Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3.
Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3.
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DOI：
10.1093/dnares/5.2.55
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发表时间：
1998-04-30
期刊：
影响因子：
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通讯作者：
Kikuchi, H
中科院分区：
文献类型：
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作者：
Kawarabayasi, Y;Sawada, M;Kikuchi, H
通过组装用于填补空白的fosmid克隆和长聚合酶链反应（PCR）产物的基于物理图谱的contigs序列，确定了一种超嗜热古细菌——阔志焦球菌OT3的完整基因组序列。基因组总长度为1738505 bp。直接从基因组DNA中扩增出的长PCR产物的限制性内切分析支持了整个基因组序列的真实性。作为潜在的蛋白质编码区，共分配了2061个开放阅读框（orf），通过对公共数据库的相似性搜索，406个（19.7%）与推测功能的基因相关，453个（22.0%）与注册但功能未知的序列相关。其余1202个orf（58.3%）与数据库中的序列没有明显的相似性。基因组中指定orf的序列比较表明，相当数量的orf是由序列重复产生的。通过相似度搜索，假设有11个orf包含内部元素。鉴定的RNA基因为1个16S-23S rRNA操纵子、2个5S rRNA基因和46个tRNA基因，其中2个具有内含子结构。所有被分配的orf和RNA编码区占全基因组的91.25%。本文中提供的数据可在互联网上找到：@www.nite.go.jp。
The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http:@www.nite.go.jp.