Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution.
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution.
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DOI：
10.1186/1471-2164-14-117
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发表时间：
2013-02-21
期刊：
影响因子：
4.4
通讯作者：
Tautz D
中科院分区：
文献类型：
--
作者：
Neme R;Tautz D
到目前为止，新基因的出现被认为主要是由现有基因的复制和分化驱动的。长期以来，人们一直认为，从非编码基因组背景中出现全新基因的可能性几乎可以忽略不计。随着全基因组测序在系统发育的广泛范围内的可用性的增加，随着时间的推移，系统地研究新基因的起源成为可能，从而重新审视这个问题。我们使用系统地层学来评估基因在连续系统发育阶段的进化趋势，主要使用注释良好的小鼠基因组作为参考。我们发现了几个重要的总体趋势，并证实了其他三种脊椎动物（人类、斑马鱼和棘鱼）的基因组。年轻的基因更短，无论是在基因长度方面，还是在开放阅读框长度方面。它们含有更少的外显子和更少的可识别结构域。另一方面，平均外显子长度不会随时间发生太大变化。只有最近进化的基因具有较长的外显子，并且它们通常与活跃的启动子区域相关，即是双向启动子的一部分。我们还重新审视了基因从头进化的可能性，甚至可以在现有基因中发生，通过使用另一种阅读框架（套印）。我们在注释的Ensembl orf中发现了几个案例，其中新的阅读框出现在比原始阅读框更高的系统地层水平上。我们讨论了其中一些重叠的基因，其中也包括Hoxa9基因，在导致啮齿动物和灵长类动物的谱系中，出现了覆盖同源盒的替代阅读框。我们认为，基因出现的总体趋势更符合孤儿基因的从头进化模型，而不是一般的重复-分化模型。因此，基因的从头进化似乎在整个进化过程中不断发生，因此应被视为新基因功能出现的一般机制。
New gene emergence is so far assumed to be mostly driven by duplication and divergence of existing genes. The possibility that entirely new genes could emerge out of the non-coding genomic background was long thought to be almost negligible. With the increasing availability of fully sequenced genomes across broad scales of phylogeny, it has become possible to systematically study the origin of new genes over time and thus revisit this question. We have used phylostratigraphy to assess trends of gene evolution across successive phylogenetic phases, using mostly the well-annotated mouse genome as a reference. We find several significant general trends and confirm them for three other vertebrate genomes (humans, zebrafish and stickleback). Younger genes are shorter, both with respect to gene length, as well as to open reading frame length. They contain also fewer exons and have fewer recognizable domains. Average exon length, on the other hand, does not change much over time. Only the most recently evolved genes have longer exons and they are often associated with active promotor regions, i.e. are part of bidirectional promotors. We have also revisited the possibility that de novo evolution of genes could occur even within existing genes, by making use of an alternative reading frame (overprinting). We find several cases among the annotated Ensembl ORFs, where the new reading frame has emerged at a higher phylostratigraphic level than the original one. We discuss some of these overprinted genes, which include also the Hoxa9 gene where an alternative reading frame covering the homeobox has emerged within the lineage leading to rodents and primates (Euarchontoglires). We suggest that the overall trends of gene emergence are more compatible with a de novo evolution model for orphan genes than a general duplication-divergence model. Hence de novo evolution of genes appears to have occurred continuously throughout evolutionary time and should therefore be considered as a general mechanism for the emergence of new gene functions.
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影响因子：
14.9
作者：
Hunter S;Jones P;Mitchell A;Apweiler R;Attwood TK;Bateman A;Bernard T;Binns D;Bork P;Burge S;de Castro E;Coggill P;Corbett M;Das U;Daugherty L;Duquenne L;Finn RD;Fraser M;Gough J;Haft D;Hulo N;Kahn D;Kelly E;Letunic I;Lonsdale D;Lopez R;Madera M;Maslen J;McAnulla C;McDowall J;McMenamin C;Mi H;Mutowo-Muellenet P;Mulder N;Natale D;Orengo C;Pesseat S;Punta M;Quinn AF;Rivoire C;Sangrador-Vegas A;Selengut JD;Sigrist CJ;Scheremetjew M;Tate J;Thimmajanarthanan M;Thomas PD;Wu CH;Yeats C;Yong SY
通讯作者：
Yong SY
影响因子：
3.3
作者：
Begun, David J.;Lindfors, Heather A.;Jones, Corbin D.
通讯作者：
Jones, Corbin D.
DOI：
10.1093/dnares/dsq006
发表时间：
2010-04
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Carninci P
通讯作者：
Carninci P
影响因子：
10.7
作者：
Domazet-Loso T;Tautz D
通讯作者：
Tautz D
影响因子：
14.9
作者：
Karolchik, D;Hinrichs, AS;Kent, WJ
通讯作者：
Kent, WJ