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

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4155-y) contains supplementary material, which is available to authorized users.

Molecular basis underlying the successful invasion of hexaploid cytotypes ofSolidago canadensisL.: Insights from integrated gene and miRNA expression profiling

“…Furthermore, we have also taken note that the coherent miRNA targets included (a) several TFs that were predicted to be targeted by miRNA regulators, for example, sca‐miR164d targets FAR1, sca‐miR530 targets MYB, sca‐miR396a targets Trihelix, and sca‐miR5139a targets VOZ1‐like, suggesting that these miRNAs may operate to enhance the adaptation of hexaploid cytotypes through an integrative miRNA‐TF‐mRNA regulatory network; (b) receptor‐like protein kinases (RLKs) that were predicted to be targets of multiple miRNAs such as sca‐miR161a, sca‐miR5139a, sca‐miR5139b, and sca‐miR8155. This target is an important enzyme gene and functions in regulating plant growth, development, signal transduction, immunity, and stress responses (Sun, Li, Wang, Zhang, & Wu, ). Notably, these RLK genes were remarkably up‐regulated in hexaploid cytotypes, suggesting that their regulator miRNAs may play key roles in the environmental adaptation of hexaploid cytotypes; (c) unigenes associated with methylation and ubiquitination processes, such as histone‐lysine N ‐methyltransferase (CL7649.Contig3_All), ubiquitin‐protein ligase (CL2235.Contig13_All), U‐box domain‐containing protein (CL2207.Contig4_All), and F‐box protein (Unigene1223_All), that were predicted to be targets of sca‐miR396d, sca‐miR444a, sca‐miR393d, and sca‐miR5139a, suggesting that these unigenes may be subjected to miRNA‐mediated DNA methylation and ubiquitination; and (d) two dirigent protein genes (CL6884.Contig1_All and CL6884.Contig3_All) that were predicted to be targets of sca‐miR169d.…”

Molecular networks in plant–pathogen holobiont

“…Upon ligand binding, these LRR‐RKs recruit another LRR‐RK, BAK1, for transducing the signal to the cytosol . Although it has been often reported that LRR‐RKs interact with each other through their extracellular domains (ECDs) , a comprehensive analysis on LRR‐RK interactions is confounded by a massive expansion of this class of receptor proteins in plants . By employing a high‐throughput in vitro interaction assay, Smakowska‐Luzan et al .…”

Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after transition from autotrophic to heterotrophic growth condition in microalgae

“…PKs play important roles in signaling networks including the perception of biotic agents, light quality and quantity, phytohormones, and various environmental conditions [42]. Fiftyseven (29 up-regulated and 28 down-regulated), sixty-two (43 up-regulated and 19 down-regulated), and fifty (43 up-regulated and 17 down-regulated) PKs were identified among the meta genes at LG, TR, and PR phases, respectively (S3 Table).…”