A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs

Abstract

BackgroundPanax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification.MethodsPolymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR.ResultsRecently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4′,6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype.ConclusionIdentification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

“…Chromosome numbers of P. ginseng are based on previous studies (Waminal et al ., ; Waminal et al . ). Images were captured with an Olympus BX53 fluorescence microscope equipped with a Leica DFC365 FS CCD camera and processed using Cytovision ver.…”

Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in Panax ginseng

“…Navy blue, orange, red, and green bands represent DAPI, Pg167TR, 45S rDNA, and 5S rDNA as described in Waminal et al (2017). The DAPI bands in the long arm of chromosomes 1 and 20 are the sites for Pgms1 (patterned arrowhead) and PgGA15 (grey arrowhead) tandem repeats, respectively.…”

“…code NN-0076-000001, https://nabic.rda.go.kr:2360/) was used to mine for microsatellite, minisatellite, and satellite repeats using the RepeatExplorer2 pipeline (Novák et al 2013) after quality trimming as described in RepeatExplorer2 guidelines. Estimation of genome representation (GR) was carried out by multiplying the total number of repeats with the repeat period size followed by normalization of the size of raw reads used with the 3.6 Gbp genome size of P. ginseng (Waminal et al 2016;Waminal et al 2017). Read mapping and sequence characterization were carried out using CLC Assembly Cell ver.…”

“…Chromosome spreads were prepared according to Waminal et al (2017). Thirty-two microliters of FISH hybridization master mix (50% formamide, 10% dextran sulfate, and 2× SSC), 25 ng of each FAM-and Cy3-modified oligoprobes, and deionized water to a total volume of 40 μL were added to slides.…”

“…With the advancement of next-generation sequencing (NGS) technologies and bioinformatics pipelines to handle NGS data such as TAREAN (Novák et al 2017), high-throughput and more efficient genome-wide repeat identification can be obtained even with low-coverage sequencing. This approach has been successfully demonstrated in some species like pea, banana and cabbage (Macas et al 2007;Hribova et al 2010;Novák et al 2013;Novák et al 2017;Perumal et al 2017;Waminal et al 2017).…”