Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy.
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.
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.
Hong-Il
HI
Choi
Nomar E
NE
Waminal
Hye Mi
HM
Park
Nam-Hoon
NH
Kim
Beom Soon
BS
Choi
Minkyu
M
Park
Doil
D
Choi
Yong Pyo
YP
Lim
Soo-Jin
SJ
Kwon
Beom-Seok
BS
Park
Hyun Hee
HH
Kim
Tae-Jin
TJ
Yang
D000595:Amino Acid Sequence; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D006570:Heterochromatin; D017404:In Situ Hybridization, Fluorescence; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005894:Panax / Q000166:cytology / Q000235:genetics*; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences / Q000235:genetics*; D057891:Tetraploidy
D018744:DNA, Plant; D006570:Heterochromatin; D018626:Retroelements
Panax ginseng; allotetraploidy; genome evolution; heterochromatin; long terminal repeat retrotransposon