Pavel Neumann

Summary

Affiliation: Institute of Plant Molecular Biology
Country: Czech Republic

Publications

  1. pmc Stretching the rules: monocentric chromosomes with multiple centromere domains
    Pavel Neumann
    Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    PLoS Genet 8:e1002777. 2012
  2. pmc Sgt1, but not Rar1, is essential for the RB-mediated broad-spectrum resistance to potato late blight
    Pudota B Bhaskar
    Department of Horticulture, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Plant Biol 8:8. 2008
  3. pmc Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing
    Eva Hřibová
    Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovska 6, Olomouc CZ 77200, Czech Republic
    BMC Plant Biol 10:204. 2010
  4. pmc Plant centromeric retrotransposons: a structural and cytogenetic perspective
    Pavel Neumann
    Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branisovska 31, České Budějovice CZ 37005, Czech Republic
    Mob DNA 2:4. 2011
  5. ncbi request reprint Chromosome sorting and PCR-based physical mapping in pea (Pisum sativum L.)
    Pavel Neumann
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Chromosome Res 10:63-71. 2002
  6. ncbi request reprint PIGY, a new plant envelope-class LTR retrotransposon
    Pavel Neumann
    Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ, 37005, Czech Republic
    Mol Genet Genomics 273:43-53. 2005
  7. ncbi request reprint Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced
    Pavel Neumann
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Branisovska 31, Ceske Budejovice, 37005 Czech Republic
    Plant Mol Biol 53:399-410. 2003
  8. pmc Experimental evidence for splicing of intron-containing transcripts of plant LTR retrotransposon Ogre
    Veronika Steinbauerová
    Institute of Plant Molecular Biology, Biology Centre ASCR, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
    Mol Genet Genomics 280:427-36. 2008
  9. pmc Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula
    Jiri Macas
    Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    BMC Genomics 8:427. 2007
  10. doi request reprint Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats
    Jiri Macas
    Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    Gene 448:198-206. 2009

Collaborators

Detail Information

Publications22

  1. pmc Stretching the rules: monocentric chromosomes with multiple centromere domains
    Pavel Neumann
    Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    PLoS Genet 8:e1002777. 2012
    ..Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function...
  2. pmc Sgt1, but not Rar1, is essential for the RB-mediated broad-spectrum resistance to potato late blight
    Pudota B Bhaskar
    Department of Horticulture, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Plant Biol 8:8. 2008
    ..Several late blight resistance genes have been cloned recently. However, there is almost no information available about the resistance pathways mediated by any of those genes...
  3. pmc Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing
    Eva Hřibová
    Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovska 6, Olomouc CZ 77200, Czech Republic
    BMC Plant Biol 10:204. 2010
    ..This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement...
  4. pmc Plant centromeric retrotransposons: a structural and cytogenetic perspective
    Pavel Neumann
    Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branisovska 31, České Budějovice CZ 37005, Czech Republic
    Mob DNA 2:4. 2011
    ..abstract:..
  5. ncbi request reprint Chromosome sorting and PCR-based physical mapping in pea (Pisum sativum L.)
    Pavel Neumann
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Chromosome Res 10:63-71. 2002
    ..These experiments enabled assignment of the linkage groups IV and VII to chromosomes 4 and 7, respectively...
  6. ncbi request reprint PIGY, a new plant envelope-class LTR retrotransposon
    Pavel Neumann
    Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ, 37005, Czech Republic
    Mol Genet Genomics 273:43-53. 2005
    ..Another new env-class retrotransposon similar to PIGY was also identified among genomic sequences of Medicago truncatula...
  7. ncbi request reprint Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced
    Pavel Neumann
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Branisovska 31, Ceske Budejovice, 37005 Czech Republic
    Plant Mol Biol 53:399-410. 2003
    ..Considering this retroelement's constitutive expression and observed high mutual similarity of the element genomic sequences, it is possible to speculate about its recent amplification in the genomes of pea and other legume plants...
  8. pmc Experimental evidence for splicing of intron-containing transcripts of plant LTR retrotransposon Ogre
    Veronika Steinbauerová
    Institute of Plant Molecular Biology, Biology Centre ASCR, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
    Mol Genet Genomics 280:427-36. 2008
    ..This is one of very few known cases of spliced LTR retrotransposons and the only one where splicing does not involve parts of the element's coding sequences, thus resembling intron splicing found in most cellular genes...
  9. pmc Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula
    Jiri Macas
    Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    BMC Genomics 8:427. 2007
    ....
  10. doi request reprint Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats
    Jiri Macas
    Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    Gene 448:198-206. 2009
    ....
  11. pmc Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
    Petr Novak
    Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    BMC Bioinformatics 11:378. 2010
    ..However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization...
  12. doi request reprint A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons
    Veronika Steinbauerová
    Institute of Plant Molecular Biology, Biology Centre ASCR, Branisovska 31, Ceske Budejovice, Czech Republic
    Genetica 139:1543-55. 2011
    ..In addition, the protein domain which is otherwise associated with DNA transposons have been detected in part of the Tat-like extra ORFs, pointing to their origin from an insertion event of a mobile element...
  13. ncbi request reprint Ogre elements--a distinct group of plant Ty3/gypsy-like retrotransposons
    Jiri Macas
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Gene 390:108-16. 2007
    ....
  14. pmc Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement
    Pavel Neumann
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Genetics 173:1047-56. 2006
    ..Similar elements were also detected in several other Vicia species but in most cases in significantly lower numbers. However, there was no obvious correlation of the abundance of Ogre sequences with the genome size of these species...
  15. doi request reprint Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data
    Jiri Macas
    Institute of Plant Molecular Biology, Biology Centre ASCR, Branisovska 31, CZ 37005, Ceske Budejovice, Czech Republic
    Bioinformatics 26:2101-8. 2010
    ..k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats...
  16. ncbi request reprint Characterization of Stowaway MITEs in pea (Pisum sativum L.) and identification of their potential master elements
    Jiri Macas
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Budejovice, Czech Republic
    Genome 48:831-9. 2005
    ..Based on this feature, the Psmar-1 elements are believed to be the most likely candidates for the master elements of the Stowaway MITEs in pea...
  17. pmc Next generation sequencing-based analysis of repetitive DNA in the model dioecious [corrected] plant Silene latifolia
    Jiri Macas
    Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    PLoS ONE 6:e27335. 2011
    ....
  18. ncbi request reprint Karyotype analysis of four Vicia species using in situ hybridization with repetitive sequences
    Alice Navrátilová
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    Ann Bot 91:921-6. 2003
    ..This fact, together with observed variations in positions and numbers of rDNA loci, suggests considerable divergence between karyotypes of the species studied...
  19. doi request reprint RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
    Petr Novak
    Institute of Plant Molecular Biology, Biology Centre ASCR, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    Bioinformatics 29:792-3. 2013
    ....
  20. ncbi request reprint Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice
    Kiyotaka Nagaki
    Department of Horticulture, University of Wisconsin Madison, USA
    Mol Biol Evol 22:845-55. 2005
    ..Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed...
  21. pmc The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference
    Pavel Neumann
    Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 176:749-61. 2007
    ..These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric heterochromatin...
  22. ncbi request reprint Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice
    Hye Ran Lee
    Department of Horticulture, University of Wisconsin Madison, Madison, WI, USA
    Mol Biol Evol 23:2505-20. 2006
    ..We detected transcripts derived from both strands of the CentO repeats. The CentO transcripts are processed into siRNA, suggesting a potential role of this satellite repeat family in epigenetic chromatin modification...