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

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

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

Content Provider	Springer Nature Link
Author	Heitkam, Tony Petrasch, Stefan Zakrzewski, Falk Kögler, Anja Wenke, Torsten Wanke, Stefan Schmidt, Thomas
Copyright Year	2015
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.
Starting Page	791
Ending Page	806
Page Count	16
File Format	PDF
ISSN	09673849
Journal	Chromosome Research
Volume Number	23
Issue Number	4
e-ISSN	15736849
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-11-18
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Camellia japonica RepeatExplorer Fluorescent in situ hybridization Satellite DNA Tandem repeats Cell Biology Human Genetics Animal Genetics and Genomics Plant Genetics & Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics

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