Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L

Abstract

BackgroundF-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects.ResultsIn current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction.ConclusionThe results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.

Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

“…The ARID domain is related to sequence-specific DNA binding [ 52 ], the PHD domain specifically recognize methylated (modified) histone codes and may be important readers of histone codes [ 53 ], and the PLU-1 domain plays a critical role in gene regulation and chromatin stability [ 54 ]. In the JMJD6 subfamily, four JmjC genes ( GhJMJ3A/GhJMJ3D and GhJMJ18A/GhJMJ18D ) containing the F-box domain are consistent with previous study [ 55 ].…”

The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress

“…However, here, we found that 67% of the TaFBX genes do not have any additional known domains. This result is in accordance with the protein structure that has been observed in cotton and in wheat with, respectively, 54% and 76% of the FBX containing only the F-box domain [32,43]. A similar percentage was observed by Jain et al (2007) [41] in the rice FBX family.…”

“…In contrast, only 14% and 30% of the FBX genes were identified without other known domains in Arabidopsis and chickpea, respectively [31,77]. The second most abundant subfamily was found to be the FBD subfamily in our study, such as in Hong et al (2020) [43], while this is the Kelch domain in cotton [32].…”

“…The FBX family has been recorded in a large number of animal and plant species [ 5 ]; for example, 9 in humans, 74 in mice, 20 in yeast and 27 FBX in Drosophila [ 28 , 29 ]. In plants, the FBX family is much larger, with 897 predicted genes in Arabidopsis , 971 in rice, 417 in corn, 228 in Physcomitrella patens moss, 285 in chickpea, 592 in cotton and 425 genes in poplar [ 25 , 30 , 31 , 32 ]. In contrast to other E3 ligases families, the FBX family has, therefore, undergone a significant expansion in the plant kingdom in comparison with other eukaryotes [ 33 , 34 ].…”

Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113

“…The proposed systemic nomenclature will be helpful not only in introducing uniformity and communicating research findings effectively in the Arabidopsis FBP gene family but can also be applied to FBP gene families of other plant species whose genome sequencing have been completed and have well-defined chromosome maps. The genomic distribution of Arabidopsis FBPs depicts a positive relation between FBP number and chromosomal length as opposed to the study, which found out uneven FBPs distribution on cotton chromosomes ( Zhang et al, 2019 ; Figure 5 ). Targeting the genes involved in anther or pollen development can manipulate male fertility, which is of immense importance in crop breeding and increasing the crop yield ( Gómze et al, 2015 ).…”