National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
China National Center for Bioinformation, Beijing, China.
Mol Biol Evol. 2023 Apr 4;40(4). doi: 10.1093/molbev/msad080.
The genus Antirrhinum has been used as a model to study self-incompatibility extensively. The multi-allelic S-locus, carrying a pistil S-RNase and dozens of S-locus F-box (SLF) genes, underlies the genetic control of self-incompatibility (SI) in Antirrhinum hispanicum. However, there have been limited studies on the genomic organization of the S-locus supergene due to a lack of high-quality genomic data. Here, we present the chromosome-level reference and haplotype-resolved genome assemblies of a self-incompatible A. hispanicum line, AhS7S8. For the first time, 2 complete A. hispanicum S-haplotypes spanning ∼1.2 Mb and containing a total of 32 SLFs were reconstructed, whereas most of the SLFs derived from retroelement-mediated proximal or tandem duplication ∼122 Mya. Back then, the S-RNase gene and incipient SLFs came into linkage to form the pro-type of type-1 S-locus in the common ancestor of eudicots. Furthermore, we detected a pleiotropic cis-transcription factor (TF) associated with regulating the expression of SLFs, and two miRNAs may control the expression of this TF. Interspecific S-locus and intraspecific S-haplotype comparisons revealed the dynamic nature and polymorphism of the S-locus supergene mediated by continuous gene duplication, segmental translocation or loss, and TE-mediated transposition events. Our data provide an excellent resource for future research on the evolutionary studies of the S-RNase-based self-incompatibility system.
金鱼草属（Antirrhinum）被广泛用作研究自交不亲和性的模式植物。多等位基因 S 基因座携带柱头 S-RNase 和数十个 S 基因座 F-box (SLF) 基因，是金鱼草（Antirrhinum hispanicum）自交不亲和性（SI）遗传控制的基础。然而，由于缺乏高质量的基因组数据，对 S 基因座超基因的基因组组织的研究有限。在这里，我们展示了一个自交不亲和的金鱼草品系 AhS7S8 的染色体水平参考基因组和单倍型解析基因组组装。首次重建了 2 个完整的金鱼草 S 单倍型，跨越约 1.2 Mb，共包含 32 个 SLF，而大多数 SLF 来源于约 1.22 亿年前 retroelement 介导的近端或串联重复。当时，S-RNase 基因和初生 SLF 进入连锁，在真双子叶植物的共同祖先中形成了 1 型 S 基因座的原型。此外，我们检测到一个与调控 SLF 表达相关的多效顺式转录因子（TF），两个 miRNA 可能控制这个 TF 的表达。种间 S 基因座和种内 S 单倍型比较揭示了 S 基因座超基因的动态性质和多态性，这是由连续基因复制、片段易位或缺失以及 TE 介导的转位事件介导的。我们的数据为未来基于 S-RNase 的自交不亲和性系统的进化研究提供了一个极好的资源。
