State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
Genes (Basel). 2020 Dec 12;11(12):1500. doi: 10.3390/genes11121500.
Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid (S), its diploid parents, and the F hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in , 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S, which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution.
长非编码 RNA（lncRNAs）在各种生物过程中发挥着关键的调控作用。然而，lncRNAs 的存在及其在植物多倍体中的功能仍在很大程度上是未知的。因此，我们检查了初生异源四倍体（S）、其二倍体亲本和 F1 杂种中 lncRNAs 的图谱，以揭示 lncRNAs 在植物种间杂交和全基因组加倍中的功能。结果表明，在 中鉴定出了均匀转录自所有 19 条染色体的 2206 个 lncRNAs，其中 44.6%来自基因间区。基于在异源多倍化中的表达趋势，我们发现大多数 lncRNAs（94.6%）在杂交后呈现出不同程度的上调表达。然而，在基因组加倍后，很少有 lncRNAs（33 个，2.1%）是非累加表达的，这表明杂交对 lncRNAs 的影响显著，而不是基因组加倍。此外，还预测了 253 个顺式调控靶基因这些在 S 中差异表达的 lncRNAs，它们主要参与叶绿体的生物调控（如叶绿素合成和光捕获系统）。总体而言，这项研究为 lncRNAs 在植物进化过程中的杂交和多倍体化过程中的功能提供了新的见解。
