Genome-wide identification and transcriptomic profiling of auxin concentration and signaling related genes in moso bamboo (Phyllostachys heterocycla). Phyllostachys edulis

Auxin is essential for plant growth and development by altering downstream gene expression. Although large progresses have been made on auxin-concentration, distribution and signaling pathways in model plants like Arabidopsis and rice, little is known in moso bamboo which belongs to grass family, and has great economic and social value. Here we performed genome-wide analysis of the key components related to auxin action, and identified 13 YUCCA genes for auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) proteins 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) family members for auxin transport, 10 auxin binding factors (AFB) for auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) and 41 auxin response transcription factors (ARF) genes for auxin signaling in moso bamboo genome. We further performed phylogenetic analysis of those auxin action related genes from Arabidopsis, Oryza sativa and moso bamboo. To know those genes’ ability to response exogenous auxin and to generate a comprehensive transcriptome overview of auxin response in moso Bamboo, we performed RNA_seq analysis. Our data showed that auxin regulates genes related its biosynthesis, transport, signaling. Moreover, we present the interaction between auxin and other phytohormones at the level of transcription. In summary, we identified the key gene families involved in the auxin action pathways in moso bamboo, and generated a transcriptional overview of the auxin response in moso bamboo. Our data open up an opportunity to uncover the precise roles of auxin action pathways in this important species. Overall design: bamboo (Phyllostachys heterocycla) one-month-old seedlings were sprayed with 5μM NAA for 4 hours with 1-hour interval, and the root part were dissected for RNA extraction.

生长素（auxin）通过调控下游基因表达，对植物生长发育至关重要。尽管在拟南芥（Arabidopsis）、水稻（Oryza sativa）等模式植物中，有关生长素的浓度、分布及信号通路的研究已取得长足进展，但对于属于禾本科且兼具重要经济与社会价值的毛竹（moso bamboo）而言，相关研究仍较为匮乏。本研究对毛竹基因组中与生长素作用相关的关键组分开展全基因组分析，共鉴定得到13个参与生长素合成的YUCCA基因、14个PIN-FORMED/PIN-like（PIN/PILS）蛋白家族成员、7个介导生长素转运的AUXIN1/LIKE-AUX1（AUX1/LAX）家族成员、10个参与生长素感知的生长素结合蛋白（AFB）、43个auxin/indole-3-aceticacid（AUX/IAA）基因以及41个生长素响应转录因子（ARF）。我们进一步对来自拟南芥、水稻以及毛竹的上述生长素作用相关基因开展了系统发育分析。为明确这些基因对外源生长素的响应能力，并全面解析毛竹中生长素响应的转录组全貌，我们开展了RNA测序（RNA_seq）分析。研究数据显示，生长素可调控与其自身合成、转运及信号通路相关的基因。此外，我们还在转录水平揭示了生长素与其他植物激素之间的互作关系。综上，本研究鉴定得到了毛竹中参与生长素作用通路的关键基因家族，并构建了毛竹生长素响应的转录组全景图谱。本研究数据为解析生长素作用通路在这一重要物种中的精准功能提供了新的契机。实验设计：将生长1个月的毛竹（Phyllostachys heterocycla）幼苗以5μM萘乙酸（NAA）喷雾处理，每间隔1小时喷施一次，持续处理4小时，随后采集根部组织用于RNA提取。