Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var . rapa

Abstract

The Lateral Organ Boundaries Domain (LBD) genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species. However, members of the LBD gene family have yet to be identified in Brassica rapa var. rapa. In the present study, fifty-nine LBD genes were identified and distributed on 10 chromosomes. The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa; the theoretical pI for these proteins varies from 4.83 to 9.68. There were 17 paralogous gene pairs in the BrrLBD family, suggesting that the amplification of the BrrLBD gene family involved large-scale gene duplication events. Members of the BrrLBD family were divided into 7 subclades (class I a to e, class II a and b). Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs. The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR (qRT-PCR). Most BrrLBD genes in the same subclade had similar gene expression profiles. However, the expression patterns of 7 genes differed from their duplicates, indicating that although the gene function of most BrrLBD genes has been conserved, some BrrLBD genes may have undergone evolutionary change.

Keywords: Brassica rapa var. rapa; Expression profiles; LBD; LBD gene sequence analysis; Transcription factors.

Fig. 1

Phylogenetic tree of LBD proteins from turnip and Arabidopsis. The evolutionary history of LBD proteins was inferred by using 59 BrrLBD protein and 43 AtLBD protein sequences to construct a Neighbor-Joining (NJ) cluster tree. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Evolutionary analyses were conducted in MEGA7.

Fig. 2

Chromosome distribution of BrrLBD genes. Turnip Chromosomes are shown in different colors in the outer circle, where the numbers represent the chromosome length in 100 Kb. The BrrLBD genes are marked at the approximate positions with specific color lines on the circle. Filled blocks in different colors represent the syntenic relationships of BrrLBD genes.

Fig. 3

The gene structure and motif composition of BrrLBD genes. (3A) Phylogenetic tree and classification of BrrLBD proteins was constructed by MEGA 7.0.21. (3B) Gene structure of BrrLBD genes. The yellow boxes and black lines represent the CDS and intron. (3C) Conserved motif compositions of BrrLBD proteins were identified using MEME. Each color represents a specific motif.

Fig. 4

Expression patterns of BrrLBD genes in root, shoot apical meristem (SAM), leaf, and flower buds (Flower). All data obtained from quantitative real-time fluorescence PCR. Constitutive β-tubulin gene served as an internal control. The error bar represents standard deviations for three technical duplications.

Fig. 5

Subcellular localization of 35S:BrrLBD-GFP in Nicotiana benthamiana leaves. BrrLBD16-GFP, BrrLBD18-GFP, BrrLBD29-GFP and BrrLBD33-GFP were localized in the nucleus.