In silico analysis of R2R3-MYB transcription factors in the basal eudicot model, Aquilegia coerulea.

IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
3 Biotech Pub Date : 2024-11-01 Epub Date: 2024-10-29 DOI:10.1007/s13205-024-04119-y
Banisha Phukela, Hanna Leonard, Yuval Sapir
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引用次数: 0

Abstract

R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, Aquilegia coerulea is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized Arabidopsis thaliana R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as A. thaliana R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus Aquilegia. AqcoeR2R3-MYB genes are present in all seven chromosomes of A. coerulea, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in A. coerulea. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04119-y.

基生裸子植物模型 Aquilegia coerulea 中 R2R3-MYB 转录因子的硅学分析。
R2R3-MYBs是一类重要的转录因子,调控整个植物界的关键发育过程;然而,迄今为止还没有对Ranunculaceae(毛茛科)早期分化的裸子植物支系中的R2R3-MYBs进行过全面的分析。本研究选取 Aquilegia coerulea 作为研究对象,通过分析 R2R3-MYBs 的基因组分布、组织结构、基因结构、理化性质、蛋白质结构、进化和可能的扩展模式,了解 R2R3-MYBs 的保守和分化程度。全基因组分析表明,根据全长蛋白质序列的系统进化分析,存在 82 个推定同源物,分为 21 个亚群。该结构域在所有同源物中基本保持不变,与拟南芥 R2R3-MYB 的特征差异很小。当使用全长蛋白质序列时,系统发生树的拓扑结构保持不变,表明 R2R3-MYB 的进化仅由结构域区域驱动。同一亚群中存在相似的外显子-内含子结构和保守基团也证明了这一点。此外,通过将 AqcoeR2R3-MYB 成员与单子叶植物和核心裸子植物进行比较,发现了一些功能支系的进化扩展,如大连油菜 R2R3-MYB 亚群 6(SG6),它是花色素生物合成和花色的上游调控因子。SG6 类基因在被子植物中的进化历史重建突显了 Aquilegia 属中发生的独立复制事件。AqcoeR2R3-MYB基因存在于A. coerulea的所有七条染色体中,其中大部分是局部和节段复制的结果。对这些重复基因对的选择分析表明,除一个基因对外,其他基因对均有纯化选择,而对 R2R3-MYB 的理化分析表明,MYB 之间存在差异,表明其功能多样化。这项研究为进一步研究旁系拷贝及其在 A. coerulea 不同花性状进化中可能扮演的角色铺平了道路。它为基础裸子植物中 R2R3-MYBs 的功能基因组研究奠定了基础,并促进了被子植物之间的比较研究。这项工作还为破译支配花形态多样性的新型遗传调控途径提供了一个框架:在线版本包含补充材料,可查阅 10.1007/s13205-024-04119-y。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
3 Biotech
3 Biotech Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)
CiteScore
6.00
自引率
0.00%
发文量
314
期刊介绍: 3 Biotech publishes the results of the latest research related to the study and application of biotechnology to: - Medicine and Biomedical Sciences - Agriculture - The Environment The focus on these three technology sectors recognizes that complete Biotechnology applications often require a combination of techniques. 3 Biotech not only presents the latest developments in biotechnology but also addresses the problems and benefits of integrating a variety of techniques for a particular application. 3 Biotech will appeal to scientists and engineers in both academia and industry focused on the safe and efficient application of Biotechnology to Medicine, Agriculture and the Environment.
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