Characterization of the genome of bald cypress.
Characterization of the genome of bald cypress.
复制标题
DOI：
10.1186/1471-2164-12-553
复制
发表时间：
2011-11-11
期刊：
影响因子：
4.4
通讯作者：
Peterson DG
中科院分区：
文献类型：
--
作者：
Liu W;Thummasuwan S;Sehgal SK;Chouvarine P;Peterson DG
秃柏（Taxodium distichum var. distichum）是一种具有巨大生态和经济价值的针叶树。它是柏科的一员，柏科还包括柏树、红木、红杉、土jas和杜松。虽然秃柏树的基因组是人类基因组的三倍多，但它的1C DNA含量是所有针叶树中最少的。为了进一步了解秃柏树的基因组，深入了解柏科基因组的进化过程，我们进行了Cot分析，并使用Cot过滤技术对Taxodium DNA进行了研究。此外，我们构建了一个6.7个基因组等效的BAC文库，我们用已知的紫杉属基因和选择重复序列进行筛选。秃柏树基因组由90%的重复DNA组成，大多数序列在低到中拷贝数中被发现。最丰富的重复序列在每个基因组中少于25000个拷贝。大约7.4%的基因组是单拷贝/低拷贝DNA（即在1到5个拷贝中发现的序列）。高重复克隆的测序表明，大多数紫杉属重复序列与以前鉴定的植物重复序列高度不同。秃柏树BAC文库包含606,336个克隆（平均插入大小为113 kb），总共提供了6.7倍的秃柏树基因组等效覆盖率。用已知基因进行Macroarray筛选，平均每个探针每个基因组当量产生约1.5个阳性克隆。使用Cot-1 DNA进行文库筛选显示，大约83%的BAC克隆包含每个基因组迭代103至104次的重复序列。秃柏的BAC库是第一个为松科以外的针叶树物种生成的。Taxodium BAC文库在裸子比较基因组学、物理定位、基因组测序和基因/多态性发现方面具有重要的应用价值。秃柏树的单/低拷贝（SL）成分是拟南芥基因组的4.6倍。与其他裸子植物一样，紫杉属中大量的SL DNA可能是古代重复拷贝和基因/假基因复制之间分歧的结果。
Bald cypress (Taxodium distichum var. distichum) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias, thujas, and junipers. While the bald cypress genome is more than three times the size of the human genome, its 1C DNA content is amongst the smallest of any conifer. To learn more about the genome of bald cypress and gain insight into the evolution of Cupressaceae genomes, we performed a Cot analysis and used Cot filtration to study Taxodium DNA. Additionally, we constructed a 6.7 genome-equivalent BAC library that we screened with known Taxodium genes and select repeats. The bald cypress genome is composed of 90% repetitive DNA with most sequences being found in low to mid copy numbers. The most abundant repeats are found in fewer than 25,000 copies per genome. Approximately 7.4% of the genome is single/low-copy DNA (i.e., sequences found in 1 to 5 copies). Sequencing of highly repetitive Cot clones indicates that most Taxodium repeats are highly diverged from previously characterized plant repeat sequences. The bald cypress BAC library consists of 606,336 clones (average insert size of 113 kb) and collectively provides 6.7-fold genome equivalent coverage of the bald cypress genome. Macroarray screening with known genes produced, on average, about 1.5 positive clones per probe per genome-equivalent. Library screening with Cot-1 DNA revealed that approximately 83% of BAC clones contain repetitive sequences iterated 103 to 104 times per genome. The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The Taxodium BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single/low-copy (SL) component of bald cypress is 4.6 times the size of the Arabidopsis genome. As suggested for other gymnosperms, the large amount of SL DNA in Taxodium is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication.