Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri)

Abstract

Background The lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene family has not yet been characterized for the Chinese White Pear. Results In our study, a total of 60 PbrLBDs were identified in the pear genome. The PbrLBD gene family was divided into two classes based on gene structure and phylogenetic analysis: class I (53) and class II (7). Cis-acting element analysis results suggested that PbrLBDs may participate in various biological processes, such as flavonoid biosynthetic and stress response. Synteny analysis results indicated that segmental duplication played a key role in the expansion of the PbrLBD gene family. The mean Ks and 4DTv values showed that the PbrLBD gene family had undergone only one recent whole-genome duplication event occurring at 30–45 MYA. Purifying selection was a primary force during the PbrLBD gene family evolution process. Transcriptome data analysis revealed that 10 PbrLBDs were expressed in all six examined tissues, and 73.33% of members in the PbrLBD gene family were expressed in pear sepal. qRT-PCR was conducted to verify the expression levels of 11 PbrLBDs in these six tissues. Specifically, PbrLBD20, PbrLBD35 and PbrLBD53 genes were down-regulated when anthocyanin concentrations were high, whereas PbrLBD33 was significantly up-regulated in pear when anthocyanin concentrations were high. Furthermore, PbrLBD20, one of the candidate genes related to anthocyanins was localized in the nucleus. Conclusions Our analysis provides valuable information for understanding the evolution of the PbrLBD gene family, and provides new insights into the regulation of pear pigment metabolism and lays a foundation for the future disclosure of the molecular mechanism of LBD gene regulating flavonoid metabolism.

Genome-wide analyses of LATERAL ORGAN BOUNDARIES in cassava reveal the role of LBD47 in defence against bacterial blight

“…thaliana and M . esculenta were further classified into nine subclasses (Ia-If and IIa-IIb) based on their phylogenetic relationships ( Fig 1 ), and were consistent with those previously reported [ 67 ]. Homologous genes in the same class or subclass might share the same function.…”

Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)

“…We designed fifteen pairs specific primers (Additional file 4 : Table S1) using Primer5.0 software and checked by using NCBI online software ( https://www.ncbi.nlm.nih.gov/ ) . The reaction system and protocol of qRT-PCR were consistent with our previously study [ 59 , 62 ]. The relatively expression level of PbrPUBs were estimated using 2 −∆∆CT method [ 63 ].…”

“…The RPKM values were measured by featureCount software and in-house python scripts. Then, we used Heatmap.2 package to show the expression pattern of PbrPUBs (log 2 (RPKM + 1)) [ 59 ].…”

Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial–Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis

“…Considering similarities among the AS2/LOB domains, it is, however, undeniable that these family members may retain partially overlapping functions at the molecular level. They have often been described as transcription factors [40][41][42][43][44][45][46][47]. Recent results on AS2, however, suggest that the term "transcription factor" is not appropriate for a member of this family; they are better described as novel functional factors that could play a role in gene expression.…”