A comprehensive account of the LBD gene family of Gossypium was provided in this work. Expression analysis and functional characterization revealed that LBD genes might play different roles in G. hirsutum and G. barbadense. The Lateral Organ Boundaries Domain (LBD) proteins comprise a plant-specific transcription factor family, which plays crucial roles in physiological processes of plant growth, development, and stress tolerance. In the present work, a systematical analysis of LBD gene family from two allotetraploid cotton species, G. hirsutum and G. barbadense, together with their genomic donor species, G. arboreum and G. raimondii, was conducted. There were 131, 128, 62, and 68 LBDs identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. The LBD proteins could be classified into two main classes, class I and class II, based on the structure of their lateral organ boundaries domain and traits of phylogenetic tree, and class I was further divided into five subgroups. The gene structure and motif composition analyses conducted in both G. hirsutum and G. barbadense revealed that LBD genes kept relatively conserved within the subfamilies. Synteny analysis suggested that segmental duplication acted as an important mechanism in expansion of the cotton LBD gene family. Cis-element analysis predicated the possible functions of LBD genes. Public RNA-seq data were investigated to analyze the expression patterns of cotton LBD genes in various tissues as well as gene expression under abiotic stress treatments. Furthermore, RT-qPCR results found that GhLBDs had various expression regulation under MeJA treatments. Expression analysis indicated the differential functions of cotton LBD genes in response to abiotic stress and hormones.

中文翻译：

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棉属植物LBD基因家族的综合表征及基因表达模式

在这项工作中提供了对棉属植物 LBD 基因家族的全面描述。表达分析和功能表征表明 LBD 基因可能在 G. hirsutum 和 G. barbadense 中发挥不同的作用。横向器官边界域 (LBD) 蛋白包含植物特异性转录因子家族，在植物生长、发育和胁迫耐受的生理过程中起关键作用。在目前的工作中，对来自两种异源四倍体棉花 G. hirsutum 和 G. barbadense 及其基因组供体物种 G. arboreum 和 G. raimondii 的 LBD 基因家族进行了系统分析。G. hirsutum、G. barbadense、G. arboreum 和 G. raimondii 分别鉴定出 131、128、62 和 68 个 LBD。LBD 蛋白可分为两大类，I类和II类，根据其横向器官边界域的结构和系统发育树的特征，I类进一步分为5个亚群。在 G. hirsutum 和 G. barbadense 中进行的基因结构和基序组成分析表明 LBD 基因在亚科中保持相对保守。Synteny分析表明，片段重复是棉花LBD基因家族扩增的重要机制。顺式元素分析预测了 LBD 基因的可能功能。研究公共 RNA-seq 数据以分析棉花 LBD 基因在各种组织中的表达模式以及非生物胁迫处理下的基因表达。此外，RT-qPCR 结果发现 GhLBDs 在 MeJA 处理下具有多种表达调控。