Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica

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• 作者：Tony Heitkam ; Stefan Petrasch ; Falk Zakrzewski ; Anja K?gler…
• 关键词：Camellia japonica ; RepeatExplorer ; Fluorescent in situ hybridization ; Satellite DNA ; Tandem repeats
• 刊名：Chromosome Research
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：23
• 期：4
• 页码：791-806
• 全文大小：3,608 KB
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• 作者单位：Tony Heitkam (1)
  Stefan Petrasch (1)
  Falk Zakrzewski (1)
  Anja K?gler (1)
  Torsten Wenke (1)
  Stefan Wanke (1)
  Thomas Schmidt (1)
  
  1. Institute of Botany, Technische Universit?t Dresden, 01069, Dresden, Germany
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Human Genetics
  Animal Genetics and Genomics
  Plant Genetics and Genomics
  
• 出版者：Springer Netherlands
• ISSN：1573-6849

文摘

Northern Europe’s oldest and largest Camellia japonica growing at the Pillnitz Castle (Germany) for over 200 years is of botanical and cultural importance and is a reference for C. japonica molecular scale analysis. In order to provide a fundament for genome analysis of the genus Camellia, we characterize the C. japonica tandem repeat fraction, constituting 12.5 % of the Pillnitz camellia’s genome. A genomic library of the Pillnitz C. japonica was produced and Illumina sequenced to generate 36 Gb of paired-end reads. We performed graph-based read clustering implemented in the RepeatExplorer pipeline to estimate the C. japonica repeat fraction of 73 %. This enabled us to identify and characterize the most prominent satellite DNAs, Camellia japonica satellite 1- (CajaSat1–CajaSat4), and the 5S ribosomal DNA (rDNA) by bioinformatics, fluorescent in situ and Southern hybridization. Within the Camellia genus, satellite spreading, array expansion and formation of higher-order structures highlight different modes of repeat evolution. The CajaSat satellites localize at prominent chromosomal sites, including (peri)centromeres and subtelomeres of all chromosomes, thus serving as chromosomal landmarks for their identification. This work provides an insight into the C. japonica chromosome organization and significantly expands the Camellia genomic knowledge, also with respect to the tea plant Camellia sinensis. Keywords Camellia japonica RepeatExplorer Fluorescent in situ hybridization Satellite DNA Tandem repeats