Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia:: A somatic view of the germline
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia:: A somatic view of the germline
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DOI：
10.1101/gr.074534.107
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发表时间：
2008-04-01
期刊：
影响因子：
7
通讯作者：
Sperling, Linda
中科院分区：
文献类型：
--
作者：
Duret, Laurent;Cohen, Jean;Sperling, Linda
纤毛虫是已知的唯一具有生发和体细胞功能的单细胞真核生物。二倍体但沉默的微核将遗传信息传递给下一代。多倍体巨核表达来自基因组流线型版本的遗传信息，但在每代有性繁殖时都被替换。四虫草履虫的大核基因组最近通过散弹枪法测序，提供了进入基因库的途径。72mb的组合代表了体细胞DNA的一致序列，它是在性事件发生后通过合子基因组的可重复重排产生的，包括消除重复序列，精确切除独特拷贝的内部消除序列（IES），以及将细胞基因扩增到高拷贝数。我们报告使用霰弹枪测序数据（bbb10(6)读数代表13倍覆盖的一个完全纯合子克隆）来评估这些发育基因组重排产生的体细胞DNA的可变性。虽然DNA扩增看起来是一致的，但两种DNA消除过程都会产生序列异质性。与之前已知的42个相比，IES切除产生的可变性允许鉴定数百个假定的新IES，并揭示了错误切除编码序列片段的情况。我们证明编码区域的IESs在选择压力下引入翻译在切除失败的情况下过早终止。
Ciliates are the only unicellular eukaryotes known to separate germinal and somatic functions. Diploid but silent micronuclei transmit the genetic information to the next sexual generation. Polyploid macronuclei express the genetic information from a streamlined version of the genome but are replaced at each sexual generation. The macronuclear genome of Paramecium tetraurelia was recently sequenced by a shotgun approach, providing access to the gene repertoire. The 72-Mb assembly represents a consensus sequence for the somatic DNA, which is produced after sexual events by reproducible rearrangements of the zygotic genome involving elimination of repeated sequences, precise excision of unique-copy internal eliminated sequences (IES), and amplification of the cellular genes to high copy number. We report use of the shotgun sequencing data (>10(6) reads representing 13 x coverage of a completely homozygous clone) to evaluate variability in the somatic DNA produced by these developmental genome rearrangements. Although DNA amplification appears uniform, both of the DNA elimination processes produce sequence heterogeneity. The variability that arises from IES excision allowed identification of hundreds of putative new IESs, compared to 42 that were previously known, and revealed cases of erroneous excision of segments of coding sequences. We demonstrate that IESs in coding regions are under selective pressure to introduce premature termination of translation in case of excision failure.