The DBB Family in Populus trichocarpa: Identification, Characterization, Evolution and Expression Profiles

Abstract

The B-box proteins (BBXs) encode a family of zinc-finger transcription factors that regulate the plant circadian rhythm and early light morphogenesis. The double B-box (DBB) family is in the class of the B-box family, which contains two conserved B-box domains and lacks a CCT (CO, CO-like and TOC1) motif. In this study, the identity, classification, structures, conserved motifs, chromosomal location, cis elements, duplication events, and expression profiles of the PtrDBB genes were analyzed in the woody model plant Populus trichocarpa. Here, 12 PtrDBB genes (PtrDBB1-PtrDBB12) were identified and classified into four distinct groups, and all of them were homogeneously spread among eight out of seventeen poplar chromosomes. The collinearity analysis of the DBB family genes from P. trichocarpa and two other species (Z. mays and A. thaliana) indicated that segmental duplication gene pairs and high-level conservation were identified. The analysis of duplication events demonstrates an insight into the evolutionary patterns of DBB genes. The previously published transcriptome data showed that PtrDBB genes represented distinct expression patterns in various tissues at different stages. In addition, it was speculated that several PtrDBBs are involved in the responsive to drought stress, light/dark, and ABA and MeJA treatments, which implied that they might function in abiotic stress and phytohormone responses. In summary, our results contribute to the further understanding of the DBB family and provide a reference for potential functional studies of PtrDBB genes in P. trichocarpa.

Keywords: DBB; Populus trichocarpa; expression patterns; phylogenetic relationships; stress response.

Figure 1

Multiple sequence alignment of 12 PtrDBB conserved domains.

Figure 2

Phylogenetic tree of DBB protein from Populus trichocarp, Arabidopsis thaliana, Oryza sativa, Zea mays, Physcomitrella patens, Selaginella moellendorffii, Picea abies and Amborella trichopoda.

Figure 3

Analysis of phylogenetic relationship and DBB gene structures by MEGA-X in view of the PtrDBB protein sequences in P. trichocarp. Left: a neighbor-joining (NJ) phylogenetic tree was constructed. All the PtrDBB genes were divided into four clades, and different groups were represented by different colors. Right: the analysis of exon/intron structures of 12 PtrDBB genes. The yellow and green rectangles represent exons and introns, respectively. The black lines represents untranslated regions (UTRs).

Figure 4

Distribution of conserved motifs for PtrDBB proteins (1–8). The analysis of PtrDBBs conserved motifs was carried out by the MEME. Eight motifs were displayed by boxes of different colors, and the lengths of the motif were represented in proportion. The annotation information of each motif is marked in the bottom right corner.

Figure 5

Predicted structures of 12 PtrDBB proteins (>99% confidence).

Figure 6

Chromosomal distribution of poplar DBB genes. Different colors indicated the grouping of PtrDBB genes. Six segmental duplication pairs were connected by orange lines.

Figure 7

Duplication events of DBB genes. (A) Synteny of poplar DBB genes. (B) Synteny of P. trichocarpa and Z. mays, P. trichocarpa and A. thaliana DBB gene regions. Segmental duplicated DBB gene pairs, and duplicated blocks were linked by red lines and gray lines, respectively.

Figure 8

Ks and Ka/Ks value distribution of the DBB genes in the genomes of poplar paralogous gene pairs (Ptr-Ptr) and orthologous gene pairs between P. trichocarpa and Z. mays (Ptr-Zm), P. trichocarpa and A. thaliana (Ptr-At), viewed from the frequency distribution.

Figure 9

Expression patterns of 12 PtrDBB genes in different vegetative tissues and stages of reproductive development. Samples were from 14 tissues, including the following: FM, female catkin, prior to seed release; F, female catkins, post-fertilization; M, male catkins; ML, mature leaf; REF, roots < 0.5 cm diameter from field-grown trees; RTC, roots from plants in tissue culture; G43h, germinated 43 h post-imbibition; ApB, actively growing shoot apex; AxB, axillary bud; YFB, newly initiated female floral buds; YMB, newly initiated male floral buds; Xylem1, developing xylem; Phloem3, developing phloem/cambium; PC, phloem, cortex, and epidermis.

Figure 10

Analysis of cis-elements of PtrDBBs using the Plantcare database.

Figure 11

The expression of 12 PtrDBB genes under different stresses (light/dark, drought, ABA, and MeJA treatments). Compared with untreated samples (expression levels = 1) after sampling to analyze the relative expression levels. X-axes and Y-axes mean time points after light/dark stress, drought stress, ABA, and MeJA treatments, and data were normalized to reference gene Ptr18S, respectively. Three independent biological replicates were conducted.