PMID- 24456463
OWN - NLM
STAT- MEDLINE
DCOM- 20141112
LR  - 20140312
IS  - 1365-313X (Electronic)
IS  - 0960-7412 (Linking)
VI  - 77
IP  - 6
DP  - 2014 Mar
TI  - Major repeat components covering one-third of the ginseng (Panax ginseng C.A. 
      Meyer) genome and evidence for allotetraploidy.
PG  - 906-16
LID - 10.1111/tpj.12441 [doi]
AB  - 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.
CI  - (c) 2014 The Authors The Plant Journal (c) 2014 John Wiley & Sons Ltd.
FAU - Choi, Hong-Il
AU  - Choi HI
AD  - 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.
FAU - Waminal, Nomar E
AU  - Waminal NE
FAU - Park, Hye Mi
AU  - Park HM
FAU - Kim, Nam-Hoon
AU  - Kim NH
FAU - Choi, Beom Soon
AU  - Choi BS
FAU - Park, Minkyu
AU  - Park M
FAU - Choi, Doil
AU  - Choi D
FAU - Lim, Yong Pyo
AU  - Lim YP
FAU - Kwon, Soo-Jin
AU  - Kwon SJ
FAU - Park, Beom-Seok
AU  - Park BS
FAU - Kim, Hyun Hee
AU  - Kim HH
FAU - Yang, Tae-Jin
AU  - Yang TJ
LA  - eng
SI  - GENBANK/KF357942
SI  - GENBANK/KF357943
SI  - GENBANK/KF357944
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140224
PL  - England
TA  - Plant J
JT  - The Plant journal : for cell and molecular biology
JID - 9207397
RN  - 0 (DNA, Plant)
RN  - 0 (Heterochromatin)
RN  - 0 (Retroelements)
SB  - IM
MH  - Amino Acid Sequence
MH  - Base Sequence
MH  - Chromosomes, Artificial, Bacterial
MH  - Chromosomes, Plant/*genetics
MH  - DNA, Plant/genetics
MH  - Evolution, Molecular
MH  - Genome, Plant/*genetics
MH  - Heterochromatin
MH  - In Situ Hybridization, Fluorescence
MH  - Models, Genetic
MH  - Molecular Sequence Data
MH  - Panax/cytology/*genetics
MH  - Phylogeny
MH  - Retroelements/*genetics
MH  - Sequence Analysis, DNA
MH  - Terminal Repeat Sequences/*genetics
MH  - Tetraploidy
OTO - NOTNLM
OT  - Panax ginseng
OT  - allotetraploidy
OT  - genome evolution
OT  - heterochromatin
OT  - long terminal repeat retrotransposon
EDAT- 2014/01/25 06:00
MHDA- 2014/11/13 06:00
CRDT- 2014/01/25 06:00
PHST- 2013/12/11 00:00 [received]
PHST- 2014/01/07 00:00 [revised]
PHST- 2014/01/13 00:00 [accepted]
PHST- 2014/01/25 06:00 [entrez]
PHST- 2014/01/25 06:00 [pubmed]
PHST- 2014/11/13 06:00 [medline]
AID - 10.1111/tpj.12441 [doi]
PST - ppublish
SO  - Plant J. 2014 Mar;77(6):906-16. doi: 10.1111/tpj.12441. Epub 2014 Feb 24.