Major repeat components covering one‐third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy |
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Authors: | Hong‐Il Choi Nomar E Waminal Hye Mi Park Nam‐Hoon Kim Beom Soon Choi Minkyu Park Doil Choi Yong Pyo Lim Soo‐Jin Kwon Beom‐Seok Park Hyun Hee Kim Tae‐Jin Yang |
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Institution: | 1. Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, , Seoul, 151‐921 Korea;2. National Instrumentation Center for Environmental Management, Seoul National University, , Seoul, 151‐742 Korea;3. Department of Horticulture, Chungnam National University, , Daejeon, 305‐764 Korea;4. Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, , Suwon, 441‐707 Korea;5. Department of Life Science, Plant Biotechnology Institute, Sahmyook University, , Seoul, 139–742 Korea |
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Abstract: | Ginseng (Panax ginseng) is a famous medicinal herb, but the composition and structure of its genome are largely unknown. Here we characterized the major repeat components and inspected their distribution in the ginseng genome. By analyzing three repeat‐rich bacterial artificial chromosome (BAC) sequences from ginseng, we identified complex insertion patterns of 34 long terminal repeat retrotransposons (LTR‐RTs) and 11 LTR‐RT derivatives accounting for more than 80% of the BAC sequences. The LTR‐RTs were classified into three Ty3/gypsy (PgDel, PgTat and PgAthila) and two Ty1/Copia (PgTork and PgOryco) families. Mapping of 30‐Gbp Illumina whole‐genome shotgun reads to the BAC sequences revealed that these five LTR‐RT families occupy at least 34% of the ginseng genome. The Ty3/Gypsy families were predominant, comprising 74 and 33% of the BAC sequences and the genome, respectively. In particular, the PgDel family accounted for 29% of the genome and presumably played major roles in enlargement of the size of the ginseng genome. Fluorescence in situ hybridization (FISH) revealed that the PgDel1 elements are distributed throughout the chromosomes along dispersed heterochromatic regions except for ribosomal DNA blocks. The intensity of the PgDel2 FISH signals was biased toward 24 out of 48 chromosomes. Unique gene probes showed two pairs of signals with different locations, one pair in subtelomeric regions on PgDel2‐rich chromosomes and the other in interstitial regions on PgDel2‐poor chromosomes, demonstrating allotetraploidy in ginseng. Our findings promote understanding of the evolution of the ginseng genome and of that of related species in the Araliaceae. |
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Keywords: | Panax ginseng long terminal repeat retrotransposon heterochromatin allotetraploidy genome evolution |
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