Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae.
Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae.
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作者：
Alu逆转录酶的历史已经通过遗传诊断核苷酸取代的系统积累而编排，以形成离散的亚家族，每个亚家族具有不同的核苷酸共有序列。最古老的亚科是Strepsirrhini和后来的Catarrhini和Platyrrhini分裂后产生的Strepsirrhini。在卡他鼻类动物中，Escherichia S谱系产生了Escherichia Y，而在阔鼻类动物中，Escherichia Ta谱系产生了Escherichia。Platyrrhine Alu亚科Ta 7、Ta 10和Ta 15基于标准化命名法被指定名称。然而，随着随后的全基因组测序（WGS）的加强，使用程序COSEG的大规模分析，以表征Alu亚家族，同时确定了整个谱系的亚家族。第一个具有WGS的宽鼻类基因组是普通的绒猴（Callithrix jacchus; [caljac 3]），导致Alu亚科以任意顺序命名为sf 0至sf 94。虽然通过比对共有序列很容易解决，但随着越来越多的基因组被独立分析，这种命名惯例可能变得越来越令人困惑。在这项研究中，我们报告了Alu亚科的特性，为宽鼻三个家庭的分支Cebidae，Callithrichidae，Aotidae。我们调查了一个物种/基因组从每个公认的家庭Callithrichidae和Aotidae和两个亚科（Cebinae和Saimiriinae）的家庭Cebidae。此外，我们构建了一个全面的网络Alu亚科的进化在三个家庭的进化分支的阔鼻，为未来的研究提供了一个工作框架。Alu在三个家族分支中的扩张一直由Alu Ta 15及其衍生物主导。
The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset (Callithrix jacchus; [caljac3]), resulted in Alu subfamily names sf0 to sf94 in an arbitrary order. Although easily resolved by alignment of the consensus sequences, this naming convention can become increasingly confusing as more genomes are independently analyzed. In this study, we reported Alu subfamily characterization for the platyrrhine three-family clade of Cebidae, Callithrichidae, and Aotidae. We investigated one species/genome from each recognized family of Callithrichidae and Aotidae and of both subfamilies (Cebinae and Saimiriinae) of the family Cebidae. Furthermore, we constructed a comprehensive network of Alu subfamily evolution within the three-family clade of platyrrhines to provide a working framework for future research. Alu expansion in the three-family clade has been dominated by AluTa15 and its derivatives.
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DOI：
10.1073/pnas.2010632118
发表时间：
2021-02-16
影响因子：
11.1
作者：
Orkin JD;Montague MJ;Tejada-Martinez D;de Manuel M;Del Campo J;Cheves Hernandez S;Di Fiore A;Fontsere C;Hodgson JA;Janiak MC;Kuderna LFK;Lizano E;Martin MP;Niimura Y;Perry GH;Valverde CS;Tang J;Warren WC;de Magalhães JP;Kawamura S;Marquès-Bonet T;Krawetz R;Melin AD
通讯作者：
Melin AD
影响因子：
3.5
作者：
Storer, Jessica M. M.;Walker, Jerilyn A. A.;Rewerts, Lydia C. C.;Brown, Morgan A. A.;Beckstrom, Thomas O. O.;Herke, Scott W. W.;Roos, Christian;Batzer, Mark A. A.
通讯作者：
Batzer, Mark A. A.
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
高质量的BONOBO基因组完善了对人类进化的分析。
影响因子：
64.8
作者：
Mao Y;Catacchio CR;Hillier LW;Porubsky D;Li R;Sulovari A;Fernandes JD;Montinaro F;Gordon DS;Storer JM;Haukness M;Fiddes IT;Murali SC;Dishuck PC;Hsieh P;Harvey WT;Audano PA;Mercuri L;Piccolo I;Antonacci F;Munson KM;Lewis AP;Baker C;Underwood JG;Hoekzema K;Huang TH;Sorensen M;Walker JA;Hoffman J;Thibaud-Nissen F;Salama SR;Pang AWC;Lee J;Hastie AR;Paten B;Batzer MA;Diekhans M;Ventura M;Eichler EE
通讯作者：
Eichler EE
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O