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

Macas, Jiří; Kejnovský, Eduard; Neumann, Pavel; Novák, Petr; Koblížková, Andrea; Vyskot, Boris

doi:https://dx.doi.org/10.1371/journal.pone.0027335

Number of the records: 1

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

1.

SYSNO ASEP	0367358
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia
Author(s)	Macas, Jiří (BC-A)_{RID, ORCID, SAI} Kejnovský, Eduard (BFU-R)_{RID, ORCID} Neumann, Pavel (BC-A)_{RID, ORCID} Novák, Petr (BC-A)_{RID, ORCID} Koblížková, Andrea (BC-A) Vyskot, Boris (BFU-R)_{RID, ORCID}
Number of authors	6
Source Title	PLoS ONE. - : Public Library of Science - ISSN 1932-6203 Roč. 6, č. 11 (2011), e27335
Number of pages	12 s.
Language	eng - English
Country	US - United States
Keywords	Plant genome ; Sequencing-Based Analyses ; Repetitive DNA ; Silene latifolia
Subject RIV	EB - Genetics ; Molecular Biology
R&D Projects	OC10037 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	LC06004 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	LH11058 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	GAP501/10/0102 GA ČR - Czech Science Foundation (CSF)
	GAP305/10/0930 GA ČR - Czech Science Foundation (CSF)
CEZ	AV0Z50510513 - UMBR-M, BC-A (2005-2011)
	AV0Z50040702 - BFU-R (2007-2013)
UT WOS	000297350800044
DOI	10.1371/journal.pone.0027335
Annotation	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.
Workplace	Biology Centre (since 2006)
Contact	Dana Hypšová, eje@eje.cz, Tel.: 387 775 214
Year of Publishing	2012

Number of the records: 1