Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome.
Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome.
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DOI：
10.1186/gb-2004-5-10-r79
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发表时间：
2004
期刊：
影响因子：
12.3
通讯作者：
Pereira V
中科院分区：
文献类型：
--
作者：
Pereira V
对拟南芥基因组中LTR反转录转座子的分布和年龄的分析表明，假病毒科沿着染色体随机插入并且最近很活跃，而元病毒科在过去更加活跃并且优先靶向异染色质。多细胞生物的基因组进化和大小变异深受反转录转座子活性的影响。在具有紧凑基因组的高等真核生物中，反转录转座子的拷贝数低于较大基因组中的拷贝数，这可能是由于转座的抑制或插入的消除，并且沿染色体非随机分布。限制逆转录转座子拷贝数和染色体分布的进化机制仍然知之甚少。我研究了紧凑拟南芥基因组中长末端重复（LTR）反转录转座子的进化动力学，使用自动化方法获得不同组元素的全基因组、年龄和物理分布概况，然后比较年轻和年老插入的分布。假病毒科的元件沿着染色体随机插入，并且最近一直很活跃，但插入往往会从常染色质区域丢失，在那里它们不太可能固定，半衰期估计约为 470,000 年。相比之下，后病毒科成员（尤其是 Athila）优先针对异染色质，并且在过去更加活跃。不同的进化机制限制了单个基因组内逆转录转座子的拷贝数和染色体分布。在拟南芥中，它们的非随机基因组分布是由于对常染色质插入的选择和异染色质的优先靶向。常染色质插入的持续更新和针对异染色质的元件活性的下降都限制了反转录转座子 DNA 对拟南芥基因组大小扩展的贡献。
An analysis of the distribution and age of LTR retrotransposons in the Arabidopsis genome revealed that Pseudoviridae insert randomly along the chromosome and have been recently active whereas Metaviridae were more active in the past and preferentially target heterochromatin. Genome evolution and size variation in multicellular organisms are profoundly influenced by the activity of retrotransposons. In higher eukaryotes with compact genomes retrotransposons are found in lower copy numbers than in larger genomes, which could be due to either suppression of transposition or to elimination of insertions, and are non-randomly distributed along the chromosomes. The evolutionary mechanisms constraining retrotransposon copy number and chromosomal distribution are still poorly understood. I investigated the evolutionary dynamics of long terminal repeat (LTR)-retrotransposons in the compact Arabidopsis thaliana genome, using an automated method for obtaining genome-wide, age and physical distribution profiles for different groups of elements, and then comparing the distributions of young and old insertions. Elements of the Pseudoviridae family insert randomly along the chromosomes and have been recently active, but insertions tend to be lost from euchromatic regions where they are less likely to fix, with a half-life estimated at approximately 470,000 years. In contrast, members of the Metaviridae (particularly Athila) preferentially target heterochromatin, and were more active in the past. Diverse evolutionary mechanisms have constrained both the copy number and chromosomal distribution of retrotransposons within a single genome. In A. thaliana, their non-random genomic distribution is due to both selection against insertions in euchromatin and preferential targeting of heterochromatin. Constant turnover of euchromatic insertions and a decline in activity for the elements that target heterochromatin have both limited the contribution of retrotransposon DNA to genome size expansion in A. thaliana.
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DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
影响因子：
1.5
作者：
Kapitonov, VV;Jurka, J
通讯作者：
Jurka, J
影响因子：
64.8
作者：
Bustamante, CD;Nielsen, R;Hartl, DL
通讯作者：
Hartl, DL
影响因子：
10.7
作者：
Blumenstiel, JP;Hartl, DL;Lozovsky, ER
通讯作者：
Lozovsky, ER
影响因子：
10.7
作者：
Filatov, DA;Charlesworth, D
通讯作者：
Charlesworth, D