De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome.
De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome.
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DOI：
10.1186/1471-2229-12-61
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发表时间：
2012-05-01
影响因子：
5.3
通讯作者：
Simon P
中科院分区：
文献类型：
--
作者：
Iorizzo M;Senalik D;Szklarczyk M;Grzebelus D;Spooner D;Simon P
细胞器基因组的序列分析揭示了植物细胞进化的重要方面。本研究的范围是开发一种方法，从头组装的胡萝卜线粒体基因组使用下一代序列数据从总基因组DNA。来自胡萝卜454全基因组文库的测序数据用于开发线粒体基因组的从头组装。一种新的生物信息学工具的开发允许可视化重叠群连接和从头组装的阐明。Southern杂交表明，重组跨越两个大的重复。基因组注释允许鉴定44个蛋白质编码基因，3个rRNA和17个tRNA。质体基因组序列的鉴定允许细胞器基因组比较。线粒体基因间序列分析允许检测到胡萝卜质体基因组特异性的DNA片段。PCR扩增和序列分析在不同的伞形科物种揭示了一致的保护线粒体基因组中的这一片段和插入在胡萝卜属质体基因组中，线粒体的DNA转移到质体的证据。与逆转录转座子元件的序列相似性表明转座子样事件将该序列转移到质体基因组中的可能性。本研究证实了全基因组测序是高等植物线粒体基因组从头组装的一种实用方法。此外，还报道了区室间基因组相互作用的一个新方面，为DNA转移到被子植物质体基因组中提供了第一个证据。这里使用的方法可以更广泛地用于测序和组装不同物种的线粒体基因组。这些信息将使我们能够更好地了解房室间的相互作用和细胞进化。
Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.
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影响因子：
5.4
作者：
Archibald JM;Richards TA
通讯作者：
Richards TA
影响因子：
4.4
作者：
Aury JM;Cruaud C;Barbe V;Rogier O;Mangenot S;Samson G;Poulain J;Anthouard V;Scarpelli C;Artiguenave F;Wincker P
通讯作者：
Wincker P
影响因子：
11.6
作者：
Alverson, Andrew J.;Rice, Danny W.;Palmer, Jeffrey D.
通讯作者：
Palmer, Jeffrey D.
影响因子：
10.7
作者：
Goremykin, Vadim V.;Salamini, Francesco;Viola, Roberto
通讯作者：
Viola, Roberto
DOI：
10.1073/pnas.042694899
发表时间：
2002-07-23
影响因子：
11.1
作者：
Adams, KL;Qiu, YL;Palmer, JD
通讯作者：
Palmer, JD