Organization and molecular evolution of a disease-resistance gene cluster in coffee trees
© Ribas et al; licensee BioMed Central Ltd. 2011
Received: 14 December 2010
Accepted: 16 May 2011
Published: 16 May 2011
Most disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Recently in coffee tree (Coffea arabica), a region spanning the S H 3 locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. Using comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the S H 3 locus.
Sequence analysis of the S H 3 region in three coffee genomes, Ea and Ca subgenomes from the allotetraploid C. arabica and Cc genome from the diploid C. canephora, revealed the presence of 5, 3 and 4 R genes in Ea, Ca, and Cc genomes, respectively. All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the S H 3 locus in C. arabica. Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species. The orthology relationship among the S H 3-CNL copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the S H 3 locus were traced back. Gene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of C. arabica. Significant positive selection was detected in the solvent-exposed residues of the S H 3-CNL copies.
The ancestral S H 3-CNL copy was inserted in the S H 3 locus after the divergence between Solanales and Rubiales lineages. Moreover, the origin of most of the S H 3-CNL copies predates the divergence between Coffea species. The S H 3-CNL family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the S H 3 locus. Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of S H 3-CNL in coffee trees.
In their natural environment, plants encounter a vast array of pathogenic microorganisms such as viruses, bacteria, oomycetes, fungi and nematodes. To defend themselves against infection by these pathogens, plants employ a network of intertwined mechanisms. One such line of defense is based on dominant disease resistance (R) genes that mediate resistance to pathogens possessing corresponding avirulence (Avr) genes . The largest class of known R genes includes those that encode the nucleotide binding site (NBS) and the leucine-rich repeat (LRR) domains. The deduced NBS-LRR proteins can be subdivided in classes based on their amino-terminal features [2, 3]. The most frequent classes possess a TIR domain with similarity to either the intracellular signaling domains of Drosophila Toll and the mammalian Interleukin-1 Receptor or a CC domain (coiled-coil) in the N-terminal and are named TNL (TIR-NBS-LRR) and CNL (CC-NBS-LRR), respectively [1, 3, 4]. Each domain of NBS-LRR protein is predicted to have a specific function. The NBS domain is suggested to have NTP-hydrolyzing activity (ATPase or GTPase, etc), regulating signal transduction through conformational changes [4, 5]. The LRR domain contains tandemly arrayed repeats in the carboxy-terminal region of R-genes and its predicted biochemical function is to mediate protein-protein interaction. It was hypothesized and experimentally confirmed that the LRR domain is involved in the specific recognition of pathogen effectors [6–9]. Both TIR and CC domains are assumed to be involved in protein-protein interactions and signal transduction [10, 11].
Genes encoding NBS-LRR protein represent one of the largest and most variable gene families found in plants, with most plant genomes containing several hundred family members. NBS-LRR genes are unevenly distributed in plant genomes and are mainly organized in multi-gene clusters [2, 12–16]. Furthermore, results of nucleotide polymorphism analyses demonstrated extremely high levels of inter and intraspecific variation of NBS-LRR genes, which presumably evolved rapidly in response to changes in pathogen populations [16–18]. The clustered distribution of R-genes is assumed to provide a reservoir of genetic variation from which new pathogen specificity can evolve via gene duplication, unequal crossing-over, ectopic recombination or diversifying selection . However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Several comparative sequence analyses of R-gene clusters have been performed across haplotypes or related genomes in different plant species including Arabidopsis [20, 21], wild potato , tomato [23–25], Brassicaceae , wheat , rice  soybean  and common bean . Available data suggest that different R genes can follow strikingly different evolutionary trajectories. Kuang et al. [31, 32] divided NBS-LRR-genes into two evolutionary categories: Type I includes genes whose evolution is accelerated by frequent sequence exchange among paralogs. Consequently, their sequences have chimeric structure and a clear allelic/orthologous relationship between different genotypes cannot be easily established. Type II includes slowly evolving genes whose sequence mainly evolves through the accumulation of amino acid substitution. Orthology relationships are highly conserved among accessions .
The evolutionary rate of each domain of individual NBS-LRR-encoding genes has been shown to be heterogeneous . The NBS domain appears to be subject to purifying selection, whereas the LRR region tends to be highly variable . Nucleotide polymorphisms found in the LRR region of R genes have been shown to be responsible for pathogen specificity . In particular, codons encoding putative solvent-exposed residues in the LRR domain are hypervariable among different R proteins and show significantly elevated ratios of non-synonymous to synonymous substitutions, suggesting that the LRR domain is subject to positive selection for amino acid diversification [19, 35–39].
Coffee is one of the world's most important agricultural commodities and is the main livelihood of more than 80 million people worldwide. Although the Coffea subgenus Coffea includes more than 95 species , commercial coffee production relies mainly on two related species: Coffea arabica L. and C. canephora Pierre, which account for 65% and 35% of world coffee production, respectively (International Coffee Organization, http://www.ico.org). C. arabica L. (2n = 4x = 44), the only polyploid species in the Coffea genus, is an allotetraploid containing two diploid subgenomes, Ca and Ea, which originated from two different diploid species (2n = 2x = 22), C. canephora and C. eugenioides, respectively . While diversification in the Coffea subgenus Coffea probably occurred in the second half of the Middle Pleistocene (450,000-100,000 years BP), it is most likely that the allopolyploid speciation of C. arabica took place in relatively recent times i.e. from historical times to 50,000 years ago [41, 42].
Among the diseases affecting cultivated coffee, coffee leaf rust, caused by the obligate parasitic fungus Hemileia vastatrix Berk. & Br. (Uredinales), is one of the most serious diseases and greatly limits Arabica coffee production in almost all coffee growing countries around the world. Therefore, the development of coffee varieties resistant to coffee leaf rust has been a breeding objective of the highest priority in many countries . A number of resistance genes to coffee leaf rust have been identified in the cultivated or wild Coffea gene pool. In particular, one resistance gene (i.e. S H 3 resistance factor) has been successfully introgressed from C. liberica into agronomically important Arabica cultivars. In the last few years, the genetic and physical maps of the S H 3 locus were completed [44–46]. Furthermore, using fluorescence in situ hybridization in C. arabica, the S H 3 locus was located in a distal position on a chromosome belonging to the homeologous group 1 . Recently, a region of 800 kb spanning the S H 3 locus was sequenced and annotated . Tandem arrays of CNL R genes were identified suggesting that the S H 3 locus corresponds to a complex multi-gene cluster.
The purpose of the present study was to gain insight into the genomic organization and evolution of the S H 3 R gene cluster in coffee. The agronomic importance of this locus as well as the recent origin and the perennial characteristic of coffee species make these objectives especially appealing. Sequences of the S H 3 region in three different genomes, the Ca and Ea subgenomes of C. arabica and the Cc genome of C. canephora were analyzed to investigate the genomic organization and evolution of the S H 3 locus. In addition, we performed comparative analyses of the identified NBS-LRR encoding sequences to identify the forces that drive evolution in the S H 3 R gene cluster. Our results highlight the importance of intra and inter subgenomic gene conversion as an important evolutionary mechanism for the evolution of disease resistance genes.
Organization of the S H 3 R gene cluster
Origin and evolution of the S H 3 R gene cluster
Locus S H 3 was compared with the putative orthologous region in the tomato genome (Solanum lycopersicum) which is, to date, the closest species to Coffea for which whole genome sequence is available (http://solgenomics.net). Micro-synteny was found between the coffee S H 3 locus and two tomato genomic regions which shared 53.2 and 23.4% of the Coffea genes, respectively (data not shown), but no CNL genes were found in these regions of the tomato genome.
Sequence characterization of the S H 3-CNL family
Exon, intron size (bp) and protein size (aa) of the S H 3-CNL members identified in the three genomes analyzed.
Cloning of S H 3- CNL_A2 members from diploid species of coffee
To study interspecific diversity, the SH3-CNL_A2 member was selected at random for further analysis. The S H 3- CNL_A2 member was cloned from six coffee species (C. anthonyi, C sp. Congo, C. canephora, C. eugenioides, C. liberica, C. pseudozanguebarie). The cloned fragments were around 4 kb in size. Their sequences were determined and compared with those from Ca, Ea and Cc genomes.
Sequence diversity analysis of the S H 3- CNL family
Gene conversions detected among S H 3-CNL members with the RDP method .
A1_Cc × A2_Cc
2.72 × 10-14
A1_Cc × B_Cc
6.57 × 10-3
A2_Ca × A1_Ca
2.13 × 10-3
A2_Ca × A1_Ca
4.15 × 10-3
A1_Ea × A2_Ea
9.46 × 10-8
A3_Ea × B1_Ea
7.63 × 10-4
A2_Ea × A1_Ea
7.62 × 10-3
Ca + Ea
B2_Ea × A1_Ca
8.99 × 10-14
Ca + Ea
A1_Ea × A2_Ca
7.82 × 10-8
To check the type of selection that acted on genes in the S H 3-CNL family, the ratio between non-synonymous (Ka) and synonymous substitutions (Ks) was estimated using DNAsp v.5. The Ka/Ks substitution rate was calculated for each pair between ortholog and/or paralog members in C. arabica and C. canephora species. We also calculated the Ka/Ks between each pair of A2 members cloned from diploid coffee species together with A2 members from sequenced genomes (C. arabica and C. canephora). The analysis was performed on the complete coding sequence as well as on different domains (CC, NBS, LRR). Analysis also focused on codons encoding the solvent-exposed amino acids of the β-strand/β-turn motifs (x residues in xxLxLxx motifs) in the LRR domains.
Organization and evolution of the S H 3-CNL family
Comparative analyses of R-gene clusters across different haplotypes or species demonstrated that the evolution of resistant genes is a dynamic process mostly involving duplication, deletion, sequence exchange, point mutation, diversified selection, recombination, gene conversion and retroelement insertion [21, 23, 24, 28–30, 32, 33, 51, 52]. The cluster arrangement of R-genes represents an important reservoir of diversity and a source of genetic variation allowing the generation of novel resistance specificities via gene conversion, gene duplication, unequal crossing-over, ectopic recombination or diversifying selection [12, 19]. To explore the organization and to characterize the mechanisms involved in the evolution of the S H 3 locus, where a putative R-gene cluster was identified  a ~550 kb sequence was analyzed in three coffee genomes, Ea and Ca from C. arabica and Cc from C. canephora. Sequence analysis revealed the presence of a variable number of NBS-LRR genes belonging to the CC subclass at the S H 3 locus. All these genes belong to the same family (hereafter called S H 3-CNL family). Sequence analysis of regions flanking the S H 3-CNL genes helped determine the orthology relationship among the copies in different genomes. At the same time, several traces of ancient duplications made it possible to trace back the duplication/deletion events which, consistently with the birth and death evolution model, shaped the S H 3 locus from the most recent common ancestor of all S H 3-CNL copies. Since the structure of the S H 3 locus was well conserved in all three Coffea genomes analyzed, one can conclude that the origin of most of the S H 3-CNL copies predates the divergence between Coffea species.
Homologs of S H 3-CNL genes were found in several dicot species including Solanum spp., but comparative genomics failed to find a CNL R-gene in the orthologous regions of three Rosid species  and Solanum lycopersicum. Consequently, it can be suggested that the ancestral S H 3-CNL copy was inserted in the S H 3 locus after the divergence between Solanum and Coffea lineages.
In a similar study by David et al.  the authors compared the B4 locus of Phaseolus vulgaris (that has 26 CNL genes) with three sequenced legume genomes, Medicago trunculata (Mt), Lotus japonicus (Lj) and Glycine max (Gm). Their analysis revealed that conserved microsynteny existed among legumes species, except for the CNL sequences, which appeared to be completely absent in the corresponding regions of Mt and Lj and only a truncated CNL was found in syntenic regions of Gm . They suggested that CNL were inserted in the ancestor of the B4 locus after Mt, Lj, and Pv diverged but before the divergence of Pv and Gm through an ectopic recombination event between non-homologous chromosomes. Phylogenetic analysis including those legume CNL sequences and all known Pv B4-CNL sequences supported this hypothesis .
Structural instability induced by repetitive mobile elements is one of the mechanisms that could lead to diversification into R gene families. The presence of very similar sequences increases the possibilities of mispairing during recombination, giving rise to unequal crossovers and interlocus gene conversions [19, 53–55]. However, the edges of the duplications involved in the birth of new S H 3-CNL copies were not related to mobile elements and mobile elements identified in the region did not appear to play a role in the structural evolution of the S H 3 locus of Coffea species.
Gene conversion (i.e. the substitution of a portion of a gene sequence by the homologous sequence of another related gene) is more frequent among members of highly similar, tightly clustered families . Gene conversion is a common phenomenon and it has been detected between paralogs in many R-gene clusters [9, 21, 35–37, 57–62]. Sequence exchanges between different sub-genomes have previously been detected in a R1 resistance-gene cluster of one CNL subfamily in allohexaploid, Solanum demissum . In that study, seven of the 17 sequence exchanges among R1 homologs occurred between different genomes. Two explanations were proposed: first, sequence exchanges among different haplotypes could be generated through gene conversions or alternatively, they might have occurred through recombination before speciation and have been conserved in S. demissum . At the S H 3 locus, gene conversion events were detected between paralogs in all three coffee genomes analyzed and also between members of the two sub-genomes of C. arabica.
Conversion events were detected between S H 3-CNL members independently of their orientation (i.e. between members in region A and B).The inverted orientation of the loci might allow rare interlocus gene conversion or unequal exchange while minimizing the risk of gross chromosomal rearrangement . The gene orientation in a cluster of NBS-LRR has also been studied in rice  and A. thaliana . These studies demonstrated that conversion can occur between genes in the same or in opposite orientation, however conversion is more frequent in gene families arranged as direct repeats because they have higher similarity than those found in opposite orientation.
In addition, gene conversion was suggested to be more frequent in perennial than in annual plants. Yang et al., compared the gene conversion events among NBS-encoding genes in two perennial and two annual plants. A total of 823 and 468 gene conversion events involving 299 and 187 NBS-encoding genes were detected in grapevine and poplar, respectively, while only 143 and 81 gene conversion events were detected in Arabidopsis and rice, respectively . Since the long-generation time of woody species slows down the accumulation of evolutionary change, the authors suggested that an excess of recent duplications and a higher conversion rate in grapevine and poplar could generate novel resistance profiles to compensate for life history traits. According to Kuang et al. [31, 32] S H 3-CNL members should be classified as evolutionary type I (fast evolving genes) since several conversion events were detected between members.
Effect of selection on molecular evolution of the S H 3-CNL family
Natural selection influences the molecular evolution of sequences by increasing or reducing the fixation probability of a given mutation which, respectively, increases or reduces the fitness of the individuals carrying it.
The effect of natural selection on a gene sequence can be investigated by analyzing nucleotide substitutions that occurred between two variants of this gene. Since synonymous substitutions (i.e. nucleotide substitutions that do not change the amino acid sequence) are supposed to not modify the phenotype, their accumulation is considered not to be influenced by natural selection. Conversely, non-synonymous substitutions (nucleotide substitutions that modify the coded amino acid) could increase, reduce, or not influence the fitness of the individuals carrying it; consequently, their accumulation could be influenced by natural selection. The ratio of non-synonymous (Ka) to synonymous (Ks) substitution rates could be used to infer the effect of natural selection of a given gene or a part of it. When Ka and Ks have similar values (Ka/Ks ≈ 1), one could infer a neutral effect of selection; when Ka is significantly lower than Ks (0 < Ka/Ks < 1), it could be deduced that the selection purges the gene sequence of most non-synonymous substitutions (purifying selection); finally, when Ka is significantly higher than Ks (Ka/Ks > 1), the selection is assumed to favor fixation of new variants (positive or diversifying selection) [63, 64].
In many NBS-LRR genes, analysis of corresponding proteins revealed high non-synonymous:synonymous substitution ratios in the leucine-rich (LRR) domain, mainly concentrated on the putative solvent-exposed residues, indicating that the LRR domain is subject to positive selection for amino acid diversification, [19, 35, 36, 38, 39, 59, 60, 65–68]. These results are consistent with the observation that nucleotide polymorphisms found in the leucine-rich (LRR) region of R genes are often responsible for pathogen specificity .
In the S H 3-CNL family, significant positive selection was only detected when the Ka/Ks analysis was focused on solvent-exposed residues (i.e. the x residues in xxLxLxx motif from LRR domain) most frequently among paralog members. Conversely, when larger regions were considered, the effect of natural selection was diluted and not detectable.
In the co-evolutionary arms race between hosts and their pathogens, genes involved in their interaction are expected to evolve under positive selection. The positive selection detected in the solvent-exposed residue of the S H 3-CNL members could indicate involvement in recognition of pathogen attack.
The S H 3-CNL family appears to have evolved following the birth-and-death model, since duplications and deletions were inferred in the evolution of the S H 3 locus. Gene conversion between paralog members from the same or different sub-genomes, and positive selection appear to be the major forces influencing the evolution of S H 3-CNL in coffee trees.
Materials and methods
Plant material and DNA extraction
The cv. IAPAR 59 of Coffea arabica and six Coffea species were analyzed in this study: C. canephora (IF200), C. anthonyi (OD68), C sp. Congo (OB66), C. eugenioides (DA54), C. liberica (EA67), C. pseudozanguebarie (H66). Genomic DNA was isolated from leaves of greenhouse grown plants located at IRD (Institut de Recherche pour le Développement) Montpellier, France. Leaves were frozen in liquid nitrogen and DNA was extracted using a CTAB procedure  with modified extraction buffer (3% CTAB, 1.4 mM NACl, 100 mM Tris HCl, 20 mM EDTA, pH 0.8).
Several Bacterial Artificial Chromosome (BAC) clones spanning the S H 3 locus were isolated from a C. arabica (IAPAR59)  and a C. canephora (HD-200-94) (unpublished data) libraries Based on fingerprint data and overlapping sequence analysis, BAC sequences were assembled in contigs specific to the C. arabica and C. canephora genomes (hereafter called Cc for C. canephora genome; Ea and Ca for "eugenioides" and "canephora" sub-genomes of C. arabica) (Lashermes et al. 2010). Gene annotation of the BACs was already available . Sequences of the thirteen selected BACs were deposited to GeneBank [accession numbers, Genebank:GU123894 to GU123899 and HQ696507 to HQ696513].
Primer design and cloning procedure
Orthologous specific primers to amplify A2 members of the S H 3-CNL family from wild Coffea species were designed based on sequence alignments of A2 members in C. canephora and C. arabica: A2_Left: 5'-CCTTGATAAGAAACATGAATGAAATACACGA-3' and A2_right 5'-AAGGATAAATGAGAAGAACTACTGAGCCTG-3'. DNA amplification was performed with Expand™ 20Kbplus PCR System (Roche Applied Science, Mannheim Germany). PCR were performed as follows: one cycle of 1 min at 95°C, 10 cycles of 10 sec at 94°C, 45 sec at 50°C, 5 min at 68°C followed by 20 cycles of 10 sec at 94°C, 45 sec at 50°C, 7 min at 68°C plus 10 sec per cycle, and final extension of 7 min at 68°C. A10 μl aliquot from each PCR amplification was analyzed by electrophoresis in a 1.2% agarose gel. The amplicons were gel-stained using Crystal violet and the DNA bands were purified using a S.N.A. P™ purification column (Invitrogen Carlsbad, CA). The PCR products were cloned into the pCR®-XL-TOPO® kit from Invitrogen and chemically competent cells (Invitrogen Carlsbad, CA) according to the manufacturer's protocol. Eight colonies were randomly selected for screening. Colony PCR of eight random samples was used to select clones containing the complete amplicon. For this purpose, two new primers were designed to amplify the extremities of the genes in combination with the primers used to amplify the whole gene: 5'-CGACAGTGGGAACGAAACCC-3'combined with A2_Left and 5'-TGGAGGACCGGATCATGAACA-3' combined with de A2_RIGHT. The colony PCR was performed as follows: 10 min at 94°C, followed by 30 cycles of 30 sec at 94°C, 30 sec at 55°C, 4 min at 72°C and final extension of 10 min at 72°C. The colonies shown to contain the complete insert were transferred to 5 ml LB broth with 50 μg/ml kanamycin and incubated at 37°C overnight. Plasmid DNA was isolated using Promega Wizard® Plus Minipreps DNA purification System (Promega Corporation, Madison, WI, USA) according to manufacturer's instructions. Two independent PCR and sequencing were carried out to ensure quality.
Sequencing and analysis of cloned S H 3-CNL members
Plasmid DNA was sequenced at Genome Express (Grenoble, France) using M13-universal- forward and reverse primers and five other internal primers were designed using the Primer3 program (Whitehead Institute, USA) to allow whole gene sequencing. INT1-L: 5-TCCATCGTCCAAGATACAGC-3, INT2-L: 5-TTTGTTGGGATGGAAGATGA-3, INT3-L: 5-GCTGGGAGTTGCTTCAAAAG-3, INT4-L: 5-TCGAATGTGGACAGCAGAAG-3, INT5-L: 5-GCCTTGGAGACACTTCCATC-3. The cloned sequence contigs were assembled using the Staden package . The complete sequences of each clone were aligned using Bioedit v.7.0 .
Southern blot analysis
Southern blot analysis was performed as follows: 20 μg of genomic DNA was extracted as described above and digested with a restriction enzyme (only Eco RI for the panel of diploid species Eco RI, Dra I and Bam HI for the Coffea arabica cv. IAPAR-59) and separated by agarose gel electrophoresis. The digested DNA was transferred to Hybond-N+ nylon membranes for Southern hybridization as described in Noir et al. . S H 3-CNL family specific probe was obtained by PCR amplification using primers designed on the NBS domain (left primer: 5'-CGGTCTCGGTAAGACCACTC-3'and right primer 5'-CCTCTGCAAATGGAAATGCT-3'). The amplified 516 bp fragment was labeled with [32P]-dATP according to the manufacturer's recommendations (Megaprime DNA Labelling Systems kit, Amersham) and used as probe in the hybridization experiment as described in Sambrook et al. .
SMART protein motif analyses (http://smart.embl-heidelberg.de) and Pfam database (http://pfam.sanger.ac.uk/search/sequence) were used to detect motifs in the S H 3-CNL genes. COILS with a threshold of 0.9 was used to specifically detect CC domains .
In order to check the possibility of conversion events among the the S H 3-CNL members, alignments of sequences from C. arabica and C. canephora species were analyzed with the RDP3 software  using the default settings (but linear instead of circular sequences were selected, in general settings). The program uses simultaneously different recombination detection methods, including RDP and GeneConv , to both detect and characterize the recombination events that are evident within a sequence alignment without any prior user indication of a non-recombinant set of reference sequences . Pairwise P values are assigned based on the comparison of each fragment with the maximum fragment length that is expected from the sequence pair by chance.
Protein sequences were manually aligned with the BioEdit program. The amino acid sequence alignments were used to guide the alignments of nucleotides using MEGA version 4.1 . Nucleotide diversity (π) was calculated by DnaSP v.5  where each paralog was considered as an independent allele of population.
The Ka/Ks ratio was estimated by DnaSP v5.1 based on Nei and Gojobori's equation  for full-length CDS for specific domains: (CC, NBS, LRR), for the xxLxLxx motifs in the LRR domain, and for the solvent-exposed residues (i.e. only the x residues in the xxLxLxx motif). P values were calculated and the significance level was compared at 0.05 and 0.01%.
The search for putative gene orthologs of the genes at the S H 3 locus was performed by TBLASTN analysis on the tomato genome sequence (Solanum lycopersicum) available in Solanaceae Genome Network (http://www.sgn.cornell.edu).
This study was financially supported by a grant to A. Ribas of CAPES foundation from the Ministry of Education of Brazil and by CIRAD and IRD funds for doctoral support.
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