Department of Automation, Xiamen University, Xiamen 361005, China.
Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Plant Cell Physiol. 2020 May 1;61(5):882-896. doi: 10.1093/pcp/pcaa013.
Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used Pacific Biosciences (PacBio) full-length single-molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt gradient experiments. High-quality unigenes, transcription factors, non-coding RNA and Spartina-specific transcripts were identified. Co-expression network analysis found that protein kinase-encoding genes (SaOST1, SaCIPK10 and SaLRRs) are hub genes in the salt tolerance regulatory network. High salt stress induced the expression of transcription factors but repressed the expression of long non-coding RNAs. The Spartina transcriptome is closer to rice than Arabidopsis, and a higher proportion of transporter and transcription factor-encoding transcripts have been found in Spartina. Transcriptome analysis showed that high salt stress induced the expression of carbohydrate metabolism, especially cell-wall biosynthesis-related genes in Spartina, and repressed its expression in rice. Compared with rice, high salt stress highly induced the expression of stress response, protein modification and redox-related gene expression and greatly inhibited translation in Spartina. High salt stress also induced alternative splicing in Spartina, while differentially expressed alternative splicing events associated with photosynthesis were overrepresented in Spartina but not in rice. Finally, we built the SAPacBio website for visualizing full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes and alternative splicing events in Spartina. Overall, this study suggests that the salt tolerance mechanism in Spartina is different from rice in many aspects and is far more complex than expected.
互花米草（Spartina）是盐沼中唯一的盐生植物。然而，其高耐盐性的分子基础仍不清楚。在这项研究中，我们使用 Pacific Biosciences（PacBio）全长单分子长读测序和 RNA-seq 通过盐梯度实验阐明了互花米草高耐盐性的转录组动态。鉴定出高质量的 unigenes、转录因子、非编码 RNA 和互花米草特异性转录本。共表达网络分析发现，蛋白激酶编码基因（SaOST1、SaCIPK10 和 SaLRRs）是耐盐调控网络中的枢纽基因。高盐胁迫诱导转录因子的表达，但抑制长非编码 RNA 的表达。互花米草的转录组与水稻比与拟南芥更接近，并且在互花米草中发现了更多的转运蛋白和转录因子编码转录本。转录组分析表明，高盐胁迫诱导互花米草碳水化合物代谢，特别是细胞壁生物合成相关基因的表达，并抑制水稻中这些基因的表达。与水稻相比，高盐胁迫强烈诱导应激反应、蛋白质修饰和氧化还原相关基因的表达，并在互花米草中大大抑制翻译。高盐胁迫还诱导了互花米草的选择性剪接，而与光合作用相关的差异表达选择性剪接事件在互花米草中过表达，但在水稻中没有。最后，我们构建了 SAPacBio 网站，用于可视化互花米草全长转录组序列、转录因子、ncRNA、耐盐基因和选择性剪接事件。总的来说，这项研究表明，互花米草的耐盐机制在许多方面与水稻不同，而且比预期的要复杂得多。
