Jiri Macas

Summary

Affiliation: Institute of Plant Molecular Biology
Country: Czech Republic

Publications

  1. pmc Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids
    Roman Matyasek
    Institute of Biophysics, Academy of Sciences of the Czech Republic, v v i, Kralovopolska 135, Brno CZ 612 65, Czech Republic
    BMC Genomics 13:722. 2012
  2. 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
  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. ncbi 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
  5. doi 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
  6. 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
  7. ncbi 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
  8. ncbi Sequence homogenization and chromosomal localization of VicTR-B satellites differ between closely related Vicia species
    Jiri Macas
    Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, 37005, Czech Republic
    Chromosoma 115:437-47. 2006
  9. doi 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
  10. ncbi Two new families of tandem repeats isolated from genus Vicia using genomic self-priming PCR
    J Macas
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Mol Gen Genet 263:741-51. 2000

Collaborators

  • Jiming Jiang
  • Pavel Neumann
  • Jaroslav Dolezel
  • Eduard Kejnovsky
  • Roman Hobza
  • Petr Novak
  • Veronika Steinbauerová
  • Alice Navrátilová
  • Roman Matyasek
  • A Navrátilová
  • Eva Hřibová
  • Jirí Pech
  • Jaroslav Steinhaisl
  • Andrew Leitch
  • M Nouzova
  • Jaroslav Fulnecek
  • Simon Renny-Byfield
  • Ales Kovarik
  • Richard Nichols
  • Marie Angèle Grandbastien
  • Takashi Matsumoto
  • Nicolas Roux
  • Andrea Koblizkova
  • D W Galbraith

Detail Information

Publications30

  1. pmc Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids
    Roman Matyasek
    Institute of Biophysics, Academy of Sciences of the Czech Republic, v v i, Kralovopolska 135, Brno CZ 612 65, Czech Republic
    BMC Genomics 13:722. 2012
    ..Here we study rDNA complexity in species with arrays consisting of thousands of units...
  2. 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
    ....
  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. ncbi 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...
  5. doi 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
    ....
  6. 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
    ....
  7. ncbi 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
    ....
  8. ncbi Sequence homogenization and chromosomal localization of VicTR-B satellites differ between closely related Vicia species
    Jiri Macas
    Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, 37005, Czech Republic
    Chromosoma 115:437-47. 2006
    ..sativa. The other two V. grandiflora subfamilies showing a considerable divergence from V. sativa sequences were found to be accumulated at subtelomeric regions of V. grandiflora chromosomes...
  9. doi 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
    ....
  10. ncbi Two new families of tandem repeats isolated from genus Vicia using genomic self-priming PCR
    J Macas
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Mol Gen Genet 263:741-51. 2000
    ..In contrast, labeling of VicTR-B repeats in V. sativa resulted in mainly intercalary bands of various intensities and only weak telomeric signals...
  11. ncbi Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes
    Jiri Macas
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Branisovska 31, Ceske Budejovice, 37005 Czech Republic
    Chromosoma 112:152-8. 2003
    ..Thus, the subfamilies may have evolved at these loci following the spreading of the A subrepeats from the IGS to genomic regions outside the rDNA clusters...
  12. ncbi Zaba: a novel miniature transposable element present in genomes of legume plants
    J Macas
    Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
    Mol Genet Genomics 269:624-31. 2003
    ..A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions...
  13. ncbi PlantSat: a specialized database for plant satellite repeats
    Jiri Macas
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    Bioinformatics 18:28-35. 2002
    ..This is mainly due to the presence of multiple entries of homologous sequences and of single entries that contain more than one repeated unit (monomer) in the public databases...
  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. ncbi 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...
  16. 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...
  17. ncbi 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...
  18. ncbi 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...
  19. 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...
  20. pmc Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Alice Navrátilová
    Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    BMC Plant Biol 8:90. 2008
    ..While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes...
  21. 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...
  22. doi 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...
  23. doi 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
    ....
  24. ncbi Microarray-based survey of repetitive genomic sequences in Vicia spp
    M Nouzova
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Plant Mol Biol 45:229-44. 2001
    ..Correlations between the repeat distributions and the current taxonomic classification of these species are discussed...
  25. 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:..
  26. ncbi PRINS on plant chromosomes
    Jiri Macas
    Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
    Methods Mol Biol 334:133-9. 2006
    ..This approach allows the distinguishing of sequences that differ in only a few nucleotides and has proved to be valuable for studies of satellite DNA evolution in plants...
  27. ncbi 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...
  28. ncbi Construction of chromosome-specific DNA libraries covering the whole genome of field bean (Vicia faba L.)
    J Macas
    Institute of Plant Molecular Biology, Branisovska, Czech Republic
    Chromosome Res 4:531-9. 1996
    ..The suitability of the libraries for genome mapping was demonstrated by isolation of clones containing microsatellite motifs...
  29. ncbi Molecular and cytogenetic analysis of repetitive DNA in pea (pisum sativum L.)
    P Neumann
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, , Czech Republic
    Genome 44:716-28. 2001
    ..Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia...
  30. ncbi Long-range organization of plant satellite repeats investigated using strand-specific FISH
    A Navrátilová
    Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Ceske Budejovice, Czech Republic
    Cytogenet Genome Res 109:58-62. 2005
    ..In contrast to VicTR-B, orientation of the PisTR-B clusters with respect to telomeric sequences appeared to be conserved among subtelomeric regions of metacentric chromosomes and of the short arms of acrocentric chromosomes...