Genome-Wide Identification, Evolutionary Analysis and Expression Profiles of LATERAL ORGAN BOUNDARIES DOMAIN Gene Family in Lotus japonicus and Medicago truncatula.

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family has been well-studied in Arabidopsis and play crucial roles in the diverse growth and development processes including establishment and maintenance of boundary of developmental lateral organs. In this study we identified and characterized 38 LBD genes in Lotus japonicus (LjLBD) and 57 LBD genes in Medicago truncatula (MtLBD), both of which are model legume plants that have some specific development features absent in Arabidopsis. The phylogenetic relationships, their locations in the genome, genes structure and conserved motifs were examined. The results revealed that all LjLBD and MtLBD genes could be distinctly divided into two classes: Class I and II. The evolutionary analysis showed that Type I functional divergence with some significantly site-specific shifts may be the main force for the divergence between Class I and Class II. In addition, the expression patterns of LjLBD genes uncovered the diverse functions in plant development. Interestingly, we found that two LjLBD proteins that were highly expressed during compound leaf and pulvinus development, can interact via yeast two-hybrid assays. Taken together, our findings provide an evolutionary and genetic foundation in further understanding the molecular basis of LBD gene family in general, specifically in L. japonicus and M. truncatula

Distribution of conserved motifs and gene structure analysis of LBD gene family from <i>Lotus japonicus</i> and <i>Medicago truncatula</i>.

<p>(A) Conserved motifs analysis by MEME suite. The colorful boxes represent the different motifs 1–15. (B) The exons and introns splicing patterns. The green boxes and black lines represent the exon ans intron, respectively. The numbers indicate the intron phase. The motifs and gene sizes are indicated at the bottom of the figure.</p

The functional divergence analysis between classes or subclasses.

<p>The estimated mean coefficients of Type-I (θI) and type-II (θII) functional divergence based on the aligned LOB domain sequences from <i>Lotus japonicus</i> and <i>Medicago truncatula</i>.</p

The phylogenetic tree of LBD proteins form <i>Lotus japonicus</i> and <i>Medicago truncatula</i>.

<p>The amino acid sequences of the LBD proteins were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbor-joining method of MEGA 5.0 software.</p

Expression profiles of LBD genes in <i>Lotus japonicus</i>.

<p>(A) Heatmap showing LBD gene expression patterns in different tissues/organs/development stages. The scale at the bottom represents log2 value. (B) Some genes highly expressed in leaf (the blue box) were confirmed by quantitative RT-PCR. The expression level of stem sample was normalized to 1.</p

Amino acid sequence alignments of LOB domain region from <i>Lotus japonicus</i> and <i>Medicago truncatula</i>.

<p>The N-terminal LOB domain includes cysteine C block, GAS block and leucine-zipper-like regions is displayed. The valine (V) and leucine (L) residues required for motor organ specification in pea were denoted by red arrow and red frame. An arginine (R) in the GAS block required for motor organ specification was denoted by red arrow.</p

Information of <i>LBD</i> gene family identified in <i>Lotus japonicus</i>.

<p>Information of <i>LBD</i> gene family identified in <i>Lotus japonicus</i>.</p