Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes

Jiangmei Sun,Leiting Li,Shaoling Zhang,Peng Wang,Juyou Wu

doi:10.1186/s12864-017-4155-y

Jiangmei Sun, Leiting Li + Show 3 more

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https://doi.org/10.1186/s12864-017-4155-y

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Journal: BMC Genomics	Publication Date: Oct 10, 2017
Citations: 47	License type: open-access

Affiliation: Nanjing Agricultural University

Abstract

BackgroundLeucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively.ResultsAll LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%.ConclusionsOur results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.

Highlights

Leucine-rich repeat receptor-like protein kinase (LRR-receptor-like kinase (RLK)) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants
Genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that Leucine-rich repeat receptor-like protein kinase (LRR-RLK) play important roles in each stage of plant growth and development
Our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies

Summary

Introduction

Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. The patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. Since the first leucinerich repeat receptor-like kinase (LRR-RLK) gene was isolated in maize (Zea mays) [3], more and more LRR-RLK genes have been confirmed [2, 4]. LRR-RLK is the largest and most highly conserved group of the plant RLK gene family [5]. Previous studies have shown that the approximately 225 LRR-RLK gene members in Arabidopsis can be grouped into 23 subfamilies based on the sequence similarity in their kinase domains [2, 6, 7].

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