Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of U's genomes

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene Pub Date : 2025-03-05 DOI:10.1016/j.plgene.2025.100497

Prabhakaran Soundararajan , AT Vivek , Gokul Babu Suresh , Bhavya Shukla , Kanchan B.M. Singh , Shailesh Kumar , Abinaya Manivannan

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引用次数: 0

Abstract

WUSCHEL-related homeobox (WOX) is an evolutionarily important gene family involved in key developmental processes such as embryo patterning, stem cell regulation, apical meristem maintenance, etc. Brassica contains several widely diversified and economically important vegetables grown worldwide. In this study, a pangenome-wide identification and characterization of the WOX gene family among all the species of Brassica Triangle of U's have been performed. WOX gene family was identified from the genomes of 31 Brassica species/morphotypes. About 26–28, 28, and 26–31 copies of WOX genes are present in diploid progenitors such as B. rapa (AA), B. nigra(BB), and B. oleracea (CC), respectively. In allotetraploid species, the number of WOX genes exceeds more than 50 copies. However, their number varies between morphotypes at the pangenome level. Motif and gene structure analysis showed distinct and conserved patterns between homoeologous genes. Non-synonymous (Ka)/Synonymous (Ks) ratio indicated that more number of modern/WUS clade orthologs underwent positive selection followed by those of the intermediate clade. Interacting networks between the WOX and miRNA showed that the CC genome has more complex network pattern compared to the AA genome. Although the WOX-miRNA interactions observed in both AABB and AACC genomes were distinct, they exhibited similarity in overlapping connections. Transcriptome data, analyzed from unfertilized ovule to seven developmental stages of embryos and their seed coat, sourced from public databases across six genomes, illustrated that WOX genes are expressed in a spatio-temporal manner throughout these developmental stages. Furthermore, qPCR analysis of WOX genes at two stages, such as 2–3 days old (leaf and root primordia) and 3 weeks old seedlings (leaf and root) in B. juncea and B. oleracea provides details of stage- and tissues-specific expression patterns between AB and C genomes. Overall, the present study sheds light on evolution and characterization of the WOX gene family in Brassica at the pangenome level for further functional validation.

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三角芸苔WOX基因家族的全基因组鉴定、进化分析和特征分析

wuschelrelated homeobox （WOX）是一个具有重要进化意义的基因家族，参与胚胎模式、干细胞调控、根尖分生组织维持等关键发育过程。芸苔属包括几种广泛多样化和经济上重要的蔬菜种植在世界各地。在本研究中，我们对U型三角芸苔（Brassica Triangle of U’s）所有种的WOX基因家族进行了全基因组鉴定和表征。从31个芸苔种/形态型的基因组中鉴定出WOX基因家族。在二倍体祖细胞如B. rapa （AA）、B. nigra（BB）和B. oleracea （CC）中，WOX基因分别有26 - 28,28和26-31个拷贝。在异源四倍体物种中，WOX基因的拷贝数超过50份。然而，它们的数量在泛基因组水平上因形态而异。基序和基因结构分析显示同源基因之间存在明显的保守模式。非同义(Ka)/同义（Ks）比值表明，更多的现代/WUS进化枝同源物发生正向选择，其次是中间进化枝。WOX和miRNA之间的相互作用网络表明，CC基因组比AA基因组具有更复杂的网络模式。尽管在AABB和AACC基因组中观察到的WOX-miRNA相互作用是不同的，但它们在重叠连接上表现出相似性。转录组数据来源于6个基因组的公共数据库，分析了从未受精的胚珠到胚胎的7个发育阶段及其种皮的转录组数据，表明WOX基因在这些发育阶段以时空方式表达。此外，对芥菜和甘蓝2-3天龄（叶和根原基）和3周龄幼苗（叶和根）中WOX基因的qPCR分析提供了AB和C基因组之间阶段和组织特异性表达模式的细节。总的来说，本研究在泛基因组水平上阐明了芸苔属WOX基因家族的进化和特征，为进一步的功能验证提供了基础。

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来源期刊

Plant Gene Agricultural and Biological Sciences-Plant Science

CiteScore

4.50

自引率

0.00%

发文量

审稿时长

51 days

期刊介绍： Plant Gene publishes papers that focus on the regulation, expression, function and evolution of genes in plants, algae and other photosynthesizing organisms (e.g., cyanobacteria), and plant-associated microorganisms. Plant Gene strives to be a diverse plant journal and topics in multiple fields will be considered for publication. Although not limited to the following, some general topics include: Gene discovery and characterization, Gene regulation in response to environmental stress (e.g., salinity, drought, etc.), Genetic effects of transposable elements, Genetic control of secondary metabolic pathways and metabolic enzymes. Herbal Medicine - regulation and medicinal properties of plant products, Plant hormonal signaling, Plant evolutionary genetics, molecular evolution, population genetics, and phylogenetics, Profiling of plant gene expression and genetic variation, Plant-microbe interactions (e.g., influence of endophytes on gene expression; horizontal gene transfer studies; etc.), Agricultural genetics - biotechnology and crop improvement.