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Main conclusion  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.

Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium