Recognizing the pseudogenes in bacterial genomes.
Recognizing the pseudogenes in bacterial genomes.
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DOI：
10.1093/nar/gki631
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发表时间：
2005
影响因子：
14.9
通讯作者：
Ochman, H
中科院分区：
文献类型：
--
作者：
Lerat, E;Ochman, H
现在已知假基因是细菌基因组的常规特征，并且在最近出现的细菌病原体的基因组中发现特别高的数量。由于大多数假基因是通过序列比对识别的，我们使用新获得的基因组序列来识别来自4个细菌属的11个基因组中的假基因，每个细菌属至少包含1种人类病原体。假基因的数量范围从金黄色葡萄球菌MW 2中的27个到鼠疫耶尔森氏菌CO 92中的337个（例如基因组中注释基因的1-8%）。大多数假基因是由小的移码插入缺失形成的，但是由于终止密码子富含A + T，因此与更多富含G + C的基因组相比，两种低G + C的革兰氏阳性分类群（链球菌和葡萄球菌）具有相对高比例的由无义突变产生的假基因。超过一半的假基因是由其原始功能被注释为“假设”或“未知”的基因产生的;然而，几个广泛分布的参与核苷酸加工、修复或复制的基因在一个已测序的创伤弧菌基因组中成为假基因。尽管我们的许多比较涉及基因库广泛重叠的密切相关菌株，但每个基因组都包含一组基本上独特的假基因，这表明假基因在大多数细菌基因组中相对较快地形成和消除。
Pseudogenes are now known to be a regular feature of bacterial genomes and are found in particularly high numbers within the genomes of recently emerged bacterial pathogens. As most pseudogenes are recognized by sequence alignments, we use newly available genomic sequences to identify the pseudogenes in 11 genomes from 4 bacterial genera, each of which contains at least 1 human pathogen. The numbers of pseudogenes range from 27 in Staphylococcus aureus MW2 to 337 in Yersinia pestis CO92 (e.g. 1–8% of the annotated genes in the genome). Most pseudogenes are formed by small frameshifting indels, but because stop codons are A + T-rich, the two low-G + C Gram-positive taxa (Streptococcus and Staphylococcus) have relatively high fractions of pseudogenes generated by nonsense mutations when compared with more G + C-rich genomes. Over half of the pseudogenes are produced from genes whose original functions were annotated as ‘hypothetical’ or ‘unknown’; however, several broadly distributed genes involved in nucleotide processing, repair or replication have become pseudogenes in one of the sequenced Vibrio vulnificus genomes. Although many of our comparisons involved closely related strains with broadly overlapping gene inventories, each genome contains a largely unique set of pseudogenes, suggesting that pseudogenes are formed and eliminated relatively rapidly from most bacterial genomes.
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影响因子：
64.8
作者：
Rain, JC;Selig, L;Legrain, P
通讯作者：
Legrain, P
影响因子：
168.9
作者：
Makino, K;Oshima, K;Iida, T
通讯作者：
Iida, T
DOI：
10.1073/pnas.152298499
发表时间：
2002-07-23
影响因子：
11.1
作者：
Beres, SB;Sylva, GL;Musser, JM
通讯作者：
Musser, JM
影响因子：
64.8
作者：
Heidelberg JF;Eisen JA;Nelson WC;Clayton RA;Gwinn ML;Dodson RJ;Haft DH;Hickey EK;Peterson JD;Umayam L;Gill SR;Nelson KE;Read TD;Tettelin H;Richardson D;Ermolaeva MD;Vamathevan J;Bass S;Qin H;Dragoi I;Sellers P;McDonald L;Utterback T;Fleishmann RD;Nierman WC;White O;Salzberg SL;Smith HO;Colwell RR;Mekalanos JJ;Venter JC;Fraser CM
通讯作者：
Fraser CM
DOI：
10.1073/pnas.180094797
发表时间：
2000-09-12
影响因子：
11.1
作者：
Pupo, GM;Lan, RT;Reeves, PR
通讯作者：
Reeves, PR