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. 2019 May 9;10(5):355.
doi: 10.3390/genes10050355.

Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses

Ghulam Qanmber  1 , Faiza Ali  2 , Lili Lu  3 , Huijuan Mo  4 , Shuya Ma  5 , Zhi Wang  6   7 , Zuoren Yang  8   9
Affiliations

Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses

Ghulam Qanmber et al. Genes (Basel). .

Abstract

Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. The current study identified 34 HH3 genes in Gossypium hirsutum. Phylogenetic analysis classified HH3 genes of 19 plant species into eight distinct clades. Sequence logos analysis among Arabidopsis, rice, and G. hirsutum amino acid residues showed higher conservation in amino acids. Using collinearity analysis, we identified 81 orthologous/paralogous gene pairs among the four genomes (A, D, At, and Dt) of cotton. Further, orthologous/paralogous and the Ka/Ks ratio demonstrated that cotton HH3 genes experienced strong purifying selection pressure with restricted functional divergence resulting from segmental and whole genome duplication. Expression pattern analysis indicated that GhHH3 genes were preferentially expressed in cotton ovule tissues. Additionally, GhHH3 gene expression can be regulated by abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)) and phytohormonal (brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA)) treatments, suggesting that GhHH3 genes might play roles in abiotic and hormone stress resistance. Taken together, this work provides important information to decipher complete molecular and physiological functions of HH3 genes in cotton.

Keywords: GhHH3; Gossypium hirsutum; abiotic stress; cis-elements; expression pattern; gene duplication; phylogenetic analysis; phytohormonal stress.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Phylogenetic tree of histone H3 (HH3) genes from 19 plant species. (A) The phylostratum analysis of the HH3 gene family. (B) Phylogenetic tree divided all 257 HH3 genes into eight clades from HH3-a to HH3-h. Bootstrap values were also mentioned near the node of each branch.
Figure 2
Figure 2
Sequence logos of conserved amino acid residues generated for three plant species including Arabidopsis (first), rice (second), and Gossypium hirsutum (third) exhibited highly conserved sequence logos during the evolution of dicots and monocots plant species.
Figure 2
Figure 2
Sequence logos of conserved amino acid residues generated for three plant species including Arabidopsis (first), rice (second), and Gossypium hirsutum (third) exhibited highly conserved sequence logos during the evolution of dicots and monocots plant species.
Figure 3
Figure 3
Gene duplication among HH3 genes in cotton including G. arboreum (A-genome), G. hirsutum (At and Dt sub-genome), and G. raimondii (D-genome). Red lines linking two different genes represent the orthologous pairs diverged from the same ancestor. A01–A13 (mustard colored blocks) represent the chromosomes of At sub-genome and D01–D13 (light green colored blocks) exhibit the chromosomes of Dt sub-genome. Similarly, A-chr1-A-chr13 (blue colored blocks) and D-chr1-D-chr13 (red colored blocks) demonstrate G. arboreum and G. raimondii chromosomes, respectively.
Figure 4
Figure 4
Tissue specific expression patterns analysis of GhHH3 genes in different tissues of the plant. (A) Heat map generated for the expression of 34 GhHH3 genes in 22 different tissues. Data obtained from publically available transcriptomic data and the color bar (down) indicate the values of expression level. (B) Heat map of all GhHH3 relative expressions in two fuzzless/lintless mutants (M1l and M2l) as compared with wild type (WT) plants. Data were extracted from published RNA-seq data and the color bar (down) indicates the expression level. (C) Relative expression level of eight selected GhHH3 genes in different tissue estimated by qRT-PCR analysis. Error bars indicate the standard deviations (SD) of three independent biological repeats.
Figure 5
Figure 5
Expression patterns analysis of GhHH3 genes under the treatment of four different abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)). (A) Heat map of all GhHH3 gene family members generated using publically available transcriptomic data. Color bar (down) indicated the response of that gene under specific treatment. (B) Expression pattern of eight GhHH3 genes in cotton seedlings under same abiotic stresses estimated by qRT-PCR analysis. The error bars exhibit standard deviations (SD) of three independent biological repeats.
Figure 6
Figure 6
Expression analysis of selected GhHH3 genes in cotton seedlings under exposure to five different phytohormonal stress stimuli including brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA). Error bars indicated standard deviations (SD) among three independent biological experiments.
Figure 6
Figure 6
Expression analysis of selected GhHH3 genes in cotton seedlings under exposure to five different phytohormonal stress stimuli including brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA). Error bars indicated standard deviations (SD) among three independent biological experiments.
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