Data from: The evolutionary history of plant T2/S-type ribonucleases

A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution.

越来越多的T2/S-核糖核酸酶（T2/S-RNases）在植物基因组中被鉴定发现。该蛋白家族的成员已被报道具备多种功能，但绝大多数仍未得到功能注释与表征。本研究提供了T2/S-核糖核酸酶家族的系统发育关系数据与分析，并重点关注了包含被子植物中分布最广泛的自交不亲和系统雌性决定组分的类群。针对该自交不亲和机制最初鉴定出的组分开展的重点研究，为其进化背景提供了重要推测方向。其一，参与自交排斥反应的III类进化支仅存在于核心真双子叶植物中，而其余进化支则涵盖其他维管植物的家族成员。其二，内含子模式、等电点以及保守氨基酸区域等特征，可将介导自交不亲和性表达的S-核糖核酸酶（S-RNases）与其他T2/S-核糖核酸酶家族成员区分开来。其三，本研究开发并公开了一套分析方法，用于从现有基因组组装数据中筛选新的S-核糖核酸酶候选基因。我们利用基因组特征，在自交不亲和机制尚未明确的植物基因组中，鉴定出潜在的功能性S位点与残留S位点。这类潜在残留位点的广泛分布表明，功能性自交不亲和性的丧失可能在事件发生后长期留下可检测的痕迹，而这类类似分子化石的数据，可为基于核糖核酸酶的自交不亲和系统及其他类型自交不亲和机制的演化历史与分类学分布提供重要的信息来源。最后，本研究发布了一项公共资源，旨在助力S位点核糖核酸酶的搜索鉴定工作，并帮助完善其分类学分布的相关详细信息。