Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil.
Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Ann Bot. 2023 May 15;131(5):813-825. doi: 10.1093/aob/mcad036.
Satellite DNAs (satDNAs) are repetitive sequences composed by tandemly arranged, often highly homogenized units called monomers. Although satDNAs are usually fast evolving, some satDNA families can be conserved across species separated by several millions of years, probably because of their functional roles in the genomes. Tyba was the first centromere-specific satDNA described for a holocentric organism, until now being characterized for only eight species of the genus Rhynchospora Vahl. (Cyperaceae). Here, we characterized Tyba across a broad sampling of the genus, analysing and comparing its evolutionary patterns with other satDNAs.
We characterized the structure and sequence evolution of satDNAs across a robust dadated phylogeny based on Hybrid Target-Capture Sequencing (hyb-seq) of 70 species. We mined the repetitive fraction for Tyba-like satellites to compare its features with other satDNAs and to construct a Tyba-based phylogeny for the genus.
Our results show that Tyba is present in the majority of examined species of the genus, spanning four of the five major clades and maintaining intrafamily pairwise identity of 70.9% over 31 Myr. In comparison, other satellite families presented higher intrafamily pairwise identity but are phylogenetically restricted. Furthermore, Tyba sequences could be divided into 12 variants grouped into three different clade-specific subfamilies, showing evidence of traditional models of satDNA evolution, such as the concerted evolution and library models. Besides, a Tyba-based phylogeny showed high congruence with the hyb-seq topology. Our results show structural indications of a possible relationship of Tyba with nucleosomes, given its high curvature peaks over conserved regions and overall high bendability values compared with other non-centromeric satellites.
Overall, Tyba shows a remarkable sequence conservation and phylogenetic significance across the genus Rhynchospora, which suggests that functional roles might lead to long-term stability and conservation for satDNAs in the genome.
卫星 DNA（satDNA）是由串联排列的重复序列组成的，通常由高度同源的单元（称为单体）组成。尽管 satDNA 通常进化迅速，但一些 satDNA 家族可以在经过数百万年分离的物种中保守存在，这可能是因为它们在基因组中的功能作用。Tyba 是第一个为全着丝粒生物描述的着丝粒特异性 satDNA，直到现在，它仅在 Rhynchospora Vahl 属的八个物种中得到了特征描述。（莎草科）。在这里，我们对该属进行了广泛的采样，分析并比较了 Tyba 的进化模式与其他 satDNA。
我们基于杂交靶标捕获测序（hyb-seq）对 70 种物种进行了稳健的系统发育分析，对 satDNA 的结构和序列进化进行了特征描述。我们从重复序列中挖掘出类似于 Tyba 的卫星，以比较其特征与其他 satDNA，并构建了一个基于 Tyba 的属系统发育。
我们的结果表明，Tyba 存在于该属的大多数被检测物种中，跨越了五个主要分支中的四个分支，并在 3100 万年的时间内保持了家族内的 70.9%的同源性。相比之下，其他卫星家族具有更高的家族内同源性，但在系统发育上受到限制。此外，Tyba 序列可分为 12 个变体，分为三个不同的分支特异性亚家族，显示出传统的 satDNA 进化模式的证据，如协同进化和文库模型。此外，基于 Tyba 的系统发育与 hyb-seq 拓扑高度一致。我们的结果显示，Tyba 可能与核小体有关，因为它在保守区域上有很高的曲率峰值，并且与其他非着丝粒卫星相比，整体的弯曲性值较高。
总体而言，Tyba 在 Rhynchospora 属中表现出显著的序列保守性和系统发育意义，这表明功能作用可能导致 satDNA 在基因组中长期稳定和保守。
