title: Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe's oldest Camellia japonica.
abstract: 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 1-4 (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.
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Tony
authors.initials: T
authors.lastname: Heitkam
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Petrasch
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Zakrzewski
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Kögler
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Wenke
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wanke
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany. Thomas.Schmidt@tu-dresden.de.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmidt
mesh_terms: D001483:Base Sequence; D028244:Camellia / Q000235:genetics*; D032461:Chromosomes, Plant; D016384:Consensus Sequence; D019175:DNA Methylation; D004276:DNA, Satellite; D040481:Genome Components; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D020080:Tandem Repeat Sequences
chemical_list: D004276:DNA, Satellite
keywords: Camellia japonica; Fluorescent in situ hybridization; RepeatExplorer; Satellite DNA; Tandem repeats