Abstract
BackgroundRadish (Raphanus sativus L., 2n = 2x = 18) is a major root vegetable crop especially in eastern Asia. Radish root contains various nutritions which play an important role in strengthening immunity. Repetitive elements are primary components of the genomic sequence and the most important factors in genome size variations in higher eukaryotes. To date, studies about repetitive elements of radish are still limited. To better understand genome structure of radish, we undertook a study to evaluate the proportion of repetitive elements and their distribution in radish.ResultsWe conducted genome-wide characterization of repetitive elements in radish with low coverage genome sequencing followed by similarity-based cluster analysis. Results showed that about 31% of the genome was composed of repetitive sequences. Satellite repeats were the most dominating elements of the genome. The distribution pattern of three satellite repeat sequences (CL1, CL25, and CL43) on radish chromosomes was characterized using fluorescence in situ hybridization (FISH). CL1 was predominantly located at the centromeric region of all chromosomes, CL25 located at the subtelomeric region, and CL43 was a telomeric satellite. FISH signals of two satellite repeats, CL1 and CL25, together with 5S rDNA and 45S rDNA, provide useful cytogenetic markers to identify each individual somatic metaphase chromosome. The centromere-specific histone H3 (CENH3) has been used as a marker to identify centromere DNA sequences. One putative CENH3 (RsCENH3) was characterized and cloned from radish. Its deduced amino acid sequence shares high similarities to those of the CENH3s in Brassica species. An antibody against B. rapa CENH3, specifically stained radish centromeres. Immunostaining and chromatin immunoprecipitation (ChIP) tests with anti-BrCENH3 antibody demonstrated that both the centromere-specific retrotransposon (CR-Radish) and satellite repeat (CL1) are directly associated with RsCENH3 in radish.ConclusionsProportions of repetitive elements in radish were estimated and satellite repeats were the most dominating elements. Fine karyotyping analysis was established which allow us to easily identify each individual somatic metaphase chromosome. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of satellite and centromere-specific retrotransposon at centromeres. Our study provides a valuable basis for future genomic studies in radish.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0480-y) contains supplementary material, which is available to authorized users.
Highlights
Radish (Raphanus sativus L., 2n = 2x = 18) is a major root vegetable crop especially in eastern Asia
Composition of the repetitive sequences in the radish genome 5Gb sequencing data, which amounts to 4.8× coverage of the radish genome, was obtained from the HiSeq2000 platform
RepeatExplorer, a Graph-based clustering and characterization of repetitive sequence utilities was used for analyzing repetitive elements of the genome. 174 clusters were generated with cluster size threshold of 0.01%, and clusters which were annotated putative mitochondrial and plastid contaminations were removed
Summary
Repetitive DNAs, including transposable elements and tandem repeats, are the major components of the genomic sequence and the most important factors in genome size variations in higher eukaryotes [1,2,3]. Centromeres are specialized regions on chromosomes where centromeric protein and spindle microtubules attach via the kinetochore and typically contain large arrays of satellite repeats and/or retrotransposon-related repetitive sequences in eukaryotes [8,9]. They are essential for proper chromosome segregation during mitosis and meiosis. CENH3 is a good marker to identify the core centromeric sequences by chromatin immunoprecipitation (ChIP) with an anti-CENH3 antibody [11,17,18]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
