NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs
NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs
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DOI：
10.1093/molbev/msh210
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发表时间：
2004-10-01
影响因子：
10.7
通讯作者：
Leister, D
中科院分区：
文献类型：
--
作者：
Richly, E;Leister, D
NUPT（nuclear plastid DNA，核质体DNA）来源于质体到核的DNA转移，存在于各种植物中。实验数据表明，DNA转移是一个持续的，高频率的过程，但NUPT的种间多样性，没有明确的解释存在。在这里，NUPTs在四个测序的质体轴承物种和它们的基因组组织的库存。具有预测的低基因密度的大基因组包含更多的NUPT。在衣原体和疟原虫中，DNA转移发生，但有限，可能是因为每个细胞中只有一个质体。在拟南芥和水稻中，NUPT经常组织成簇。紧密簇可以包含NUPT和NUMT（核线粒体DNA），表明preNUPT和preNUMT可能在整合之前已经多联体化。这样一个假设的preNUPT-preNUMT池的组成似乎是可变的，这意味着在不同的物种中NUPT：NUMT的比例有很大的不同。松散的簇可以跨越几十kbps的核DNA，并且它们包含比从核细胞器DNA的随机基因组分布中预期的明显更多的NUPT或NUMT。NUPT/NUMT和质体/线粒体DNA之间的序列相似性水平与整合子的大小相关。这意味着最初的插入是大的，并随着进化时间的推移衰减成具有不同序列的较小片段。我们认为，紧密和松散的集群代表这个衰变过程的中间体。
NUPTs (nuclear plastid DNA) derive from plastid-to-nucleus DNA transfer and exist in various plant species. Experimental data imply that the DNA transfer is an ongoing, highly frequent process, but for the interspecific diversity of NUPTs, no clear explanation exists. Here, an inventory of NUPTs in the four sequenced plastid-bearing species and their genomic organization is presented. Large genomes with a predicted low gene density contain more NUPTs. In Chlamydomonas and Plasmodium, DNA transfer occurred but was limited, probably because of the presence of only one plastid per cell. In Arabidopsis and rice, NUPTs are frequently organized as clusters. Tight clusters can contain both NUPTs and NUMTs (nuclear mitochondrial DNA), indicating that preNUPTs and preNUMTs might have concatamerized before integration. The composition of such a hypothetical preNUPT-preNUMT pool seems to be variable, as implied by substantially different NUPTs:NUMTs ratios in different species. Loose clusters can span several dozens of kbps of nuclear DNA, and they contain markedly more NUPTs or NUMTs than expected from a random genomic distribution of nuclear organellar DNA. The level of sequence similarity between NUPTs/NUMTs and plastid/ mitochondrial DNA correlates with the size of the integrant. This implies that original insertions are large and decay over evolutionary time into smaller fragments with diverging sequences. We suggest that tight and loose clusters represent intermediates of this decay process.