The strawberry (Fragaria × ananassa) is an economically important fruit throughout the world. The large R2R3-MYB gene family participates in a variety of plant functions, including anthocyanin biosynthesis. The present study is the first genome-wide analysis of the MYB gene family in the octoploid strawberry and describes the identification and characterization of the family members using the recently sequenced F. × ananassa genome. Specifically, we aimed to identify the key MYBs involved in petal coloration in the pink-flowered strawberry, which increases its ornamental value. A comprehensive, genome-wide analysis of F. × ananassa R2R3-FaMYBs was performed, investigating gene structures, phylogenic relationships, promoter regions, chromosomal locations, and collinearity. A total of 393 R2R3-FaMYB genes were identified in the F. × ananassa genome and divided into 36 subgroups based on phylogenetic analysis. Most genes with similar functions in the same subgroup exhibited similar exon-intron structures and motif compositions. These R2R3-FaMYBs were unevenly distributed over 28 chromosomes. The expansion of the R2R3-FaMYB gene family in the F. × ananassa genome was found to be caused mainly by segmental duplication. The Ka/Ks analysis indicated that duplicated R2R3-FaMYBs mostly experienced purifying selection and showed limited functional divergence after the duplication events. To elucidate which R2R3-FaMYB genes were associated with anthocyanin biosynthesis in the petals of the pink-flowered strawberry, we compared transcriptional changes in different flower developmental stages using RNA-seq. There were 131 differentially expressed R2R3-FaMYB genes identified in the petals, of which three genes, FaMYB28, FaMYB54, and FaMYB576, appeared likely, based on the phylogenetic analysis, to regulate anthocyanin biosynthesis. The qRT-PCR showed that these three genes were more highly expressed in petals than in other tissues (fruit, leaf, petiole and stolon) and their expressions were higher in red compared to pink and white petals. These results facilitate the clarification on the roles of the R2R3-FaMYB genes in petal coloration in the pink-flowered strawberry. This work provides useful information for further functional analysis on the R2R3-FaMYB gene family in F. × ananassa.

中文翻译：

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Fragaria × ananassa R2R3-MYB 基因家族全基因组分析及其在粉花草莓花青素生物合成过程中的功能鉴定。

草莓（Fragaria × ananassa）是世界上经济上重要的水果。大型 R2R3-MYB 基因家族参与多种植物功能，包括花青素生物合成。本研究是对八倍体草莓中 MYB 基因家族的首次全基因组分析，并使用最近测序的 F. × ananassa 基因组描述了家族成员的鉴定和表征。具体而言，我们旨在确定参与粉红色花草莓花瓣着色的关键 MYB，这增加了其观赏价值。对 F. × ananassa R2R3-FaMYBs 进行了全面的全基因组分析，研究了基因结构、系统发育关系、启动子区域、染色体位置和共线性。共鉴定了 393 个 R2R3-FaMYB 基因。× ananassa 基因组，并根据系统发育分析分为 36 个亚组。同一亚组中具有相似功能的大多数基因表现出相似的外显子-内含子结构和基序组成。这些 R2R3-FaMYB 不均匀地分布在 28 条染色体上。发现 F. × ananassa 基因组中 R2R3-FaMYB 基因家族的扩增主要是由节段重复引起的。Ka/Ks 分析表明，复制的 R2R3-FaMYB 大多经历了纯化选择，并且在复制事件后显示出有限的功能差异。为了阐明哪些 R2R3-FaMYB 基因与粉红花草莓花瓣中的花青素生物合成有关，我们使用 RNA-seq 比较了不同花发育阶段的转录变化。在花瓣中鉴定出 131 个差异表达的 R2R3-FaMYB 基因，其中三个基因 FaMYB28、FaMYB54 和 FaMYB576 根据系统发育分析似乎可能调节花青素的生物合成。qRT-PCR 显示这三个基因在花瓣中的表达高于其他组织（果实、叶、叶柄和茎），与粉红色和白色花瓣相比，它们在红色中的表达更高。这些结果有助于阐明 R2R3-FaMYB 基因在粉红色花草莓花瓣着色中的作用。这项工作为 F. × ananassa 中 R2R3-FaMYB 基因家族的进一步功能分析提供了有用的信息。qRT-PCR 显示这三个基因在花瓣中的表达高于其他组织（果实、叶、叶柄和茎），与粉红色和白色花瓣相比，它们在红色中的表达更高。这些结果有助于阐明 R2R3-FaMYB 基因在粉红色花草莓花瓣着色中的作用。这项工作为 F. × ananassa 中 R2R3-FaMYB 基因家族的进一步功能分析提供了有用的信息。qRT-PCR 显示这三个基因在花瓣中的表达高于其他组织（果实、叶、叶柄和茎），与粉红色和白色花瓣相比，它们在红色中的表达更高。这些结果有助于阐明 R2R3-FaMYB 基因在粉红色花草莓花瓣着色中的作用。这项工作为 F. × ananassa 中 R2R3-FaMYB 基因家族的进一步功能分析提供了有用的信息。