P, Vazzola V, Murgia I, Gomarasca S, Piccoli MB, Morandini P., Plant Biol (Stuttg) 10(2), 2008
PMID: 18304198
Intracellular localisation of PPI1 (proton pump interactor, isoform 1), a regulatory protein of the plasma membrane H(+)-ATPase of Arabidopsis thaliana.
Bonza MC, Fusca T, Homann U, Thiel G, De Michelis MI., Plant Biol (Stuttg) 11(6), 2009
PMID: 19796364
Bonza MC, Fusca T, Homann U, Thiel G, De Michelis MI., Plant Biol (Stuttg) 11(6), 2009
PMID: 19796364
Endogenous Arabidopsis messenger RNAs transported to distant tissues.
Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Minambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F., Nat Plants 1(4), 2015
PMID: 27247031
Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Minambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F., Nat Plants 1(4), 2015
PMID: 27247031
Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
Vukasinovic N, Cvrckova F, Elias M, Cole R, Fowler JE, Zarsky V, Synek L., PLoS ONE 9(4), 2014
PMID: 24728280
Vukasinovic N, Cvrckova F, Elias M, Cole R, Fowler JE, Zarsky V, Synek L., PLoS ONE 9(4), 2014
PMID: 24728280
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.
Lomsadze A, Burns PD, Borodovsky M., Nucleic Acids Res. 42(15), 2014
PMID: 24990371
Lomsadze A, Burns PD, Borodovsky M., Nucleic Acids Res. 42(15), 2014
PMID: 24990371
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M., Bioinformatics 32(5), 2015
PMID: 26559507
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M., Bioinformatics 32(5), 2015
PMID: 26559507
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P; French-Italian Public Consortium for Grapevine Genome Characterization., Nature 449(7161), 2007
PMID: 17721507
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P; French-Italian Public Consortium for Grapevine Genome Characterization., Nature 449(7161), 2007
PMID: 17721507
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL., Nat. Genet. 43(5), 2011
PMID: 21478890
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL., Nat. Genet. 43(5), 2011
PMID: 21478890
The genome of the mesopolyploid crop species Brassica rapa.
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z; Brassica rapa Genome Sequencing Project Consortium, Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Chris Pires J, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z., Nat. Genet. 43(10), 2011
PMID: 21873998
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z; Brassica rapa Genome Sequencing Project Consortium, Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Chris Pires J, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z., Nat. Genet. 43(10), 2011
PMID: 21873998
The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IA, Zhao M, Ma J, Yu J, Huang S., 2013
Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IA, Zhao M, Ma J, Yu J, Huang S., 2013
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O, Sorensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldon T, Lehrach H, Weisshaar B, Himmelbauer H., Nature 505(7484), 2013
PMID: 24352233
Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O, Sorensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldon T, Lehrach H, Weisshaar B, Himmelbauer H., Nature 505(7484), 2013
PMID: 24352233
Using intron position conservation for homology-based gene prediction.
Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F., Nucleic Acids Res. 44(9), 2016
PMID: 26893356
Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F., Nucleic Acids Res. 44(9), 2016
PMID: 26893356
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Teil dieser Dissertation
De novo Nd-1 genome assembly reveals genomic diversity of Arabidopsis thaliana and facilitates genome-wide non-canonical splice site analysis across plant species
Pucker B (2019)
Bielefeld: Universität Bielefeld.
Pucker B (2019)
Bielefeld: Universität Bielefeld.
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