Ginseng, Panax ginseng C. A. Meyer, has been used as a king medicinal herb in east Asia and has a large genome of more than 3.5 Gbp in 24 haploid chromosomes. Its genome structure, constitution, and phylogenetic history have just gained pace in recent years. Molecular cytogenetic research was carried out in ginseng using next generation sequencing (NGS) whole genome sequence (WGS) reads. Refined fluorescence in situ hybridization (FISH) karyotype was established with repeat probes including several long terminal repeat retrotransposon (LTR-RT, PgDel2, PgDel3, PgTat1, PgTat2, PgTork) and one tandem repeat (Pg167TR) probes. FISH results showed differential accumulation of Ty3/gypsy LTR-RT into subgenomes, suggesting a non-random preferential amplification of retrotransposons and an allotetraploid origin of P. ginseng. Pg167TR was the most abundant TR and showed unique distribution pattern among the 24 chromosomes which allowed to discriminate and characterize each individual chromosome. An extensive Pg167TR repeat accumulation outside functional PgCACTA transposon seemed to indicate non-functionalization of ancient PgCACTA element and a subsequent tandem repeat amplification. Sequence comparison categorized the units into 2 subclasses, PgTRa and PgTRb. Genomic distribution of PgTRb revealed hybridization to only 12 out of 24 chromosome pairs and these support an allotetraploid origin of the ginseng genome. High-throughput and more efficient genome-wide repeat mining was accomplished with low-coverage WGS reads using RepeatExplorer algorithm. The telomeric and two chromosome-specific repeats in ginseng genome were identified and pre-labelled oligonucleotide probes (PLOP) were developed for FISH analysis. The FISH procedure using PLOP was rapid and efficient and the probes were verified as excellent molecular cytogenetic markers to identify each chromosome. These results will be useful for breeding, genetic and physical map integration, sequence assembly validation, and comparative cytogenetic studies to unravel ginseng genomic history. This work was supported by the Cooperative Research Program for Agriculture Science & Technology Development (PJ013119), Rural Development Administration, Korea.
Ginseng, Panax ginseng C. A. Meyer, has been used as a king medicinal herb in east Asia and has a large genome of more than 3.5 Gbp in 24 haploid chromosomes. Its genome structure, constitution, and phylogenetic history have just gained pace in recent years. Molecular cytogenetic research was carried out in ginseng using next generation sequencing (NGS) whole genome sequence (WGS) reads. Refined fluorescence in situ hybridization (FISH) karyotype was established with repeat probes including several long terminal repeat retrotransposon (LTR-RT, PgDel2, PgDel3, PgTat1, PgTat2, PgTork) and one tandem repeat (Pg167TR) probes. FISH results showed differential accumulation of Ty3/gypsy LTR-RT into subgenomes, suggesting a non-random preferential amplification of retrotransposons and an allotetraploid origin of P. ginseng. Pg167TR was the most abundant TR and showed unique distribution pattern among the 24 chromosomes which allowed to discriminate and characterize each individual chromosome. An extensive Pg167TR repeat accumulation outside functional PgCACTA transposon seemed to indicate non-functionalization of ancient PgCACTA element and a subsequent tandem repeat amplification. Sequence comparison categorized the units into 2 subclasses, PgTRa and PgTRb. Genomic distribution of PgTRb revealed hybridization to only 12 out of 24 chromosome pairs and these support an allotetraploid origin of the ginseng genome. High-throughput and more efficient genome-wide repeat mining was accomplished with low-coverage WGS reads using RepeatExplorer algorithm. The telomeric and two chromosome-specific repeats in ginseng genome were identified and pre-labelled oligonucleotide probes (PLOP) were developed for FISH analysis. The FISH procedure using PLOP was rapid and efficient and the prob ...
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