Počet záznamů: 1

Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data

  1. 1.
    0348727 - BC-A 2011 RIV GB eng J - Článek v odborném periodiku
    Macas, Jiří - Neumann, Pavel - Novák, Petr - Jiang, J.
    Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data.
    Bioinformatics. Roč. 26, č. 1797 (2010), s. 2101-2108 ISSN 1367-4803
    Grant CEP: GA AV ČR KJB500960802; GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004
    Výzkumný záměr: CEZ:AV0Z50510513
    Klíčová slova: next-generation sequencing * satellite repeats * K-mer analysis
    Kód oboru RIV: EB - Genetika a molekulární biologie
    Impakt faktor: 4.877, rok: 2010

    K-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). K-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome.
    Trvalý link: http://hdl.handle.net/11104/0189169