Genome-wide identification, evolution and transcriptome analysis of GRAS gene family in Chinese chestnut (Castanea mollissima)

Abstract

GRAS transcription factors play an important role in regulating various biological processes in plant growth and development. However, their characterization and potential function are still vague in Chinese chestnut (Castanea mollissima), an important nut with rich nutrition and high economic value. In this study, 48 CmGRAS genes were identified in Chinese chestnut genome and phylogenetic analysis divided CmGRAS genes into nine subfamilies, and each of them has distinct conserved structure domain and features. Genomic organization revealed that CmGRAS tend to have a representative GRAS domain and fewer introns. Tandem duplication had the greatest contribution for the CmGRAS expansion based on the comparative genome analysis, and CmGRAS genes experienced strong purifying selection pressure based on the Ka/Ks. Gene expression analysis revealed some CmGRAS members with potential functions in bud development and ovule fertility. CmGRAS genes with more homologous relationships with reference species had more cis-acting elements and higher expression levels. Notably, the lack of DELLA domain in members of the DELLA subfamily may cause de functionalization, and the differences between the three-dimensional structures of them were exhibited. This comprehensive study provides theoretical and practical basis for future research on the evolution and function of GRAS gene family.

Keywords: Castanea mollissima; GRAS family; duplication model; expression pattern; protein structure.

FIGURE 1

Chromosome distribution, phylogenetic analysis and functional enrichment analysis of CmGRAS genes. (A) Chromosome distribution of CmGRAS genes. The colour of segments in the chromosomes shows the gene density of the corresponding region. (B) The phylogenetic tree of GRAS genes in Chinese chestnut, Arabidopsis thaliana and rice was constructed by maximum likelihood method. (C) GO function enrichment analysis of CmGRAS genes. (D) KEGG function enrichment analysis of CmGRAS genes.

FIGURE 2

Phylogenetic tree, distribution of conserved motifs and gene structure of CmGRAS genes. (A) Phylogenetic analysis of CmGRAS genes. (B) Distribution of conserved motifs of CmGRAS genes. (C) Gene structure of CmGRAS genes.

FIGURE 3

Collinear relationships within Chinese chestnut genome and with the grape, oak, Arabidopsis thaliana and rice genomes. (A) Collinear relationship within Chinese chestnut genome. (B) Collinear relationship between Chinese chestnut and grape genomes. (C) Collinear relationship between Chinese chestnut and oak genomes. (D) Collinear relationship between Chinese chestnut and Arabidopsis thaliana genomes. (E) Collinear relationship between Chinese chestnut and rice genomes.

FIGURE 4

Homologous collinearity dot-plot within Chinese chestnut genome. The collinear blocks from WGD containing CmGRAS genes are marked in the gray boxes of the figure, and the median Ks of the collinear blocks are marked.

FIGURE 5

Cis-acting elements in the promoter region of CmGRAS genes. The left side dendrogram shows the phylogenetic tree of CmGRAS genes. The distribution of cis-acting elements in the 2,000 bp upstream promoter are shown. The different functions of cis-acting elements are represented by different colors, as shown on the right.

FIGURE 6

Transcriptome analysis of CmGRAS genes and protein three-dimensional structure of members in DELLA subfamily. (A) Heatmap of CmGRAS genes expression in Chinese chestnut buds 20, 25 and 30 days after flowering. The left side dendrogram shows the phylogenetic tree of CmGRAS genes. (B) Heatmap of CmGRAS genes expression in fertile and abortive ovules of Chinese chestnut buds at different stages (15-July, 20-July and 25-July). The left side dendrogram shows the phylogenetic tree of CmGRAS genes. (C) The conserved domain distribution of DELLA subfamily proteins. (D) Prediction of three-dimensional structure of DELLA subfamily proteins (by Swiss model) and the comparison of similarity.