PMID- 25928652 OWN - NLM STAT- MEDLINE DCOM- 20160515 LR - 20220321 IS - 1471-2229 (Electronic) IS - 1471-2229 (Linking) VI - 15 DP - 2015 Apr 18 TI - Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.). PG - 105 LID - 10.1186/s12870-015-0480-y [doi] LID - 105 AB - BACKGROUND: Radish (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. RESULTS: We 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. CONCLUSIONS: Proportions 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. FAU - He, Qunyan AU - He Q AD - Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. xiaoyuhqy@163.com. AD - National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China. xiaoyuhqy@163.com. FAU - Cai, Zexi AU - Cai Z AD - National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China. caizexi123@cau.edu.cn. FAU - Hu, Tianhua AU - Hu T AD - Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. hutianh@hotmail.com. FAU - Liu, Huijun AU - Liu H AD - National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China. huijunliu1022@gmail.com. FAU - Bao, Chonglai AU - Bao C AD - Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. baocl@126.com. FAU - Mao, Weihai AU - Mao W AD - Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. maowh@126.com. FAU - Jin, Weiwei AU - Jin W AD - National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China. weiweijin@cau.edu.cn. LA - eng SI - SRA/SRX957720 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20150418 PL - England TA - BMC Plant Biol JT - BMC plant biology JID - 100967807 RN - 0 (DNA, Plant) RN - 0 (Histones) RN - 0 (Plant Proteins) SB - IM MH - Centromere/metabolism MH - DNA, Plant/*genetics/metabolism MH - Histones/*genetics/metabolism MH - In Situ Hybridization, Fluorescence MH - *Karyotype MH - Metaphase MH - Open Reading Frames MH - Plant Proteins/*genetics/metabolism MH - Raphanus/cytology/*genetics/metabolism MH - Repetitive Sequences, Nucleic Acid PMC - PMC4417506 EDAT- 2015/05/01 06:00 MHDA- 2016/05/18 06:00 PMCR- 2015/04/18 CRDT- 2015/05/01 06:00 PHST- 2015/01/02 00:00 [received] PHST- 2015/03/23 00:00 [accepted] PHST- 2015/05/01 06:00 [entrez] PHST- 2015/05/01 06:00 [pubmed] PHST- 2016/05/18 06:00 [medline] PHST- 2015/04/18 00:00 [pmc-release] AID - 10.1186/s12870-015-0480-y [pii] AID - 480 [pii] AID - 10.1186/s12870-015-0480-y [doi] PST - epublish SO - BMC Plant Biol. 2015 Apr 18;15:105. doi: 10.1186/s12870-015-0480-y.