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, 21 (1), 91

Comprehensive Analysis of the Gossypium Hirsutum L. Respiratory Burst Oxidase Homolog (Ghrboh) Gene Family

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Comprehensive Analysis of the Gossypium Hirsutum L. Respiratory Burst Oxidase Homolog (Ghrboh) Gene Family

Wei Wang et al. BMC Genomics.

Abstract

Background: Plant NADPH oxidase (NOX), also known as respiratory burst oxidase homolog (rboh), encoded by the rboh gene, is a key enzyme in the reactive oxygen species (ROS) metabolic network. It catalyzes the formation of the superoxide anion (O2•-), a type of ROS. In recent years, various studies had shown that members of the plant rboh gene family were involved in plant growth and developmental processes as well as in biotic and abiotic stress responses, but little is known about its functional role in upland cotton.

Results: In the present study, 26 putative Ghrboh genes were identified and characterized. They were phylogenetically classified into six subfamilies and distributed at different densities across 18 of the 26 chromosomes or scaffolds. Their exon-intron structures, conserved domains, synteny and collinearity, gene family evolution, regulation mediated by cis-acting elements and microRNAs (miRNAs) were predicted and analyzed. Additionally, expression profiles of Ghrboh gene family were analyzed in different tissues/organs and at different developmental stages and under different abiotic stresses, using RNA-Seq data and real-time PCR. These profiling studies indicated that the Ghrboh genes exhibited temporal and spatial specificity with respect to expression, and might play important roles in cotton development and in stress tolerance through modulating NOX-dependent ROS induction and other signaling pathways.

Conclusions: This comprehensive analysis of the characteristics of the Ghrboh gene family determined features such as sequence, synteny and collinearity, phylogenetic and evolutionary relationship, expression patterns, and cis-element- and miRNA-mediated regulation of gene expression. Our results will provide valuable information to help with further gene cloning, evolutionary analysis, and biological function analysis of cotton rbohs.

Keywords: Expression patterns; Gene family; Rboh; Reactive oxygen species; Upland cotton.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Cluster analysis, gene structure and domain analysis of upland cotton rboh gene family. (A) Phylogenetic tree of G. hirsutum rbohs constructed with MEGA 6.0 by the NJ method. Bootstrap values from 1000 replicates are indicated at each branch. Group I to VI represented by red, yellow, purple, black, green, and blue, respectively. (B) Exon–intron structures of Ghrboh genes. Yellow boxes and black horizontal lines indicated exons and introns, respectively. (C) Domain compositions of upland cotton rbohs. Only major domains were presented here based on our database searches in Pfam database (http://pfam.xfam.org/)
Fig. 2
Fig. 2
Chromosomal location and synteny relationships of rboh genes from G. hirsutum, G. raimondii and G. arboretum. G. hirsutum, G. raimondii and G. arboretum chromosomes are indicated in purple, blue and red, respectively. The putative orthologous rboh genes between G. hirsutum and G. raimondii, G. hirsutum and G. arboretum, and G. raimondii and G. arboretum are connected by yellow, red and orange lines, respectively. Black lines connect the putative paralogous genes. s413_A2, s, scaffold
Fig. 3
Fig. 3
Neighbor-joining (NJ) phylogenetic tree of the rboh gene family among Gossypium. The tree was constructed with predicted full length rboh amino acid sequences from in G. hirsutum (Gh), G. arboreum (Ga), and G. raimondii (Gr)
Fig. 4
Fig. 4
Expression profiles of Ghrbohs in different tissues/organs and development stages. The log2 of FPKMs values calculated by RNA-Seq data were shown as a heat map. The colors of the bar shown to the right of the heat-map varied from red to blue representing the relative expression levels from high to low. FPKMs data was obtained from ccNET (http://structuralbiology.cau.edu.cn/gossypium/) and CottonFGD (https://cottonfgd.org/). (A) The heat-map showed the hierarchical clustering of the relative expression of 26 Ghrbohs in root, stem, leaf, petal, torus, stamen, pistil, calycle. (B) The heat-map showed the hierarchical clustering of the relative expression of 26 Ghrbohs in fibers at 5, 10, 20 and 25 dpa. (C) The heat-map showed the hierarchical clustering of the relative expression of 26 Ghrbohs in ovules at − 3, − 1, 0, 1, 3, 5, 10, 20, 25 and 35 dpa
Fig. 5
Fig. 5
Expression profiles of Ghrbohs under different stress treatments. The log2 of FPKMs values calculated by RNA-Seq data were shown as a heat map. The colors of the bar shown to the right of the heat-map varied from red to blue representing the relative expression levels from high to low. FPKMs data was obtained from ccNET (http://structuralbiology.cau.edu.cn/gossypium/) and CottonFGD (https://cottonfgd.org/). The heat-map showed the hierarchical clustering of the relative expression of Ghrbohs under hot, cold, PEG and salt treatments (A-D)
Fig. 6
Fig. 6
Cis-elements analysis of putative Ghrboh promoters. Different cis-elements with the same or similar functions were shown in the same color
Fig. 7
Fig. 7
The prediction of targeting regulatory relations between Ghrbohs and G. hirsutum miRNAs. Black lines represented ORFs of Ghrbohs. NADPH_Ox domain, EF-hand motif, Ferri_reduct domain, FAD-binding_8 domain and NAD-binding_6 domain, were represented by boxes filled with yellow, orange, green, red and grey, respectively. miRNA complementary sites (black filling) with the nucleotide positions of Ghrbohs cDNAs were pointed out. The RNA sequence of each complementary site from 5′ to 3′ and the predicted miRNA sequence from 3′ to 5′ are shown in the expanded regions

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