Table_3_Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species.DOCX

The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein–protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.

植物特异的SHORT INTERNODES/STYLISH（SHI/STY）蛋白属于一类转录因子家族，参与早期侧根的形成与发育。然而，目前针对该家族的分子进化研究尚不多见。本研究在21种陆生植物中共计鉴定出195个SHI/STY基因，其中以芸苔属（Brassica）物种为研究重点。研究人员对该家族基因的理化性质、染色体定位与复制模式、基序分布、外显子-内含子结构、遗传进化及表达模式进行了系统分析。基于系统发育分析，这些基因可划分为4个进化枝（Clade 1/2/3/4）。各进化枝的基序分布与基因结构均较为相似。亚细胞定位预测结果显示，SHI/STY蛋白定位于细胞核内。共线性分析表明，SHI/STY家族在进化过程中相对保守。全基因组复制是该家族基因扩张的主要驱动因素。SHI/STY家族经历了强烈的纯化选择，但研究同时也鉴定到了若干正向选择位点。多数SHI/STY基因的启动子区域包含多种类型的顺式作用元件，如光响应、逆境响应及激素响应元件，提示该家族基因可能参与众多生物学过程。蛋白质相互作用预测结果显示，SHI/STY蛋白可与多种重要蛋白互作，例如LPAT4、MBOATs、PPR及UBQ3。此外，本研究针对油菜开展了深入的RNA测序（RNA-seq）与实时定量聚合酶链反应（qRT-PCR）分析。分析结果显示，SHI/STY家族基因在根与芽中高表达，且其表达可受核盘菌（Sclerotinia sclerotiorum）侵染、干旱、低温及高温胁迫的调控。此外，实时定量PCR（qRT-PCR）分析结果表明，BnSHI/STY基因的表达水平在多种处理条件下均发生显著变化，包括低温、盐胁迫、干旱、吲哚乙酸（IAA，生长素）、脱落酸（ABA）以及6-苄氨基腺嘌呤（6-BA，细胞分裂素）处理。本研究为陆生植物中SHI/STY家族的进化与扩张机制提供了新的认知，同时为后续该家族基因的功能研究奠定了基础。