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Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy.
Plant J. 2014 Mar; 77(6):906-16.PJ

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.

Authors+Show Affiliations

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.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24456463

Citation

Choi, Hong-Il, et al. "Major Repeat Components Covering One-third of the Ginseng (Panax Ginseng C.A. Meyer) Genome and Evidence for Allotetraploidy." The Plant Journal : for Cell and Molecular Biology, vol. 77, no. 6, 2014, pp. 906-16.
Choi HI, Waminal NE, Park HM, et al. Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy. Plant J. 2014;77(6):906-16.
Choi, H. I., Waminal, N. E., Park, H. M., Kim, N. H., Choi, B. S., Park, M., Choi, D., Lim, Y. P., Kwon, S. J., Park, B. S., Kim, H. H., & Yang, T. J. (2014). Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy. The Plant Journal : for Cell and Molecular Biology, 77(6), 906-16. https://doi.org/10.1111/tpj.12441
Choi HI, et al. Major Repeat Components Covering One-third of the Ginseng (Panax Ginseng C.A. Meyer) Genome and Evidence for Allotetraploidy. Plant J. 2014;77(6):906-16. PubMed PMID: 24456463.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy. AU - Choi,Hong-Il, AU - Waminal,Nomar E, AU - Park,Hye Mi, AU - Kim,Nam-Hoon, AU - Choi,Beom Soon, AU - Park,Minkyu, AU - Choi,Doil, AU - Lim,Yong Pyo, AU - Kwon,Soo-Jin, AU - Park,Beom-Seok, AU - Kim,Hyun Hee, AU - Yang,Tae-Jin, Y1 - 2014/02/24/ PY - 2013/12/11/received PY - 2014/01/07/revised PY - 2014/01/13/accepted PY - 2014/1/25/entrez PY - 2014/1/25/pubmed PY - 2014/11/13/medline KW - Panax ginseng KW - allotetraploidy KW - genome evolution KW - heterochromatin KW - long terminal repeat retrotransposon SP - 906 EP - 16 JF - The Plant journal : for cell and molecular biology JO - Plant J. VL - 77 IS - 6 N2 - 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. SN - 1365-313X UR - https://www.unboundmedicine.com/medline/citation/24456463/Major_repeat_components_covering_one_third_of_the_ginseng__Panax_ginseng_C_A__Meyer__genome_and_evidence_for_allotetraploidy_ L2 - https://doi.org/10.1111/tpj.12441 DB - PRIME DP - Unbound Medicine ER -