Genome-Wide Identification and Characterization of G2-Like Transcription Factor Genes in Moso Bamboo (Phyllostachys edulis)

Abstract

G2-like (GLK) transcription factors contribute significantly and extensively in regulating chloroplast growth and development in plants. This study investigated the genome-wide identification, phylogenetic relationships, conserved motifs, promoter cis-elements, MCScanX, divergence times, and expression profile analysis of PeGLK genes in moso bamboo (Phyllostachys edulis). Overall, 78 putative PeGLKs (PeGLK1-PeGLK78) were identified and divided into 13 distinct subfamilies. Each subfamily contains members displaying similar gene structure and motif composition. By synteny analysis, 42 orthologous pairs and highly conserved microsynteny between regions of GLK genes across moso bamboo and maize were found. Furthermore, an analysis of the divergence times indicated that PeGLK genes had a duplication event around 15 million years ago (MYA) and a divergence happened around 38 MYA between PeGLK and ZmGLK. Tissue-specific expression analysis showed that PeGLK genes presented distinct expression profiles in various tissues, and many members were highly expressed in leaves. Additionally, several PeGLKs were significantly up-regulated under cold stress, osmotic stress, and MeJA and GA treatment, implying that they have a likelihood of affecting abiotic stress and phytohormone responses in plants. The results of this study provide a comprehensive understanding of the moso bamboo GLK gene family, as well as elucidating the potential functional characterization of PeGLK genes.

Keywords: GLK genes; expression profiles; moso bamboo; motif analysis; phylogenetic relationship.

Figure 1

Division of 78 PeGLK genes into 13 groups (G1–G13) based on predicted domain structures. Domains are represented by different colored boxes.

Figure 2

Phylogenetic analysis of GLK proteins of moso bamboo and maize. Tree was constructed using neighbor-joining method with MEGA7.0. Each color represents one group in the branches, and 16 groups were found in total. The numbers at nodes indicate the bootstrap values per 1000 replicates determined by the neighbor-joining method.

Figure 3

Phylogenetic relationship and gene structures of PeGLKs. Left: Neighbor-joining (NJ) phylogenetic tree was constructed by MEGA 7.0 according to PeGLK protein sequences. Proteins in tree were divided into 13 distinct subfamilies, which are distinguished by different colors. Right: Exon/intron structures of PeGLK genes were generated by online GSDS. Yellow rectangles, gray lines, and blue rectangles represent exons, introns, and untranslated regions (UTRs), respectively. The numbers at nodes indicate the bootstrap values per 1000 replicates determined by the neighbor-joining method.

Figure 4

Schematic representation of eight conserved motifs (1–8) in PeGLKs, ordered based on online MEME analysis. Lengths of motifs are displayed proportionally.

Figure 5

Predicted structures of PeGLK proteins. Structures of 10 PeGLK proteins were predicted with >98% confidence. All colored lines represent α-helix, and the arrow with plane shape is β-sheet, which displayed only in PeGLK74. Bars: 20 nm.

Figure 6

Chromosomal locations of PeGLK genes in Phyllostachys edulis.

Figure 7

Duplication events of GLK proteins. (A) Synteny of moso bamboo PeGLK genes. (B) Synteny of moso bamboo and maize GLK genes. All syntenic genes were located on a map; segmentally duplicated GLK gene pairs are linked by red lines and tandemly duplicated genes by purple lines.

Figure 8

Ks and Ka/Ks value distribution of PeGLK genes in paralogous gene pairs (Pe-Pe) of moso bamboo genome and orthologous gene pairs between moso bamboo and maize, viewed through frequency distribution of relative Ks and Ka/Ks modes.

Figure 9

Expression profiles of PeGLK genes in different tissues. Samples were from leaf, steam, rhizome, and root. Expression level of each PeGLK gene can be estimated based on scale on right. Red, yellow and blue indicate high, medium and low levels of gene expression, respectively.

Figure 10

cis-Acting elements related to LTRE, DRE, MeJA, and GA in promoter regions of PeGLKs. Left: Different colors represent numbers of four cis-acting elements of PeGLKs. Right: Four CREs were predicted; each is displayed in a different color.

Figure 11

Expression patterns of 13 representative PeGLK genes in response to abiotic stress treatments. X-axis and Y-axis indicate time points after cold and osmotic treatments, and relative expression levels are standardized to reference gene TIP41.

Figure 12

Expression patterns of 13 representative PeGLK genes in response to phytohormone treatments. X-axis and Y-axis indicate time points after MeJA and GA treatments, and relative expression levels are standardized to reference gene TIP41.