Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)

Abstract

Background Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription factors unique to plants, are involved in multiple transcriptional regulatory pathways and play important roles in lateral organ development, pathogen response, secondary growth, and hormone response. The LBD gene family has not previously been characterized in moso bamboo (Phyllostachys edulis). Results In this study, we identified 55 members of the LBD gene family from moso bamboo and found that they were distributed non-uniformly across its 18 chromosomes. Phylogenetic analysis showed that the moso bamboo LBD genes could be divided into two classes. LBDs from the same class share relatively conserved gene structures and sequences encoding similar amino acids. A large number of hormone response–associated cis-regulatory elements were identified in the LBD upstream promoter sequences. Synteny analysis indicated that LBDs in the moso bamboo genome showed greater collinearity with those of O. sativa (rice) and Zea mays (maize) than with those of Arabidopsis and Capsicum annuum (pepper). Numerous segmental duplicates were found in the moso bamboo LBD gene family. Gene expression profiles in four tissues showed that the LBD genes had different spatial expression patterns. qRT–PCR assays with the Short Time-series Expression Miner (STEM) temporal expression analysis demonstrated that six genes (PeLBD20, PeLBD29, PeLBD46, PeLBD10, PeLBD38, and PeLBD06) were consistently up-regulated during the rapid growth and development of bamboo shoots. In addition, 248 candidate target genes that function in a variety of pathways were identified based on consensus LBD binding motifs. Conclusions In the current study, we identified 55 members of the moso bamboo transcription factor LBD and characterized for the first time. Based on the short-time sequence expression software and RNA-seq data, the PeLBD gene expression was analyzed. We also investigated the functional annotation of all PeLBDs, including PPI network, GO, and KEGG enrichment based on String database. These results provide a theoretical basis and candidate genes for studying the molecular breeding mechanism of rapid growth of moso bamboo.

Identification, Classification and Characterization of LBD Transcription Factor Family Genes in Pinus massoniana

“…ClassⅠ (40, 85.1%) and ClassⅡ (7, 14.9%), in terms of gene structure and protein conserved motifs, and the structural differences between the two subclades of PmLBD genes were small, but the protein conserved motifs differed significantly. Similar to Arabidopsis [ 6 ], the number of class Ⅰ members was higher than class Ⅱ during the evolutionary process, and their phylogenetic relationships were essentially the same as those of previous studies [ 25 , 30 ]. Homology modeling of the members of the two subfamilies of PmLBD proteins showed that each subfamily consists of two chains, A and B, in a symmetrical “Y” structure and forms a similar “pocket” region at the junction.…”

“…In conclusion, because LBD genes transcriptionally control a variety of downstream genes, they are important molecular targets for plant pathogen invasion. The LBD gene family has been identified and researched in a number of species [ 3 ], including poplar [ 21 ], tomato [ 22 ], barley [ 23 ], potato [ 24 ], moso bamboo [ 25 ], and Populus trichocarpa [ 26 ], but P. massoniana has not yet been the subject of such research.…”

Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Sweet Potato

“…After the phylogenetic tree was constructed, all IbLBD genes were categorized into Class I or Class II, comprising forty-ve and eight LBD genes, respectively. We found that the number of LBD genes in Class I of Arabidopsis, moso bamboo (Phyllostachys edulis) [42], and pears (Pyrus bretschneideri) [43] was high in Class II, which was consistent with previous studies. Also, there was a difference in the Class I classi cation.…”

“…These elements may be involved in the regulation of ABA metabolism in sweet potato. Huang et al [42] discovered that all LBD gene promoters in moso bamboo contained drought-inducing elements at the MYB binding sites. These drought-inducing elements were detected in 22 sweet potato genes with certain differences in quantity.…”

The Effect of Methylation Modification of MDD on the Expression of Key Genes in the Process of Saponin Synthesis in Eleutherococcus senticosus

“…The expression of ERF and GRAS was significantly inhibited by DNA methylation, while LBD and C2H2 tended to be promoted by it. LBD is involved in the growth and development of plant organs, and its expression was positively correlated with the growth in Phyllostachys heterocycle [33], which indicating LBD might be positively correlated with the DNA methylation ratio. EsLBD1-1 and EsLBD1-2 are different transcripts in LBD family; however, their expression patterns are opposite, which may be due to protein interaction with bHLH transcription factor.…”