Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1(T): chromosome II is a true chromosome
Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1(T): chromosome II is a true chromosome
复制标题
DOI：
10.1099/00221287-143-10-3085
复制
发表时间：
1997-10-01
期刊：
影响因子：
--
通讯作者：
Kaplan, S
中科院分区：
文献类型：
--
作者：
Choudhary, M;Mackenzie, C;Kaplan, S
光合细菌Rhodobacter sphaeroides 2.4.1（T）具有两条染色体，CI（类似于3.0 Mb）和CII（类似于0.9 Mb）。在这项研究中，采用低冗余测序策略，分析了23个47 cosmetics从一个有序的CII库。这23个粘粒插入片段的长度之和类似于495 kb，其包含类似于417 kb的独特DNA。进行总共1145次测序运行，每次运行产生559+/-268个碱基的序列，得到类似于640 kb的总序列。编辑后，估计每次运行有2.8%的碱基是不明确的。去除载体和大肠杆菌的序列后，剩余的565 kb相似的R.组装类球蛋白序列，产生类似于291 kb的独特序列。这些独特序列的BLASTX分析表明，类似于131 kb（45%的独特序列）与已知基因或数据库中假设或未知功能的ORF（dORF）匹配。共发现144个与数据库强匹配的基因，其中101个代表编码多种功能的基因，例如氨基酸生物合成、光合作用、营养物质转运和各种调控功能。两个rRNA操纵子（rrnB和rrnC）和五个tRNA也被确定。然后使用GCG软件包中的CODONPREFERENCE分析未产生数据库匹配的剩余160 kb DNA序列。该分析表明，122 kb（占总独特DNA序列的42%）可以编码推定的ORF（pORF），其余38 kb（13%）可能代表非编码基因间DNA。从迄今为止获得的数据来看，CII似乎并不专门用于编码任何特定的代谢功能、生理状态或生长条件。这些数据表明，CII包含的基因，其功能与任何其他细菌染色体上发现的基因一样多样，并且还包含可能被证明是该生物体所独有的序列（pORF）。
The photosynthetic bacterium Rhodobacter sphaeroides 2.4.1(T) has two chromosomes, CI (similar to 3.0 Mb) and CII (similar to 0.9 Mb). In this study a low-redundancy sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library. The sum of the lengths of these 23 cosmid inserts was similar to 495 kb, which comprised similar to 417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each run generating 559+/-268 bases of sequence to give similar to 640 kb of total sequence. After editing, similar to 2.8% bases per run were estimated to be ambiguous. After the removal of vector and Escherichia coli sequences, the remaining similar to 565 kb of R. sphaeroides sequences were assembled, generating similar to 291 kb of unique sequences. BLASTX analysis of these unique sequences suggested that similar to 131 kb (45% of the unique sequence) had matches to either known genes, or database ORFs of hypothetical or unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of these matches represented genes encoding a wide variety of functions, e.g. amino acid biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA operons (rrnB and rrnC) and five tRNAs were also identified. The remaining 160 kb of DNA sequence which did not yield database matches was then analysed using CODONPREFERENCE from the GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could encode putative ORFs (pORFs), with the remaining 38 kb (13%) possibly representing non-coding intergenic DNA. From the data so far obtained, CII does not appear to be specialized for encoding any particular metabolic function, physiological state or growth condition. These data suggest that CII contains genes which are functionally as diverse as those found on any other bacterial chromosome and also contains sequences (pORFs) which may prove to be unique to this organism.