Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes.
Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes.
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DOI：
10.1371/journal.pone.0006515
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发表时间：
2009-08-05
期刊：
影响因子：
3.7
通讯作者：
Dujon B
中科院分区：
文献类型：
--
作者：
Rolland T;Neuvéglise C;Sacerdot C;Dujon B
在真核生物基因组中偶尔会提到水平基因转移，但此类事件的数量似乎比原核生物少得多，在原核生物中它们发挥着重要的功能和进化作用。在酵母中，很少有独立的案例被描述，其中一些对应于主要的代谢功能，但迄今为止还没有尝试过水平转移基因的系统筛选。利用五个新测序和注释的酵母科基因组之间的同线性保守性，我们在保守同线性块内仅存在于一个物种的基因中对 HGT 候选基因进行了系统搜索。基于与细菌蛋白质的相似性和重建的系统发育，我们在 255 个物种特异性基因中发现了 11 个 HGT 候选基因。这对应于至少六个转移事件，因为一些水平获得的基因似乎在酵母基因组中快速复制（例如耐热克鲁维酵母中的 YwqG 基因和克鲁维酵母中 IS607 家族的丝氨酸重组酶基因）。我们表明，所得的副本受到强大的功能选择压力的影响。讨论了与 HGT 候选物普遍较小尺寸相关的 DNA 转移和整合机制。我们对有限物种的研究结果使之前发表的半子囊菌酵母中 HGT 病例的数量增加了 50%，表明此类事件比通常认为的更为频繁。我们的限制性方法并不排除存在其他 HGT 事件的可能性。事实上，几个酵母物种共有的祖先事件肯定被忽视了，并且现有数据库中同源物的缺乏留下了插入保守同线性块中的 244 个剩余物种特异性基因的起源问题。
Horizontal gene transfer has been occasionally mentioned in eukaryotic genomes, but such events appear much less numerous than in prokaryotes, where they play important functional and evolutionary roles. In yeasts, few independent cases have been described, some of which corresponding to major metabolic functions, but no systematic screening of horizontally transferred genes has been attempted so far. Taking advantage of the synteny conservation among five newly sequenced and annotated genomes of Saccharomycetaceae, we carried out a systematic search for HGT candidates amidst genes present in only one species within conserved synteny blocks. Out of 255 species-specific genes, we discovered 11 candidates for HGT, based on their similarity with bacterial proteins and on reconstructed phylogenies. This corresponds to a minimum of six transfer events because some horizontally acquired genes appear to rapidly duplicate in yeast genomes (e.g. YwqG genes in Kluyveromyces thermotolerans and serine recombinase genes of the IS607 family in Saccharomyces kluyveri). We show that the resulting copies are submitted to a strong functional selective pressure. The mechanisms of DNA transfer and integration are discussed, in relation with the generally small size of HGT candidates. Our results on a limited set of species expand by 50% the number of previously published HGT cases in hemiascomycetous yeasts, suggesting that this type of event is more frequent than usually thought. Our restrictive method does not exclude the possibility that additional HGT events exist. Actually, ancestral events common to several yeast species must have been overlooked, and the absence of homologs in present databases leaves open the question of the origin of the 244 remaining species-specific genes inserted within conserved synteny blocks.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
3.4
作者：
Andersson JO;Roger AJ
通讯作者：
Roger AJ
映射减数分裂的单链DNA揭示了酿酒酵母中DNA双链断裂的新景观。
影响因子：
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作者：
Buhler, Cyril;Borde, Valerie;Lichten, Michael
通讯作者：
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影响因子：
64.8
作者：
Dujon, B;Sherman, D;Souciet, JL
通讯作者：
Souciet, JL
影响因子：
3.4
作者：
Fitzpatrick, David A.;Logue, Mary E.;Butler, Geraldine
通讯作者：
Butler, Geraldine