LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects
© The Author(s). 2016
Received: 22 January 2016
Accepted: 12 July 2016
Published: 12 August 2016
Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors.
We built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR-RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the C. clementina and C. sinensis LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of C. clementina and C. sinensis, respectively.
This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species.
Signaling through cell surface receptors is essential for cells to communicate and interact with the environment. Plant cells are able to perceive and transduce a wide range of signals mainly through receptor-like kinases (RLKs), which mediate cell-to-cell communication by binding to extracellular ligands or forming heteromeric complexes to mediate intracellular signaling . These modular kinase receptors belong to a large monophyletic gene family with more than 400 members identified in Arabidopsis . RLKs are typically transmembrane (TM) proteins with a variable amino-terminal extracellular domain (ECD) and a conserved cytoplasmic serine/threonine kinase domain (KD) in the carboxyl-terminal region . The ECD regions play important roles in the recognition of internal signals or environmental stimuli and, according to their features, can be used to classify RLKs . More than 21 structural classes were classified in Arabidopsis RLKs based on their ECDs, with the largest one containing leucine-rich repeats (LRRs) . Phylogenetic-based analysis of the Arabidopsis RLKs using the KDs and structural comparison of their ECDs allowed the identification of more than 40 subfamilies .
In plants, LRR-RLK proteins constitute a diverse group of transmembrane receptors involved in many biological functions usually associated with growth and development [5–9] and responses to biotic and abiotic stresses [10–13]. More than 200 LRR-RLK genes have been identified in the fully sequenced Arabidopsis genome [14–16]. Concerning plant-microbe interactions, certain LRR-RLKs play essential roles in defense responses to pathogen attacks by recognizing conserved pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs) such as flagellin and elongation factor thermo unstable (EF-Tu) [17, 18]. LRR-containing proteins are suitable for pathogen recognition because their structural plasticity allows them to bind to many distinct ligands, such as proteins, peptides or lipids . Receptor proteins that are able to recognize PAMPs/MAMPs are designated pattern-recognition receptors (PRRs)  and represent an essential step for the host to perceive and defend itself against pathogens by triggering innate immune responses. Many PRRs belong to the LRR-RLK subfamily [18, 20]. The Arabidopsis FLAGELLIN SENSING 2 (FLS2) , EF-TU RECEPTOR (EFR)  and rice XA21  are among the best-studied plant PRRs and can activate immunity responses by perceiving specific bacterial proteins (or derived peptidic epitopes). These well-characterized PRRs belong to the XII group of LRR-RLKs (LRR-XII), suggesting an important role in mediating immunity responses during plant-microbe interactions.
Citrus comprise some of the most economically important crops in the world, and the species of this group produce fruits with great commercial value, such as oranges, mandarins, lemons, grapefruits and pummelos. While Citrus clementina represents one of the major species of mandarins, consumed as fresh fruit , sweet orange (C. sinensis) has the largest commercial importance, mainly due to the orange juice market . The genomes of these species were recently sequenced and even though the identity and contribution of ancestors in the composition of the domesticated citrus genome was unclear, it is suggested that these crops are hybrids derived mainly from C. maxima and C. reticulata [26, 27]. Citrus species are mostly diploid and display a basic chromosome number of x = 9. Substantial segmental synteny is observed with other eudicots and an orthology relation of one to one across oranges and plants such as grape, strawberry and cacao suggests the inexistence of recent whole genome duplication (WGD), with the exception of a triplication genome shared by all eudicots . Citrus is part of the Sapindales order, a sister order of Brassicales into the Malvidae family, which allows the performance of studies involving genomic comparisons with Arabidopsis thaliana .
The main problem that affects the citrus culture worldwide is the huge amount of phytopathogens , which cause significant damage to the citrus agribusiness. Apomictic reproduction, high juvenility and a long cultivation period are characteristics that contribute to a narrow genetic diversity in citrus crops, which increases the probability of the appearance of diseases and makes it difficult for breeding programs to obtain materials with increased resistance to pathogens . Although there is narrow genetic diversity, there are different levels of resistance among Citrus species for different diseases, such as the Citrus canker [27–29], Alternaria brown spot , Huanglongbing  and Citrus variegated chlorosis (CVC) [32, 33]. Xylella fastidiosa, for instance, causes CVC in all commercial sweet orange varieties, but not in C. clementina, despite both species being derived from the same ancestors . The comparison of defense gene families among plants with different levels of resistance is a strategy for better understanding the host defense in plant-pathogen interactions. Considering the recent sequencing of the complete genomes of C. clementina and C. sinensis and the involvement of LRR-RLKs in defense responses, we performed in silico analyses to elucidate and compare the structural organization of LRR-RLK members from the Citrus databases. The LRR-RLK subfamily has been characterized in plants such as Arabidopsis, rice, Populus, tomato, and others [35–39], but no comprehensive study was performed for Citrus species.
Results and discussion
Identification of Citrus LRR-RLKs
Genome data of C. clementina, C. sinensis, and A. thaliana
clementina 1.0 (version 1.0)
CsiDB 2013 (version 2.0)
TAIR 10 release
Estimated genome size
Protein classification according to the presence of diagnostic domains in C. clementina, C. sinensis, and A. thaliana proteomes
TM kinases with LRR (KD)a
Evolutionary analyses and structural organization of LRR-RLKs
Total number of receptors distributed in the different groups of LRR-RLKs
In general, the number of LRR-RLK receptors for most of the subfamily groups among the Citrus species was similar to A. thaliana, except for two of them, i.e., LRR-I and LRR-XII. Regarding LRR-I, 38 members were reported for A. thaliana, while in Citrus, we identified only 9 and 11 members for C. clementina and C. sinensis, respectively. Despite having a smaller genome , A. thaliana had about four times more RLKs in this group compared to the Citrus species. Although A. thaliana LRR-I includes receptor proteins associated with defense responses, such as IMPAIRED OOMYCETE SUSCEPTIBILITY 1 (IOS1)  and FLG22-INDUCED RECEPTOR-LIKE KINASE 1 (FRK1) , the majority of members in this group has unknown functions. According to Fischer et al. , the last common ancestor of angiosperms (LCAA) probably had only 7 LRR-I in the genome and the expansion rate was related to ancestral expansion rather than species-specific events, suggesting that the high copy number found in A. thaliana was due to Brassicaceae expansion and subsequent retention in this species. For Citrus, in contrast, the number of LRR-I remained the same as suggested by LCAA, perhaps because no recent WGD was detected in Citrus plants .
Total number of LRR-RLKs, LRR-XII and LRR-I found in different plant species
The expansion or reduction in the size of gene families is a result of evolutionary events usually related to duplications, de novo creation of genes and deletions . Selective pressure to perceive changing environment signals can drive the expansion of specific RLK subfamily groups that may have important functional effects related to adaptation, for example, to fast-evolving pathogens [14, 41]. It was reported that LRR-XII is a group that keeps expanding and their members are involved in biotic stress responses . In general, we observed that in Citrus and other crop species, the number of LRR-XII is increased in relation to LCAA (Table 4), suggesting that domestication may be contributing to the expansion of this group.
Evolutionary aspects of C. clementina and C. sinensis LRR-XII
Analysis of LRR-XII orthologs
Based on the large expansion of Citrus LRR-XII and its important role in response to biotic stresses, we further focused on homology studies involving this receptor group. Initially, we searched for orthologs through integrated analyses of phylogeny, sequence similarity and chromosomal distribution in the C. clementina and C. sinensis LRR-XII subfamily.
The tree topology allowed us to distinguish two monophyletic groups, one formed by two clades (light blue and light gray), related to the LRR-XIIb members and the other formed by the remaining eleven clades, which represent the LRR-XIIa (Fig. 2 ), as can also be observed in Fig. 1 . LRR-XIIa harbors seven of the nine members from the previously assigned A. thaliana LRR-XII group. LRR-XIIb harbors the two remaining members of the group, At1g35710 and At4g08850, indicating a non-monophyletic origin for the LRR-XII subfamily. This distinct grouping of LRR-XII members was also observed in phylogenetic analysis using tomato  and A. thaliana .
The two Arabidopsis members mentioned above and the correspondent Citrus members from the same clade (light gray and light blue in Fig. 2), did not share enough similarity with the other LRR-XII members. Previous work showed that these two members fell in the LRR-XI group  and they should comprise an independent group of LRR-RLKs. Based on this approach, the resulting LRR-XII group from C. clementina and C. sinensis would comprise 123 and 126 members, respectively.
LRR-XII kinase RD motif analysis
These changes can affect the charge of the molecules and potentially modify the kinase regulatory and catalytic mechanisms . Only 7 members from C. clementina and 9 members from C. sinensis have a kinase with an alternative catalytic function (ACF), which did not show either RD or non-RD motifs. The non-RD kinases identified in Citrus LRR-XII open new possibilities for further studies involving the function of these receptors in defense responses by recognition of microbial signatures.
In addition to the identification of RD and non-RD kinases in the Citrus LRR-XII group, we analyzed the LRR-XII RD and non-RD kinase motifs in A. thaliana. Only two sequences showed the RD motif, while all the other seven were non-RD kinases, as already identified by other authors [15, 50]. These two RD kinases correspond to RLK members, which were grouped in a separated clade of the phylogenetic trees (At4g08850.1 and At1g35710.1) (Fig. 2). Additionally, all the non-RD kinases were grouped in the clade that contained LRR-XIIa (Fig. 2). Curiously, and in agreement with this classification, 98 % and 100 % of the RD members from C. clementina and C. sinensis, respectively, were grouped across LRR-XIIb. For the non-RD kinases, 97 % and 99 % from C. clementina and C. sinensis, respectively, were grouped across LRR-XIIa. This separation of the Citrus RD and non-RD kinases in two distinct clades, as observed in A. thaliana, suggests a possible common phylogenetic origin for each of the RD and non-RD kinases in the LRR-XII group.
LRR-XII tandem duplication paralogs in C. clementina and C. sinensis
The Citrus LRR-XII receptors are distributed in all chromosomes but are mainly concentrated on chromosome 3 for C. clementina and on chromosome Un (for unassigned contigs) for C. sinensis. Chromosomes 4 and Un from C. clementina and C. sinensis, respectively, displayed the majority of the tandem duplicated genes. Duplication events seem to be pronounced in domesticated plant species . Segmental duplication events must have contributed to the acquisition of novel and distinct functions in relation to the ancestor by neo-functionalization or sub-functionalization . Considering the large number of pathogens in citrus crops, the observed large expansion of Citrus LRR-XII might be regarded as a plant-specific adaptation to extracellular signal perception, for example, to recognize different PAMPs .
Identification and distribution of LRR-XII gene clusters
Gene duplication is an important strategy for adaptive evolution in plants . To identify clusters that encompass LRR-XII tandem duplicated genes, we grouped these genes in each Citrus genome into the same cluster if they were arranged in a genomic fragment with a maximum of 200 Kb. LRR-XII gene clusters are present in all chromosomes, with the exception of chromosomes 1 and 3 from C. clementina and C. sinensis, respectively (Fig. 4; Additional file 11). A distribution analysis revealed 117 of 148 LRR-XII genes of C. clementina (79 %) were found in 33 cluster regions, and for C. sinensis, 94 of 140 LRR-XII genes (67.1 %) were distributed in 30 clusters. Tandem duplications seem to be an important mechanism for expansion of the LRR-XII group, which could be confirmed by the presence of the LRR-XII gene in clusters. Approximately 70 % and 63 % of these clusters are formed by tandem duplicated paralogs in the C. clementina and C. sinensis genomes, respectively. Wang et al.  also demonstrated high clustering and the importance of duplication events in the expansion of Citrus nucleotide binding site (NBS) genes, which is a large class of intracellular immune receptor genes that also display LRR domains beyond the nucleotide-binding site domain. Clustering in NBS gene loci has been reported in many species, including Arabidopsis and rice . On the other hand for LRR-XII genes, this expansion is not widespread in plants as the NBS genes are mainly observed in rice  and citrus.
Of the 68 LRR-XII orthologous pairs identified for C. clementina and C. sinensis, 46 and 38 genes from C. clementina and C. sinensis, respectively, were located in cluster regions (Additional file 7). We identified orthologous pairs in the same clusters, which suggested high conservation and correspondence of these clusters between C. sinensis and C. clementina genomes. These data suggested blocks of elevated homology among C. clementina and C. sinensis LRR-XII sequences and chromosome regions.
Syntenic blocks in LRR-XII and Citrus genomes
This work provides the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. Lineage-specific expansion was observed in the Citrus LRR-XII group that might have occurred due to tandem duplications making the number of individuals larger compared to the majority of plant species. Considering the diverse number of pathogens affecting the domesticated citrus culture, the independent expansion of a defense-related group could be associated with an adaptive process related to plant-pathogen co-evolution. Our comparative data provided valuable information concerning these RLKs, opening new perspectives in the study of their function in diverse processes, such as development and defense responses in two worldwide important economic crops, specifically, sweet oranges and clementines.
Sequence database search
Predicted proteomes from Citrus clementina (Version 1.0, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Cclementina), Citrus sinensis (Version CsiDB201301, http://citrus.hzau.edu.cn/orange/download/data.php)  and Arabidopsis thaliana (http://arabidopsis.org) were selected and downloaded. The InterProScan 4 package software (http://www.ebi.ac.uk/interpro/download.html) was used to identify different protein signatures in each proteome dataset . To recover and analyze the dataset, we developed local relational databases for each included plant species. It allowed us to extract and interpret the large amount of data obtained in this work. In-house Perl scripts and Structured Query Language (SQL) queries were used to analyze data files during the database building and searching processes. Access to these local relational databases was implemented using DbVisualizer version 9.1.7 (http://dbvis.com/).
Domain annotation and LRR-RLK retrieval
The LRR-RLK homologues were retrieved from the relational databases by searching for protein sequences with kinase, transmembrane and leucine-rich repeat domains. To recover the identifiers with KD, we considered Pkinase (PF00069) and Pkinase_Tyr (PF07714), according to the Pfam platform , as diagnostic domains. TMs were predicted from the TMHMM website (http://www.cbs.dtu.dk/services/TMHMM/) hosted at the Center for Biological Sequence Analysis, Technical University of Denmark. The prediction of transmembrane helices in the protein sequences were conducted according to the default parameters of version 2.0, without considering the old model option (version 1).
The following LRR diagnostic domains were searched: LRR_1 - Leucine Rich Repeat (PF00560), LRRNT - Leucine rich repeat N-terminal domain (PF01462), LRV - Leucine rich repeat variant (PF01816), LRRNT_2 - Leucine rich repeat N-terminal domain (PF08263), LRR_4 - Leucine rich repeats (2 copies) (PF12799), LRR_5 - Leucine rich repeats (6 copies) (PF13306), LRR_8 - Leucine rich repeat (PF13855), LRR_9 - Leucine-rich repeat (PF14580), LRRCT - Leucine rich repeat C-terminal domain (PF01463), LRR_2 - Leucine Rich repeat (PF07723), and LRR_3 - Leucine Rich repeat (PF07725). Only proteins containing LRRs, TM and KD were then considered to be putative LRR-RLK, and for this reason, At2g24130, which did not show TM, was not included in our analyses. Alternative splicing variants were excluded from our analysis.
Kinase domain alignment and phylogenetic analysis
Sequences of conserved KDs from Arabidopsis and Citrus LRR-RLK proteins were extracted by an in-house Pearl script that consider KD coordinates annotation from the Pfam database. In addition, six human kinase protein sequences were used as an outgroup (Additional file 13). The KD sequences were aligned using MAFFT version 7 (http://mafft.cbrc.jp/alignment/software/) with G-INS-i strategy and default parameters . The aligned sequences were visualized and manually refined using Jalview version 15.0 . The proteins with a short length (<100 aa) or large inserted gap regions were removed. Gap-rich columns were further filtered using trimAl v.1.3 with the gappyout method . To optimize the datasets for evolutionary analyses, the Decrease Redundancy tool, available as a resource at ExPaSy (www.expasy.org), was used to remove identical or distantly related sequences. The Decrease Redundancy parameters were set as 99 for “% max similarity” and 30 for “% min similarity”. Phylogenetic analyses were performed using the Maximum-likelihood method, as implemented in PhyML . Twelve different evolutionary models (JTT, LG, DCMut, MtREV, MtMam, MtArt, Dayhoff, WAG, RtREV, CpREV, Blosum62 and VT) were tested using ProtTest 2.4 software . The evolutionary model best fitting the data (best fit model) was determined by comparing the likelihood of the tested models according to the Akaike Information Criterion. A discrete gamma-distribution model with four rate categories plus invariant positions was assumed with the gamma parameter and the fraction of invariant positions was estimated from the data. Tree support values were estimated using approximate likelihood ratio test (ALRT), as implemented in PhyML. The ML trees were visualized and edited using the FigTree software (tree.bio.ed.ac.uk/software/figtree). The alignments are available at FigShare (10.6084/m9.figshare.3474752).
Identification of the RD motif in the kinase domain
Identification of the Citrus RD motif in the catalytic loop from the LRR-XII kinase subdomain was performed using multiple expectation maximization for motif (MEME) suite web server using default parameters . The kinases were classified as RD or non-RD according to the presence or absence of the Arg (R) in the conserved HRD motif, respectively.
Chromosomal distribution of LRR XII
The genomic coordinates of each LRR-XII gene from C. clementina and C. sinensis were used to determine their distribution in the Citrus chromosomes. The coordinates were retrieved accessing the genome browser from each Citrus database. The MapChart graphical tool  was used to generate schematic diagrams to represent the LRR-XII gene positions in the chromosomes.
LRR-XII orthologs and tandem duplicated paralogs
The identification of orthologous pairwise sequences among Citrus species was achieved through grouping in the phylogenetic tree and the BBH method. The Blastp searches were performed using all the C. sinensis and C. clementina LRR-RLK sequence proteins from group XII. For tandem duplicated paralogs searches, the results from Blasp were analyzed together with well-supported clades from the LRR-XII phylogenetic trees. The tandem duplicated paralogs were eligible when they formed the same clade and showed proximity in their chromosomal location. The identification of the LRR-XII gene clusters was performed from the arrangement of these genes in the chromosomes of each species. The LRR-XII genes were grouped in the same cluster if the genome location between two genes was within 200 kb in the chromosomes of C. sinensis and C. clementina.
LRR-XII gene synteny identification
The synteny analyses were performed using Sibelia software. Although this tool was originally optimized to efficiently identify syntenic blocks between closely related microbial genomes , this tool was employed because the chromosome comparisons were restricted to a small gene family of Citrus species with evolutionary proximity.
The minimal nucleotide length considered in the syntenic block was adjusted to 1,000 pb. Iterative de Bruijn graphs were used to show the homology results found across the LRR-XII and the genomic regions in the chromosomes.
ACF, alternative catalytic function; ALRT, approximate likelihood ratio test; BBH, bidirectional best hits; BLAST, basic local alignment search tool; C, cysteine; CsiDB, citrus sinensis database; ECD, extracellular domain; EFR, Ef-Tu receptor; Ef-Tu, elongation factor thermo unstable; FLS2, flagellin sensing 2; FRK1, flg22-induced receptor-like kinase 1; G, glycine; HRD, histidine-arginine-aspartate; IOS1, impaired oomycete susceptibility 1; Kb, kilobase; KD, kinase domain; LRRCT, leucine-rich repeat C-terminal; LRRNT, leucine-rich repeat N-terminal; LRR-RLK, leucine-rich repeat receptor-like kinases; LRV, leucine-rich repeat variant; MAFFT, multiple alignment using fast fourier transform; MAMP, microbe-associated molecular pattern; MEME, multiple expectation maximization for motif elicitation; ML, maximum-likelihood; NBS, nucleotide binding site; PAMP, pathogen-associated molecular pattern; PRR, pattern-recognition receptor; R, arginine; RD, arginine-aspartate; RLCK, receptor-like cytoplasmic kinase; RLK, receptor-like kinase; S, serine; SB, syntenic block; SQL, structured query language; TAIR, the Arabidopsis information resource; TM, transmembrane; Un, unassigned; Y, tryptophan.
The authors thank Nicholas Holton for critical reading of the manuscript before submission. The authors have no conflict of interest.
This work was supported by research grants from Fundação de Amparo à Pesquisa do Estado de São Paulo (2013/17485-7). D.M.M is a fellow PhD from FAPESP (2013/01412-0). A.A.S., G.C.O. and M.A.T. are recipient of research fellowships from CNPq.
Research in the Zipfel laboratory is funded by the Gatsby Charitable Foundation and the Two Blades Foundation.
Availability of data and materials
Phylogenetic data have been deposited to FigShare and are accessible via https://dx.doi.org/10.6084/m9.figshare.3474752.v1. Additional supporting data are included as Additional files.
AAS and MAT planned and supervised the study. AAS, MAT, LLSS and GCO contributed to the design of the analysis. DMM and LLSS performed the analysis of the data. NVS carried out the syntenic analysis. DMM drafted the manuscript. DMM, AAS, MAT, LLSS and CZ contributed to the interpretation of the data and provided intellectual input. AAS, MAT and CZ revised the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Consent for publication
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