Genome-wide Characterization of Long Terminal Repeat -retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1-copia and Ty3-gypsy Retrotransposons
查看参考文献52篇
|
文摘
|
The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers. Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame. High heterogeneity among RT sequences of both Ty1-copia and Ty3-gypsy group retrotransposons was observed, but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements. Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (～5 000) and Ty3-gypsy (～26 000). All elements of the two types of LTR retrotransposons comprise approximately 38% of the M. domestica genome, with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%). Transcription was not detected by reverse transcription-polymerase chain reaction for either Ty1-copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine. This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome. Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon, but the latter has a higher copy number, which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution. |
|
来源
|
Journal of Integrative Plant Biology
,2008,50(9):1130-1139 【核心库】
|
|
DOI
|
10.1111/j.1744-7909.2008.00717.x
|
|
关键词
|
heterogeneity
;
Malus domestica
;
retrotransposon
;
reverse transcriptase
;
transcriptional activity
|
|
地址
|
College of Horticulture, Shenyang Agricultural University, Shenyang, 110161
|
|
语种
|
英文 |
|
文献类型
|
研究性论文 |
|
ISSN
|
1672-9072 |
|
学科
|
植物学 |
|
基金
|
国家自然科学基金
;
国家教育部高等学校博士学科点专项科研基金
|
|
文献收藏号
|
CSCD:3324769
|
参考文献 共
52
共3页
|
|
1.
Altschul SF. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs.
Nucleic Acids Res,1997,25:3389-3402
|
被引
1180
次
|
|
|
|
|
2.
Antonius-Klemola K. TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports.
Theor. Appl. Genet,2006,112:999-1008
|
被引
11
次
|
|
|
|
|
3.
Beguiristain T. Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco:consequences for retrotransposon control and evolution in plants.
Plant Physiol,2001,127:212-221
|
被引
20
次
|
|
|
|
|
4.
Bennetzen JL. Mechanisms and rates of genome expansion and contraction in flowering plants.
Genetica,2002,115:29-36
|
被引
7
次
|
|
|
|
|
5.
Casacuberta JM. Quasispecies in retrotransposons:a role for sequence variability in Tnt1 evolution.
Genetica,1997,100:109-117
|
被引
1
次
|
|
|
|
|
6.
Chang L. Detection of strawberry RNA and DNA viruses by RT-PCR using total nucleic acid as a template.
J. Phytopathol,2007,155:431-436
|
被引
19
次
|
|
|
|
|
7.
Dixit A. Reverse transcriptase domain sequences from mungbean(Vigna radiata)LTR retrotransposons:sequence characterization and phylogenetic analysis.
Plant Cell Rep,2006,25:100-111
|
被引
2
次
|
|
|
|
|
8.
Feschotte C. Plant transposable elements:where genetics meets genomics.
Nat. Rev,2002,3:329-341
|
被引
2
次
|
|
|
|
|
9.
Finnegan DJ. Eukaryotic transposable elements and genome evolution.
Trends Genet,1989,5:103-107
|
被引
27
次
|
|
|
|
|
10.
Flavel AJ. Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants.
Nucleic Acids Res,1992,20:3639-3644
|
被引
1
次
|
|
|
|
|
11.
Flavell AJ. Plant transposable elements and the genome.
Curr. Opin. Genet. Dev,1994,4:838-844
|
被引
11
次
|
|
|
|
|
12.
Flavell AJ. Extreme heterogeneity of Ty1-copia group retrotransposons in plants.
Mol. Gen. Genet,1992,231:233-242
|
被引
16
次
|
|
|
|
|
13.
Havecker ER. The diversity of LTR retrotransposons.
Genome Biol,2004,5:225
|
被引
13
次
|
|
|
|
|
14.
Heslop-Harrison JS. The chromosomal distribution of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution.
Genetica,1997,100:197-204
|
被引
4
次
|
|
|
|
|
15.
Hill P. Retrotransposon populations of Vicia species with varying genome size.
Mol. Genet. Genomics,2005,273:371-381
|
被引
6
次
|
|
|
|
|
16.
Hirochika H. Ty1-copia group retrotransposons as ubiquitous components of plant genomes.
Jpn. J. Genet,1993,68:35-46
|
被引
6
次
|
|
|
|
|
17.
Hirochika H. Retrotransposons of rice involved in mutations induced by tissue culture.
Proc. Natl. Acad. Sci. USA,1996,93:7783-7788
|
被引
64
次
|
|
|
|
|
18.
Hirochika H. Autonomous transposition of the tobacco retrotransposon Tto1 in rice.
Plant Cell,1996,8:725-734
|
被引
7
次
|
|
|
|
|
19.
Kobayashi S. Retrotransposon-induced mutations in grape skin color.
Science,2004,304:982
|
被引
106
次
|
|
|
|
|
20.
Kumar A. Plant retrotransposons.
Annu. Rev. Genet,1999,33:479-532
|
被引
97
次
|
|
|
|
|
了解气象卫星更多信息，请访问