Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, La Coruña, Spain.
Heredity (Edinb). 2011 Aug;107(2):127-42. doi: 10.1038/hdy.2010.174. Epub 2011 Mar 2.
The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at -25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinant.
5S 核糖体 DNA 与其他多基因家族之间的连接已在许多真核生物谱系中被检测到，但它是否提供任何选择优势尚不清楚。在这项工作中，我们报告了来自四个不同属的 10 种剃刀贝物种（软体动物：双壳类：Pharidae）中 5S 核糖体 DNA（5S rDNA）和 U1 小核 DNA（U1 snDNA）的连接单元的发生。我们获得了几个包含这两种基因家族部分或完整重复的克隆，其中两种类型的基因均具有相同的方向。我们提供了全面的剃刀贝 5S rDNA 克隆集合，包括连接和非连接组织，以及第一个双壳类 U1 snDNA 序列。我们预测了二级结构，并对上游和下游保守元件进行了特征描述，包括从 5S rDNA 和 U1 snDNA 转录起始位点开始的 -25 个核苷酸区域。对 5S rDNA 的分析表明，一些非转录间隔区（NTS）与来自其他物种（和属）的 NTS 比与它们来自的物种的 NTS 更为密切相关，表明了诞生和死亡进化和祖先多态性。功能区域内的核苷酸保守性表明，纯化选择、不等交换和基因转换的参与。考虑到这一点和其他研究，我们讨论了这两个多基因家族在 Pharidae 谱系中连接的可能机制。5S rDNA 经常与其他多基因家族连接的原因似乎是基因组内随机过程的结果，其高拷贝数是决定因素。
