Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration
Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration
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DOI：
10.1007/s00438-008-0364-z
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发表时间：
2008-10-01
影响因子：
3.1
通讯作者：
Havey, Michael J.
中科院分区：
文献类型：
--
作者：
Jakse, Jernej;Meyer, Jenelle D. F.;Havey, Michael J.
洋葱（Allium cepa）基因组的测序具有挑战性，因为它是栽培植物中最大的核基因组之一。我们对洋葱基因组DNA进行了初步测序，以估计基因密度并调查重复DNA的性质和分布。两个洋葱BAC的完整序列富含AT（64.8%），并显示了长的退化逆转录病毒元件和转座子，类似于其他较大的植物基因组。对随机BAC进行末端测序，并且460个末端中仅3个显示出与蛋白质数据库的显著（e < -25）非细胞器命中。BAC末端序列富含AT（63.4%），与完全测序的BAC相似。洋葱基因组DNA的总长度为499，997 bp，估计平均密度为每168 kb一个基因，是迄今为止报道的最低密度之一。甲基过滤是非常有效的相对于随机鸟枪读在减少匿名序列的频率从82%到55%，并增加非细胞器蛋白质命中从4%到42%。我们的研究结果没有发现基因密集区的证据，并表明甲基过滤的基因组片段的测序应该是一种有效的方法来揭示洋葱基因组中的基因序列。
Sequencing of the onion (Allium cepa) genome is challenging because it has one of the largest nuclear genomes among cultivated plants. We undertook pilot sequencing of onion genomic DNA to estimate gene densities and investigate the nature and distribution of repetitive DNAs. Complete sequences from two onion BACs were AT rich (64.8%) and revealed long tracts of degenerated retroviral elements and transposons, similar to other larger plant genomes. Random BACs were end sequenced and only 3 of 460 ends showed significant (e < -25) non-organellar hits to the protein databases. The BAC-end sequences were AT rich (63.4%), similar to the completely sequenced BACs. A total of 499,997 bp of onion genomic DNA yielded an estimated mean density of one gene per 168 kb, among the lowest reported to date. Methyl filtration was highly effective relative to random shotgun reads in reducing frequencies of anonymous sequences from 82 to 55% and increasing non-organellar protein hits from 4 to 42%. Our results revealed no evidence for gene-dense regions and indicated that sequencing of methyl-filtered genomic fragments should be an efficient approach to reveal genic sequences in the onion genome.