Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

0367358 - BC 2012 RIV US eng J - Journal Article
Macas, Jiří - Kejnovský, Eduard - Neumann, Pavel - Novák, Petr - Koblížková, Andrea - Vyskot, Boris
Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia.
PLoS ONE. Roč. 6, č. 11 (2011), e27335. ISSN 1932-6203. E-ISSN 1932-6203
R&D Projects: GA MŠMT(CZ) OC10037; GA MŠMT(CZ) LC06004; GA MŠMT(CZ) LH11058; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GAP305/10/0930
Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50040702
Keywords : Plant genome * Sequencing-Based Analyses * Repetitive DNA * Silene latifolia
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 4.092, year: 2011

We performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data.
Permanent Link: http://hdl.handle.net/11104/0202067