Table_1_Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis ‘Old Blush’ After Exposure to a Gradual Drought Stress Followed by Recovery.XLSX

Rose is one of the most fundamental ornamental crops, but its yield and quality are highly limited by drought. The key transcription factors (TFs) and co-expression networks during rose’s response to drought stress and recovery after drought stress are still limited. In this study, the transcriptomes of leaves of 2-year-old cutting seedlings of Rosa chinensis ‘Old Blush’ from three continuous droughted stages (30, 60, 90 days after full watering) and rewatering were analyzed using RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network, which was associated with the physiological traits of drought response to discovering the hub TFs involved in drought response. More than 45 million high-quality clean reads were generated from the sample and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that drought stress caused significant changes in signal transduction, plant hormones including ABA, auxin, brassinosteroid (BR), cytokinin, ethylene (ET), jasmonic acid (JA) and salicylic acid (SA), primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules showed a high degree of correlation with physiological traits. In addition, 42 TFs including members of NACs, WRKYs, MYBs, AP2/ERFs, ARFs, and bHLHs with high connectivity in navajowhite1 and blue modules were screened. This study provides the transcriptome sequencing report of R. chinensis ‘Old Blush’ during drought stress and rewatering process. The study also identifies the response of candidate TFs to drought stress, providing guidelines for improving the drought tolerance of the rose through molecular breeding in the future.

月季（Rose）是全球最为重要的观赏作物之一，但其产量与品质极易受到干旱胁迫的限制。目前关于月季响应干旱胁迫以及干旱后恢复过程中的关键转录因子（Transcription Factors, TFs）与共表达网络的研究仍较为匮乏。本研究以2年生扦插苗中国月季‘月月红’（Rosa chinensis ‘Old Blush’）为材料，对其在连续干旱的3个阶段（充分浇水后30、60、90天）以及复水处理下的叶片转录组进行了RNA测序分析。本研究采用加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis, WGCNA）构建共表达网络，并将其与干旱响应相关生理性状进行关联分析，以筛选参与干旱响应的核心转录因子。本次实验共从样本中获得超过4500万条高质量清洁读段，并将其与月季参考基因组进行比对，最终共鉴定得到46433个差异表达基因（Differentially Expressed Genes, DEGs）。基因本体（Gene Ontology, GO）富集分析与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路分析结果显示，干旱胁迫会显著改变信号转导、包括脱落酸（Abscisic Acid, ABA）、生长素、油菜素甾醇（Brassinosteroid, BR）、细胞分裂素、乙烯（Ethylene, ET）、茉莉酸（Jasmonic Acid, JA）以及水杨酸（Salicylic Acid, SA）在内的多种植物激素通路、初生与次生代谢过程，且在复水后可得到一定程度的恢复。基因共表达分析共鉴定得到18个基因模块，其中4个模块与干旱响应生理性状呈现高度相关性。此外，本研究还在navajowhite1与blue模块中筛选得到42个核心转录因子，涵盖NAC家族、WRKY家族、MYB家族、AP2/ERF家族、ARF家族以及bHLH家族等。本研究提供了中国月季‘月月红’在干旱胁迫及复水过程中的转录组测序数据，并筛选得到一批响应干旱胁迫的候选转录因子，为未来通过分子育种手段提升月季耐旱性提供了理论依据与研究方向。