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

0348727 - BC 2011 RIV GB eng J - Journal Article
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. E-ISSN 1460-2059
R&D Projects: GA AV ČR KJB500960802; GA MŠMT(CZ) OC10037; GA MŠMT(CZ) LC06004
Institutional research plan: CEZ:AV0Z50510513
Keywords : next-generation sequencing * satellite repeats * K-mer analysis
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 4.877, year: 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.
Permanent Link: http://hdl.handle.net/11104/0189169