Data_Sheet_3_Deciphering Evolutionary Dynamics of WRKY I Genes in Rosaceae Species.PDF

WRKY transcription factors participate in various regulation processes at different developmental stages in higher plants. Here, 98 WRKY I genes were identified in seven Rosaceae species. The WRKY I genes are highly enriched in some subgroups and are selectively expanded in Chinese pear [Pyrus bretschneideri (P. bretschneideri)] and apple [Malus domestica (M. domestica)]. By searching for intra-species gene microsynteny, we found the majority of chromosomal segments for WRKY I-containing segments in both P. bretschneideri and M. domestica genomes, while paired segments were hardly identified in the other five genomes. Furthermore, we analyzed the environmental selection pressure of duplicated WRKY I gene pairs, which indicated that the strong purifying selection for WRKY domains may contribute to the stability of its structure and function. The expression patterns of duplication PbWRKY genes revealed that functional redundancy for some of these genes was derived from common ancestry and neo-functionalization or sub-functionalization for some of them. This study traces the evolution of WRKY I genes in Rosaceae genomes and lays the foundation for functional studies of these genes in the future. Our results also show that the rates of gene loss and gain in different Rosaceae genomes are far from equilibrium.

WRKY转录因子（WRKY transcription factors）可参与高等植物不同发育阶段的多种调控进程。本研究在7个蔷薇科（Rosaceae）物种中鉴定得到98个WRKY I型基因。WRKY I型基因在部分亚组中高度富集，且在中国梨[梨属白梨（Pyrus bretschneideri，P. bretschneideri）]与苹果[苹果属栽培苹果（Malus domestica，M. domestica）]中发生了选择性扩张。通过种内基因微共线性（intra-species gene microsynteny）分析，我们发现白梨与栽培苹果基因组中绝大多数携带WRKY I型基因的染色体区段存在共线性特征，而其余5个物种中几乎未检测到成对共线性区段。此外，本研究对复制的WRKY I型基因对开展了环境选择压力分析，结果显示针对WRKY结构域的强烈纯化选择（purifying selection）可能有助于维持其结构与功能的稳定性。对复制的PbWRKY基因的表达模式分析表明，部分基因的功能冗余源自共同祖先，而其余部分则经历了新功能化（neo-functionalization）或亚功能化（sub-functionalization）过程。本研究追溯了蔷薇科基因组中WRKY I型基因的进化历程，为后续此类基因的功能研究奠定了基础。本研究结果同时显示，不同蔷薇科基因组的基因得失速率远未达到均衡状态。