Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina. The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.

中文翻译：

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杂交和异源多倍体化后小 RNA 表达的进化：来自 Spartina 物种（禾本科，Chloridoideae）的见解。

在 Spartina 异源多倍体物种形成的背景下，在基因组合并和基因组复制后，靶向发育过程的 mi-RNA 的差异表达和重复相关 siRNA 的逐步下调。小 RNA 对基因表达调控和基因组稳定性的作用引起了越来越多的兴趣，并且正在各种植物系统中进行探索。尽管影响所有植物谱系进化历史的网状进化和多倍体突出，但很少有研究分析这方面的 RNAi 机制。在这里，我们使用 Spartina 系统在最近的异源多倍体物种形成的背景下探索了小 RNA 的多样性和表达，这为探索杂交和基因组复制后的直接变化提供了独特的机会。对六倍体亲本物种（互花链球菌和 S. maritima）、它们的 F1 杂种 S. x townsendii 和新异十二倍体 S. anglica 进行了小 RNA-Seq 分析。我们鉴定了 594 个 miRNA、2197 个 miRNA 靶基因和 3730 个重复相关 siRNA（主要针对 I 类/Copia-Ivana-Copia-SIRE 和 LINEs 元件）。对于 mi- 和 ra-siRNA，我们检测到基因组合并和基因组复制后的差异表达模式。这些错误调节包括 F1 杂合体中 miRNA 的非加性表达和异源多倍体靶向发育过程的额外变化。重复相关 siRNA 的表达表明在异源多倍体化过程中转座因子抑制的增强。共，