Genomics Lab, School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54770, Pakistan.
Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA.
Sci Rep. 2022 Jul 19;12(1):12328. doi: 10.1038/s41598-022-16602-8.
Zinc finger (Zf)-BED proteins are a novel superfamily of transcription factors that controls numerous activities in plants including growth, development, and cellular responses to biotic and abiotic stresses. Despite their important roles in gene regulation, little is known about the specific functions of Zf-BEDs in land plants. The current study identified a total of 750 Zf-BED-encoding genes in 35 land plant species including mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. The gene family size was somewhat proportional to genome size. All identified genes were categorized into 22 classes based on their specific domain architectures. Of these, class I (Zf-BED_DUF-domain_Dimer_Tnp_hAT) was the most common in the majority of the land plants. However, some classes were family-specific, while the others were species-specific, demonstrating diversity at different classification levels. In addition, several novel functional domains were also predicated including WRKY and nucleotide-binding site (NBS). Comparative genomics, transcriptomics, and proteomics provided insights into the evolutionary history, duplication, divergence, gene gain and loss, species relationship, expression profiling, and structural diversity of Zf-BEDs in land plants. The comprehensive study of Zf-BEDs in Gossypium sp., (cotton) also demonstrated a clear footprint of polyploidization. Overall, this comprehensive evolutionary study of Zf-BEDs in land plants highlighted significant diversity among plant species.
锌指（Zf）-BED 蛋白是一个新的转录因子超家族，控制着植物的许多活动，包括生长、发育以及对生物和非生物胁迫的细胞反应。尽管它们在基因调控中具有重要作用，但对陆地植物中 Zf-BED 的特定功能知之甚少。本研究在 35 种陆地植物（包括苔藓、苔藓植物、石松类、裸子植物和被子植物）中总共鉴定了 750 个 Zf-BED 编码基因。基因家族的大小与基因组大小有些成比例。所有鉴定的基因都根据其特定的结构域结构分为 22 类。其中，第 I 类（Zf-BED_DUF-domain_Dimer_Tnp_hAT）在大多数陆地植物中最为常见。然而，有些类是家族特异性的，而有些类是物种特异性的，在不同的分类水平上表现出多样性。此外，还预测了几个新的功能域，包括 WRKY 和核苷酸结合位点（NBS）。比较基因组学、转录组学和蛋白质组学为研究 Zf-BED 在陆地植物中的进化历史、复制、分化、基因获得和丢失、物种关系、表达谱和结构多样性提供了深入的了解。对陆地植物中的 Zf-BED 在 Gossypium sp.（棉花）中的综合研究也表明了多倍化的明显足迹。总体而言，对陆地植物中 Zf-BED 的综合进化研究突出了植物物种之间的显著多样性。
