From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates.
From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates.
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DOI：
10.1093/gbe/evy231
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发表时间：
2018-11-01
影响因子：
3.3
通讯作者：
Casola C
中科院分区：
文献类型：
--
作者：
Casola C
从基因组的非编码区进化出新的蛋白质编码基因是自然界遗传创新最令人信服的证据之一。一种流行的鉴定新生基因的方法是系统地层学，它包括根据基因沿物种系统发育的分布确定基因的大约起源时间（年龄）。几项研究表明，仅使用系统地层学来确定基因（包括新生基因）的年龄存在重大缺陷。然而，基于系统地层学的新生基因调查的假阳性率仍然未知。在这里，我重新分析了三项研究的结果，其中两项研究采用以系统地层学为中心的方法确定了数十到数百种啮齿动物特异性新生基因。在这些研究中发现的大多数假定的新生基因不再包括在最近更新的小鼠基因集中。通过对同源性信息和序列相似性搜索的结合，作者表明，在剩余的381个假定的新生基因中，约有60%与其他脊椎动物的基因具有同源性，这些基因起源于基因复制，并且/或者与非啮齿动物没有同源性信息。这些结果导致小鼠每百万年产生约12个新生基因的估计速率。与之前的研究相反（Wilson BA, Foy SG, Neme R, Masel J. 2017）。正如新基因出生的预适应假说所预测的那样，年轻基因是高度无序的。我发现没有证据支持新生基因形成的预适应假说。本研究中确认的近一半的新生基因位于较老的基因中，这表明对先前存在的调控区域的选择和较高的GC含量可能有助于新基因的起源。
The evolution of novel protein-coding genes from noncoding regions of the genome is one of the most compelling pieces of evidence for genetic innovations in nature. One popular approach to identify de novo genes is phylostratigraphy, which consists of determining the approximate time of origin (age) of a gene based on its distribution along a species phylogeny. Several studies have revealed significant flaws in determining the age of genes, including de novo genes, using phylostratigraphy alone. However, the rate of false positives in de novo gene surveys, based on phylostratigraphy, remains unknown. Here, I reanalyze the findings from three studies, two of which identified tens to hundreds of rodent-specific de novo genes adopting a phylostratigraphy-centered approach. Most putative de novo genes discovered in these investigations are no longer included in recently updated mouse gene sets. Using a combination of synteny information and sequence similarity searches, I show that ∼60% of the remaining 381 putative de novo genes share homology with genes from other vertebrates, originated through gene duplication, and/or share no synteny information with nonrodent mammals. These results led to an estimated rate of ∼12 de novo genes per million years in mouse. Contrary to a previous study (Wilson BA, Foy SG, Neme R, Masel J. 2017. Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth. Nat Ecol Evol. 1:0146), I found no evidence supporting the preadaptation hypothesis of de novo gene formation. Nearly half of the de novo genes confirmed in this study are within older genes, indicating that co-option of preexisting regulatory regions and a higher GC content may facilitate the origin of novel genes.
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校正的肌肉校准力精度在啮齿动物的分子树中精确的放置。
影响因子：
4.6
作者：
Kimura Y;Hawkins MT;McDonough MM;Jacobs LL;Flynn LJ
通讯作者：
Flynn LJ
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
4.3
作者：
Li CY;Zhang Y;Wang Z;Zhang Y;Cao C;Zhang PW;Lu SJ;Li XM;Yu Q;Zheng X;Du Q;Uhl GR;Liu QR;Wei L
通讯作者：
Wei L
影响因子：
3.3
作者：
Begun, David J.;Lindfors, Heather A.;Jones, Corbin D.
通讯作者：
Jones, Corbin D.
影响因子：
7
作者：
Knowles, David G.;McLysaght, Aoife
通讯作者：
McLysaght, Aoife