Evolutionary analysis of the DHHCs in Saccharinae

Abstract

The DHHC domain genes are crucial for protein lipid modification, a key post-translational modification influencing membrane targeting, subcellular trafficking, and protein function. Despite their significance, the DHHC gene family in Saccharinae remains understudied. Here, we identified 32 (110 alleles), 28, 53, and 48 DHHC genes in Saccharum spontaneum Np-X, Erianthus rufipilus, Miscanthus sinensis, and Miscanthus lutarioriparius, respectively. Collinearity analysis uncovered the loss of two M. lutarioriparius genes, homologues of EruDHHC1C and EruDHHC3A. Phylogenetic and classification analyses categorized DHHC family members into six subgroups (A-F). Ka/Ks ratio analysis indicated that gene duplication in these species was primarily driven by whole-genome duplication (WGD) and dispersed duplication (DSD), with DHHC genes evolving under strong purifying selection. Gene expression and trait correlation analysis revealed a significant negative correlation between SspDHHC28A expression in S. spontaneum and sucrose content, suggesting a role in photosynthesis product transport during rapid growth. This study deepens our understanding of the DHHC gene family's functional dynamics and evolutionary path in Saccharinae, laying a foundation for future research.

Keywords: DHHC; Evolutionary; Gene duplications; Saccharinae; Sucrose storage.

Fig. 1

Collinearity between chromosomes 1 and 3 of E. rufipilus and S. spontaneum, M. sinensis, and M. lutarioriparius and the labeling of missing genes.

Fig. 2

Three-dimensional structural model of the DHHC protein. The structural images were generated by PyMOL software. (a) The purple region in the 3D structural schematic is a typical DHHC structural domain: C-x2-C-x9-HC-x2-C-x2-C-x4-DHHC-x5-C-x4-N-x3-F. (b) Multiple sequence comparison of DHHC proteins; The red dashed boxes indicate conserved core structural domains.

Fig. 3

A maximum likelihood (ML) phylogenetic tree of four species was constructed based on the full-length sequence in RAxML, with branching support values added at the branches. The tree was divided into six classic outer rings with different colors: green, yellow, light purple, deep purple, pink, and blue-gray for the DHHC proteins. Circles, crosses, diamonds and squares denote S. spontaneum, E. rufipilus, M. sinensis, and M. lutarioriparius, respectively.

Fig. 4

Analysis of cis-regulatory elements in DHHC promoters. Dark blue squares indicate a high number of cis-acting regulatory elements, light blue squares indicate a low number of cis-regulatory elements, and white squares indicate no cis-regulatory elements.

Fig. 5

Statistics of Ka/Ks values for four species of Saccharinae. The x-axis represents the duplication type. WGD: whole-genome duplicates; TD: tandem duplicates; PD: proximal duplicates; TRD: transposed duplicates; DSD: dispersed duplicates, y-axis is the Ka/Ks ratio. (a) Ka/Ks box plot of S. spontaneum. (b) Ka/Ks box plot of E. rufipilus. (c) Ka/Ks box plot of M. sinensis. d. Ka/Ks box plot of M. lutarioriparius.

Fig. 6

Heatmap normalised to DHHC gene expression in S. spontaneum. (a) A heatmap of expression among tissues at different growth periods is presented. The number of stem nodes, from top to bottom, is indicated by the letters “Stem3, 6, 9.” These letters correspond to the stalks, which are arranged from young to old. roll leaf indicates a young leaf and a mature leaf indicates a spreading mature leaf. (b) A heatmap of the various regions of the leaf blade (base, middle, tip) is presented.

Fig. 7

(a) Heatmap of DHHC gene expression and expression trends in the genomes of four Saccharinae species. w19n and w37n are the 19th and 37th weeks of sampling, respectively; 5, 8, and Ex5 are the tissues sampled when the 5th stem node, 8th stem node, and 5th stem node were first labeled mature stem nodes, respectively. (b) The X-axis is the expression of the gene and the Y-axis is the phenotypic value of the agronomic trait. The correlations between DHHC genes and agronomic traits were significant for the green markers and highly significant for the red markers according to the P value. CCS: commercial cane sugar, CCS Sept: late sugar content. Delta_CCS_June_March: Yield changes in sugar content of sugarcane from March to June.