Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
Institute for Systems Biology, Seattle, WA 98109, USA.
Genes (Basel). 2023 Jan 18;14(2):249. doi: 10.3390/genes14020249.
The history of 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, J, gave rise to S after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The S lineage gave rise to Y in catarrhines and to Ta in platyrrhines. Platyrrhine 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 subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset ; [caljac3]), resulted in 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 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 subfamily evolution within the three-family clade of platyrrhines to provide a working framework for future research. expansion in the three-family clade has been dominated by Ta15 and its derivatives.
逆转座子的历史是由系统积累的遗传诊断核苷酸取代来编排的，形成离散的亚家族，每个亚家族都有独特的核苷酸共识序列。最古老的亚家族 J，在灵长目动物中的 Strepsirrhini 和后来的 Catarrhini 和 Platyrrhini 分支之后，产生了 S。S 谱系在猫科动物中产生了 Y，在 Platyrrhini 中产生了 Ta。 Platyrrhine 亚家族 Ta7、Ta10 和 Ta15 是根据标准化命名法命名的。然而，随着全基因组测序（WGS）的后续加强，使用 COSEG 程序对亚家族进行大规模分析以对其进行特征描述，同时确定了整个亚家族的谱系。第一只有 WGS 的 Platyrrhine 基因组，即普通狨猴；[caljac3]），导致亚家族名称 sf0 到 sf94 以任意顺序排列。尽管通过对齐共识序列很容易解决，但随着更多基因组被独立分析，这种命名约定会变得越来越混乱。在这项研究中，我们报告了 Platyrrhine 三家族分支（卷尾猴科、狨科和夜猴科）的亚家族特征。我们调查了每一个被认可的狨科和夜猴科家族以及卷尾猴科的两个亚家族（卷尾猴亚科和松鼠猴亚科）的一个物种/基因组。此外，我们构建了一个 Platyrrhine 三家族分支中亚家族进化的综合网络，为未来的研究提供了一个工作框架。在三家族分支中，Ta15 及其衍生物的扩张占据主导地位。
