DataSheet2_Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume.ZIP

Prunus mume is an illustrious ornamental woody plant with colorful flowers, delicate fragrances, and graceful tree forms. Low temperature limits its geographical distribution. The basic helix-loop-helix (bHLH) proteins exist in most eukaryotes as a transcription factor superfamily, which play a crucial role in metabolism, physiology, development, and response to various stresses of higher organisms. However, the characteristics of the bHLH gene family and low-temperature response remain unknown in P. mume. In the present study, we distinguished 95 PmbHLH genes in the P. mume whole-genome and analyzed their features. PmbHLHs were divided into 23 subfamilies and one orphan by phylogenetic analysis. Similar gene structures and conserved motifs appeared in the same subfamily. These genes were situated in eight chromosomes and scaffolds. Gene duplication events performed a close relationship to P. mume, P. persica, and P. avium. Tandem duplications probably promoted the expansion of PmbHLHs. According to predicted binding activities, the PmbHLHs were defined as the Non-DNA-binding proteins and DNA-binding proteins. Furthermore, PmbHLHs exhibited tissue-specific and low-temperature induced expression patterns. By analyzing transcriptome data, 10 PmbHLHs which are responsive to low-temperature stress were selected. The qRT-PCR results showed that the ten PmbHLH genes could respond to low-temperature stress at different degrees. There were differences in multiple variations among different varieties. This study provides a basis to research the evolution and low-temperature tolerance of PmbHLHs, and might enhance breeding programs of P. mume by improving low-temperature tolerance.

梅（Prunus mume）是一类极具观赏价值的木本植物，兼具花色艳丽、香气清雅与株型雅致的特点。低温环境是制约其地理分布的关键因素。碱性螺旋-环-螺旋（basic helix-loop-helix, bHLH）蛋白作为一类转录因子超家族广泛存在于绝大多数真核生物中，在高等生物的代谢、生理活动、生长发育以及各类胁迫响应过程中发挥关键调控作用。然而，梅中bHLH基因家族的特征及其低温响应机制尚未明确。本研究从梅全基因组中鉴定出95个PmbHLH基因，并对其序列特征展开分析。通过系统发育分析，可将PmbHLH家族成员划分为23个亚家族及1个孤立基因簇。同一亚家族内的基因具有相似的基因结构与保守基序。这些PmbHLH基因分布于8条染色体及基因组scaffold序列上。基因复制事件分析显示，梅、桃（Prunus persica）与甜樱桃（Prunus avium）三者之间存在紧密的进化关联。串联复制事件可能是推动PmbHLH家族扩张的主要动力之一。根据预测的DNA结合活性，可将PmbHLH家族成员分为非DNA结合型蛋白与DNA结合型蛋白两大类。此外，PmbHLH基因呈现出组织特异性表达模式，并可被低温胁迫诱导表达。通过转录组数据分析，本研究筛选出10个响应低温胁迫的PmbHLH基因。实时荧光定量PCR（quantitative real-time PCR, qRT-PCR）结果显示，这10个PmbHLH基因均能不同程度地响应低温胁迫，且不同梅品种间的基因表达变异程度存在显著差异。本研究为解析PmbHLH基因家族的进化机制与低温耐受功能奠定了理论基础，同时可为通过改良低温耐受性以推进梅育种工作提供新思路。