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Review
. 2022 Jul 25;23(1):538.
doi: 10.1186/s12864-022-08776-2.

Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

Hanqiu Ge  1 , Jingjing Xu  1 , Mingzhu Hua  1 , Wenwen An  1 , Junping Wu  2 , Baohua Wang  3 , Ping Li  4 , Hui Fang  5
Affiliations
Review

Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

Hanqiu Ge et al. BMC Genomics. .

Abstract

Background: Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum.

Results: Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum.

Conclusions: In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.

Keywords: ACP genes; Bioinformatics; Gene family analysis; Sorghum bicolor (L.) Moench.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Chromosomal location of ACP genes in sorghum. The number on the left of chromosome is physical position of genes
Fig. 2
Fig. 2
The prediction of subcellular localization for ACP genes in sorghum. The color and the size of the circle indicate the values of reliable index of the prediction results
Fig. 3
Fig. 3
Subcellular localizations of SbACPs in tobacco leaf epidermal cells by confocal laser-scanning microscopy. The 5 selected SbACP-GFP fusion proteins were predominantly localized to the chloroplast. GFP, green fluorescent protein
Fig. 4
Fig. 4
Clustering of SbACPs in three species. Sb: sorghum; At: Arabidopsis; Zm: maize. All protein members were divided into four clusters: cluster A on pink background, cluster B on blue background, cluster C on orange background and cluster D on green background. The genes marked with purple asterisk were the members of sorghum ACP family
Fig. 5
Fig. 5
Phylogenetic tree (A), conserved motifs (B) and gene structure (C) analysis of SbACP family. The scaleplates under B and C indicate the length of SbACP proteins and genes, respectively
Fig. 6
Fig. 6
Interchromosomal relationships of SbACPs genes. Grey lines indicate all syntenic blocks in the sorghum genome. Red lines indicate collinear blocks of ACP genes in the sorghum genome
Fig. 7
Fig. 7
Syntenic analysis of ACP genes between sorghum and three representative plant species. A Syntenic analysis of ACP genes between sorghum and Arabidopsis. B Syntenic analysis of ACP genes between sorghum and rice. C Syntenic analysis of ACP genes between sorghum and maize. Gray lines in the background indicate the collinear blocks within sorghum and other plant genomes, whereas red lines highlight syntenic ACP gene pairs
Fig. 8
Fig. 8
Conserved domains of SbACP gene family. The red background stands for conservative amino acids, and the skyblue background stands for less conservative amino acids. The black boxes represent alpha spirals (helix A, helix B, helix C, helix D)
Fig. 9
Fig. 9
Prediction of three-dimensional structure of ACP proteins in sorghum
Fig. 10
Fig. 10
Analysis of cis-acting elements in 1.5 kb promoter regions of SbACP genes
Fig. 11
Fig. 11
qRT-PCR analysis of SbACPs under salt treatment. *, **, *** and ****, represent significant differences at P < 0.05, P < 0.01, P < 0.001 and P < 0.0001, respectively. One-way ANOVA was used to analyze the significance of relative expression difference of SbACP1-9 at 0, 6, 12 and 24 h under salt treatment and control
Fig. 12
Fig. 12
qRT-PCR analysis of SbACPs under drought treatment. *, **, *** and ****, represent significant differences at P < 0.05, P < 0.01, P < 0.001 and P < 0.0001, respectively. One-way ANOVA was used to analyze the significance of relative expression difference of SbACP1-9 at 0, 6, 12 and 24 h under drought treatment and control
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