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.

Download Full-text

Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus

Genes ◽

10.3390/genes11030280 ◽

2020 ◽

Vol 11 (3) ◽

pp. 280 ◽

Cited By ~ 1

Author(s):

Tao Xie ◽

Lei Zeng ◽

Xin Chen ◽

Hao Rong ◽

Jingjing Wu ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Expression Patterns ◽

Hormone Treatment ◽

Evolutionary Analysis ◽

Bioinformatics Analyses ◽

Element Analysis ◽

Specific Expression ◽

Lateral Organ ◽

Organ Boundaries

The plant specific LATERAL ORGAN BOUNDARIES (LOB)-domain (LBD) proteins belong to a family of transcription factors that play important roles in plant growth and development, as well as in responses to various stresses. However, a comprehensive study of LBDs in Brassica napus has not yet been reported. In the present study, 126 BnLBD genes were identified in B. napus genome using bioinformatics analyses. The 126 BnLBDs were phylogenetically classified into two groups and nine subgroups. Evolutionary analysis indicated that whole genome duplication (WGD) and segmental duplication played important roles in the expansion of the BnLBD gene family. On the basis of the RNA-seq analyses, we identified BnLBD genes with tissue or developmental specific expression patterns. Through cis-acting element analysis and hormone treatment, we identified 19 BnLBD genes with putative functions in plant response to abscisic acid (ABA) treatment. This study provides a comprehensive understanding on the origin and evolutionary history of LBDs in B. napus, and will be helpful in further functional characterisation of BnLBDs.

Download Full-text

Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera

Journal of Genetics ◽

10.1007/s12041-016-0660-z ◽

2016 ◽

Vol 95 (3) ◽

pp. 515-526 ◽

Cited By ~ 9

Author(s):

HUI CAO ◽

CAI-YUN LIU ◽

CHUN-XIANG LIU ◽

YUE-LING ZHAO ◽

RUI-RUI XU

Keyword(s):

Vitis Vinifera ◽

Gene Family ◽

Lateral Organ ◽

Organ Boundaries

Download Full-text

A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri

Royal Society Open Science ◽

10.1098/rsos.171463 ◽

2018 ◽

Vol 5 (7) ◽

pp. 171463 ◽

Cited By ~ 2

Author(s):

Yunpeng Cao ◽

Shumei Li ◽

Yahui Han ◽

Dandan Meng ◽

Chunyan Jiao ◽

...

Keyword(s):

Gene Family ◽

Gene Structure ◽

Functional Divergence ◽

Sugar Content ◽

Expression Patterns ◽

Evolutionary Relationship ◽

World Market ◽

Pear Fruit ◽

Rosaceae Species ◽

Chinese White

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears ( Pyrus bretschneideri ) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRK s into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11 , PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRK s that might contribute to fructose efflux in the pear fruit.

Download Full-text

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

Plant Diversity ◽

10.1016/j.pld.2019.11.004 ◽

2020 ◽

Vol 42 (1) ◽

pp. 52-60

Author(s):

Qin Yu ◽

Simin Hu ◽

Jiancan Du ◽

Yongping Yang ◽

Xudong Sun

Keyword(s):

Gene Family ◽

Brassica Rapa ◽

Genome Wide ◽

Lateral Organ ◽

Identification And Characterization ◽

Organ Boundaries

Download Full-text

Comparison and evolution analysis of two rice subspecies LATERAL ORGAN BOUNDARIES domain gene family and their evolutionary characterization from Arabidopsis

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2005.09.016 ◽

2006 ◽

Vol 39 (1) ◽

pp. 248-262 ◽

Cited By ~ 47

Author(s):

Yi Yang ◽

Xiaobo Yu ◽

Ping Wu

Keyword(s):

Gene Family ◽

Evolution Analysis ◽

Lateral Organ ◽

Organ Boundaries

Download Full-text

Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes

10.1101/195669 ◽

2017 ◽

Author(s):

Daniel S. Carvalho ◽

James C. Schnable ◽

Ana Maria R. Almeida

Keyword(s):

Gene Family ◽

Functional Divergence ◽

Gene Tree ◽

Gene Families ◽

Gene Family Evolution ◽

Phylogenetic Methods ◽

Combined Use ◽

Approaches To Study ◽

Additional Support ◽

Network Approaches

AbstractThe study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations of branches with low support in a conventional gene tree. The network approach used here may also better reflect known and suspected patterns of functional divergence relative to phylogenetic methods. Overall, we believe that the combined use of phylogenetic and network tools provide more robust assessments of gene family evolution.

Download Full-text

Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species

PeerJ ◽

10.7717/peerj.11811 ◽

2021 ◽

Vol 9 ◽

pp. e11811

Author(s):

Jun Xu ◽

Ping Hu ◽

Ye Tao ◽

Puwen Song ◽

Huanting Gao ◽

...

Keyword(s):

Gene Family ◽

Phylogenetic Relationship ◽

Gene Structure ◽

Related Species ◽

Polyploid Wheat ◽

Relationship Analysis ◽

Triticeae Species ◽

Genome Wide ◽

Lateral Organ ◽

Organ Boundaries

Background Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. Methods Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a–e, II a and II b). Results The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.

Download Full-text

Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress in Brassica napus

Molecules ◽

10.3390/molecules24101985 ◽

2019 ◽

Vol 24 (10) ◽

pp. 1985 ◽

Cited By ~ 3

Author(s):

Xiaoke Ping ◽

Tengyue Wang ◽

Na Lin ◽

Feifei Di ◽

Yangyang Li ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Vital Role ◽

Gene Family Evolution ◽

Rna Seq ◽

Chain Reaction ◽

Element Analysis ◽

Cis Element ◽

Genome Wide ◽

Polymerase Chain

Lignin is an important biological polymer in plants that is necessary for plant secondary cell wall ontogenesis. The laccase (LAC) gene family catalyzes lignification and has been suggested to play a vital role in the plant kingdom. In this study, we identified 45 LAC genes from the Brassica napus genome (BnLACs), 25 LAC genes from the Brassica rapa genome (BrLACs) and 8 LAC genes from the Brassica oleracea genome (BoLACs). These LAC genes could be divided into five groups in a cladogram and members in same group had similar structures and conserved motifs. All BnLACs contained hormone- and stress- related elements determined by cis-element analysis. The expression of BnLACs was relatively higher in the root, seed coat and stem than in other tissues. Furthermore, BnLAC4 and its predicted downstream genes showed earlier expression in the silique pericarps of short silique lines than long silique lines. Three miRNAs (miR397a, miR397b and miR6034) target 11 BnLACs were also predicted. The expression changes of BnLACs under series of stresses were further investigated by RNA sequencing (RNA-seq) and quantitative real-time polymerase chain reaction (qRT-PCR). The study will give a deeper understanding of the LAC gene family evolution and functions in B. napus.

Download Full-text