Table_1_Seed Germination Mechanism of Carex rigescens Under Variable Temperature Determinded Using Integrated Single-Molecule Long-Read and Illumina Sequence Analysis.XLSX

The turfgrass species Carex rigescens has broad development and utilization prospects in landscaping construction. However, seed dormancy and a low germination rate have inhibited its application. Furthermore, the molecular mechanisms of seed germination in C. rigescens have not been thoroughly studied. Therefore, in the present study, PacBio full-length transcriptome sequencing combined with Illumina sequencing was employed to elucidate the germination mechanism of C. rigescens seeds under variable temperatures. In general, 156,750 full-length non-chimeric sequences, including those for 62,086 high-quality transcripts, were obtained using single-molecule long read sequencing. In total, 40,810 high-quality non-redundant, 1,675 alternative splicing, 28,393 putative coding sequences, and 1,052 long non-coding RNAs were generated. Based on the newly constructed full-length reference transcriptome, 23,147 differentially expressed genes were identified. We screened four hub genes participating in seed germination using weighted gene co-expression network analysis. Combining these results with the physiological observations, the important roles of sucrose and starch metabolic pathways in germination are further discussed. In conclusion, we report the first full-length transcriptome of C. rigescens, and investigated the physiological and transcriptional mechanisms of seed germination under variable temperatures. Our results provide valuable information for future transcriptional analyses and gene function studies of C. rigescens.

作为草坪草的细叶苔草（Carex rigescens）在园林绿化建设中具备广阔的开发利用前景。然而，种子休眠与低萌发率却制约了其推广应用。此外，目前对于细叶苔草种子萌发的分子机制尚未得到充分解析。为此，本研究采用PacBio全长转录组测序结合Illumina测序的技术手段，以解析变温条件下细叶苔草种子的萌发机制。经单分子长读长测序，共计获得156,750条全长非嵌合序列，其中包含62,086条高质量转录本。本次测序共生成40,810条高质量非冗余序列、1,675个可变剪接（alternative splicing）事件、28,393条推定编码序列以及1,052条长链非编码RNA（long non-coding RNAs）。基于新构建的全长参考转录组，本研究共鉴定出23,147个差异表达基因（differentially expressed genes）。本研究通过加权基因共表达网络分析（weighted gene co-expression network analysis）筛选出4个参与种子萌发的枢纽基因（hub genes）。结合生理观测结果，本研究进一步探讨了蔗糖与淀粉代谢通路在种子萌发过程中的关键作用。综上，本研究首次完成了细叶苔草全长转录组的构建，并解析了变温条件下其种子萌发的生理与转录调控机制。本研究结果为后续细叶苔草的转录组学分析及基因功能研究提供了重要参考依据。