Sequences Used

We downloaded the draft genome sequences and the original gene annotations of C. clementina (clementine) [21] and C. sinensis USA (sweet orange from USA) from the Citrus Genome Database (http://www.citrusgenomedb.org/) and those of C. sinensis China (Chinese sweet orange [19]) from the C. sinensis annotation project (http://citrus.hzau.edu.cn/orange/). The sizes of assembled genomes of C. clementina, C. sinensis China and C. sinensis USA are 301, 328 and 319 million base pairs, respectively. The C. clementina genomes assembled into nine major scaffolds and 95.8% of the sequences were assigned to those nine scaffolds. About 72.9% of the C. sinensis China genome assigned to nine chromosomes. The genome of C. sinensis USA only assembled to 12,574 scaffolds and the N50 of scaffolds is 250 kb. The original gene annotations of C. clementina, C. sinensis China and C. sinensis USA have 24,533, 29,385 and 25,397 genes respectively. We also downloaded the re-sequence data of three mandarin and three pomelo genomes from the C. sinensis annotation project (http://citrus.hzau.edu.cn/orange/download/data.php). The re-sequence data is single end Illumina reads with length of 101 bp.

Identification of NBS Genes in Citrus Genomes

We first screened the original predicted Citrus open reading frames (ORFs) using hmmsearch [22] with the hidden Markov models (HMM) of Pfam [23] for NBS domain presence (NB-ARC, PF00931) using an e-value cut-off of 0.1 for the hmmsearch. Then, the proteins selected by the HMM were searched against the Swiss protein database [24] using BLASTP [25]. Only the proteins that have a significant match (e-value < 1E-5 in BLASTP search) with the NBS proteins or resistant proteins in the Swiss protein database were identified as potential NBS-containing proteins. To recover possible NBS genes that may be missed in the original gene annotations, we mapped the identified NBS genes to the draft genome using TBLASTN. The matched sequences with e-value < 1E-5 were then predicted using Genewise [26]. The new potential NBS genes predicted by Genewise were also confirmed by BLASTP searching through the Swiss protein database. Finally, we scanned all potential NBS genes for NBS domain using hmmsearch [22] and only keep the NBS genes with e value lower than more stringent cutoff of 1E-5.

Identification of Orthologous NBS genes in C. clementina and C. sinensis

Orthologous NBS genes of C. clementina and C. sinensis were identified using the reciprocal best blast method [27]. We used NBS genes of C. clementina as query sequences to search against the NBS genes of C. sinensis and vice versa. Protein pairs with reciprocal best hits of e-value < 1E-20 were defined as orthologs.

To calculate the rates of nonsynonymous, synonymous and their rate ratio (dN, dS and dN/dS) of orthologous pairs, we first aligned orthologous protein sequence pairs using mafft, and then converted the protein alignments to codon-based alignments using PAL2NAL [28]. We calculated the dN, dS and dN/dS rate ratios using the codeml program in PAML version 4.7 [29].

Phylogenetic Analysis

We constructed the best fit phylogenetic tree of NBS genes of the three Citrus genomes using only the conserved NBS domain. Only 1,099 NBS domain sequences that have both the P-loop and the MHDV motifs and were longer than 70% (200 amino acids) of the full-length NBS domain were included. Next, NBS domain sequences were aligned in mafft [30] using an auto alignment model and a best fit maximum likelihood phylogenetic tree of NBS genes was constructed using FastTree [31] with default parameters (JTT+CAT). The resultant best fit phylogenetic tree was divided into 3 main groups based upon clade support. For each group, we constructed a new ML tree with Streptomyces coelicolor protein P25941 as the outgroup using FastTree [31]. The average identity of each group was calculated using alistat implemented in SQUID (http://selab.janelia.org/software.html).

To evaluate the confidence level of the phylogenetic tree, we resampled the alignments 1000 times using SEQBOOT [32]. Then, we constructed the phylogenetic tree from each resampled alignments using FastTree [31]. The bootstrap values were calculated by comparing resampled phylogenetic trees to the original tree using CompareToBootstrap program in the FastTree [31].

We further partitioned the NBS gene tree into clades using the depth-first phylogeny partition method in PhyloPart [33] with distance threshold 0.025. This clustered the NBS genes into 114 clades, which contain more than 2 genes, and 8 orphan genes.

Domain and Motif Annotation

The Toll-Interleukin receptor (TIR) domains in Citrus NBS-containing proteins were identified using hmmsearch [22] with the HMM model of Pfam domain PF01582 and a 0.1 e-value cut-off. The Leucine-Rich Repeat (LRR) domains in Citrus NBS containing proteins were identified using the HMM models of Pfam LRR domains with e-value cut-off of 0.1. As long as there is a significant hit to one of LRR domain models (e-value < 0.1), it was define as an LRR-containing protein. We used MARCOIL [34] with a threshold probability of 90 and COILS [35] with a threshold of 0.9 to search for Coiled Coil (CC) domains in the N-terminal region of Citrus NBS-containing protein. We considered a protein as a CC-containing protein if either MARCOIL or COILS reported a CC domain in it.

We identified 20 motifs amongst the NBS genes in each of the three main phylogenetic groups separately using MEME SUITE [36]. The motif width was set to between 6 and 50 for MEME. Then, we searched the motif structure of all genes in each group using MAST with default parameters (-ev 10—mt 0.0001).

Pseudogene Identification

We identified possible pseudogenes using PseudoPipe [37] with default parameters (-e 0.1). The PseudoPipe algorithm identifies pseudo genes by integrating sequence similarity, intron-exon structure, plus presence of stop codons and frame-shifts. We used all Citrus NBS genes to search Citrus genomes for potential NGS pseudo genes.

Transposon Identification

All long terminal repeat (LTR) retrotransponsons in each Citrus genome were identified using LTR finder [38] with default parameters (-o 3-t 1—e 1-m 2-u -2). Then, we used a script program to match the location of the LTR transposons to the NBS-LRR genes in each Citrus genome.

NBS Gene Synteny Identification

Gene synteny was identified and defined using MCScanX [39] with default parameters (-A-u 5000). First, NBS genes between two genomes were aligned using BLASTP and matches with E-value < 1e-5 were sorted according to their chromosome positions. Synteny scores were then calculated for each block based upon gene position. Two genes were considered in the same block if there were fewer than 25 genes separating them. MCScanX reported blocks with at least 5 collinear gene pairs.

Gene Cluster Analysis

We grouped the NBS genes in each Citrus genome into the same cluster if the genome location between two genes was within 200 kb. We also identified the conserved gene clusters between the C. clementina and C. sinensis. If all genes in a cluster of C. clementina have orthologs in the corresponding cluster of C. sinensis and vice versa, then these two clusters were called completely conserved clusters. If only part of genes in the clusters have orthologs, we called these two clusters partially conserved.

Gene Conversion Detection

We first aligned the sequences of NBS genes in the same cluster using mafft [30]. Then, we used GENECONV [40] version 1.81a with default settings (N = 10,000) to detect gene conversions. GENECONV identifies gene conversions by finding identical fragments between pairs of sequences in a nucleotide alignment. A global P value ≤ 0.05 was used to assess the statistical significance of the observed conversions. GENECONV requires at least three sequences for analyses in order to account for shared ancestral states. Thus, we only detected conversions in clusters containing three or more genes.

Tests for Sites under Positive Selection

The amino acid sequences of NBS genes from the same clade were aligned with mafft [30]. Then we converted the protein alignments to codon-based alignment using PAL2NAL [28]. The positively selected sites were statistically identified using the Bayesian approach implemented in codeml within PAML [29]. We also further examined sites in the ω > 1 class with >90% posterior probability.

Mapping of Re-sequencing Data of Mandarin and Pomelo

We mapped the raw reads of each re-sequenced sample to the draft genome of C. sinensis China using BWA [41] with default parameters (-k 19-d 100-A 1-B 4-O 6). Then, the mapped reads of NBS genes regions were extracted using BEDtools [42]. Two types of coverage of each NBS gene in C. sinensis were calculated. One coverage type divides the length of mapped sequences by the whole gene sequence length and the other type divides the length of mapped sequences by the length of exon sequence only.

Citrus DNA Extraction and PCR Amplication

Citrus leaf samples were collected from the six Citrus plants in USHRL's (USDA Horticultural Research Laboratory, Fort Pierce, Florida): C. sinensis (sweet, navel orange), C. aurantium (karum jamir, sour orange), C. reticulata (mandarin orange), C. clementina (clementina), C. aurantiifolia (sweet lime), C. japonica (Yuzu, kumquat), and C. maxima (pomelo). Total DNA was extracted from leaf midribs following the Plant Mini Kit standard protocol from Qiagen Inc. (Valencia, CA), followed by DNA quantity and quality evaluation with Nanodrop. We chose the NBS gene, Cs1g09350, which was conserved in C. clementina and C. sinensis for validating the conservation of NBS gene among different Citrus genomes. Primers used in this study were designed using Oligo 7.23 (Molecular Biology Insights, Inc., Cascade, CO, USA). DNA Polymerase (Invitrogen, Carlsbad, CA, USA) was used to amplify the NBS-LRR genes from Citrus DNA. For PCR, 20 μL reactions using standard conditions provided by the manufacturer for DNA Polymerase. PCR was performed using an initial denaturation at 95°C for 3 minutes, 35 cycles of 94°C for 20 seconds, 50–52°C for 20 seconds (specified by different primer sets) and 68°C for 3 minutes, follow by final extension at 68°C for 10 minutes. The cloning and sequencing analysis of amplified PCR products were conducted as previously described [43]

Identification and classification of Citrus NBS Genes

We searched the C. clementina, C. sinensis China and C. sinensis USA genomes for genes containing the NBS domain using hmmsearch. Then, the NBS-containing genes were confirmed through homology searches against the Swiss protein database (see “Materials and Methods”). We identified similar numbers of NBS domain-containing genes amongst these three genomes. We found 618, 650 and 508 NBS genes from C. clementina, C. sinensis China and C. sinensis USA genomes respectively (Table 1). Among them, 413, 499 and 484 NBS genes were predicted in the original gene annotations and 205, 151 and 24 NBS genes in C. clementina, C. sinensis China and C. sinensis USA respectively were newly predicted in this project (S1 Table).

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Table 1. Classification of Citrus NBS genes.

https://doi.org/10.1371/journal.pone.0121893.t001

NBS genes could be classified into different classes based on their domain structures [6]. We searched the Toll-Interleukin receptor (TIR) and Coiled Coil (CC) domains in the N-terminal region and the Leucine-Rich Repeat (LRR) domains in the C-terminal of NBS genes. We identified 117 NBS genes with CC-NBS-LRR (CNL) domains, 82 NBS genes with TIR-NBS-LRR (TNL) domains, 68 NBS genes with NBS-LRR (NL) and 351 others NBS genes without LRR domains (N, CN and TN) from C. clementina (Table 1). We also identified 113 CNL, 77 TNL, 62 NL and 398 others NBS genes from C. sinensis China and 60 CNL, 30 TNL, 85 NL and 333 others NBS genes from C. sinensis USA (Table 1). In comparison to other genomes, there are many more Citrus NBS genes without the LRR domain. There are only 43.2%, 38.8% and 34.4% NBS genes with existing LRR domains in C. clementina, C. sinensis China and C. sinensis USA, respectively, while 72% NBS genes in Arabidopsis thaliana [6] and 78% NBS genes in Populus trichocarpa [44] have LRR domain.

The structures of TNL and CNL NBS genes are significantly different. The TNL NBS genes tend to have more introns than that of CNL NBS genes as previously found in Arabidopsis [6] and Populus [44]. The average numbers of introns in TNL NBS genes are 4.39, 4.70 and 4.47, while the numbers of introns in CNL NBS genes are 0.89, 1.15 and 1.38 in C. clementina, C. sinensis China and C. sinensis USA respectively (S1 Fig.). The median numbers of introns of different types of NBS genes in the three Citrus genomes are similar: four in TNL NBS genes and one in CNL NBS genes.

The NBS genes were unevenly distributed in the Citrus scaffolds/chromosomes. There were 158, 217 and 110 NBS genes, totaling 78.3% of 618 NGS genes, distributed in scaffolds_3, _5 and _7 of C. clementina, respectively. There were 125, 121 and 75 NBS genes distributed in chromosomes 1, 3 and 5 of C. sinensis China. The majority (95 out of 107) of NBS genes with TIR domain in C. clementina was distributed in scaffold 3. There were 33 and 51 (out of 102) NBS genes with TIR domain in C. sinensis China distributed on chromosome 5 and chromosome unknown, respectively.

Phylogenetic and Clade Analysis of the Citrus NBS Genes

To avoid mutation saturation effects in nucleotide sequences over time which can lead to an underestimation of the number of mutation events due to higher substitution rates versus proteins, we used the protein sequences of NBS domains, which are the most conserved part of NBS genes, to construct a phylogenetic tree of NBS genes. We only selected NBS domain sequences longer than 200 amino acid residues and contain both P-loop and MHDV motifs. Finally, 442 C. clementina, 393 C. sinensis China, and 264 C. sinensis USA NBS domain sequences were used for phylogenetic analysis (S2 Table). A Maximum Likelihood (ML) phylogenetic tree of these 1,099 NBS genes was then constructed using FastTree [31]. As shown in Fig. 1, the un-rooted phylogenetic tree can be divided into three main groups. Most NBS genes containing the TIR domain are in one branch and the non-TIR NBS genes comprise the other two branches (Fig. 1), in which most of them contain a CC domain. Therefore, we denoted the three branches as TIR, CC1 and CC2.

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Fig 1. Maximum likelihood phylogenetic tree of Citrus NBS-LRR genes constructed from multiple sequences alignment of NBS domain.

There are three gene groups in the phylogenetic tree: CC1 (pink fan-shape), CC2 (orange fan-shape) and TIR (light grey fan-shape). Clades were classified using PhyloPart as shown in alternating color and represented by alternative light yellow and grey colors in the middle circle. The outer circle shows species with C. clementina in red, C. sinensis China in green and C. sinensis USA in blue. Nodes with bootstrap support of 100 are indicated with grey circles on the tree.

https://doi.org/10.1371/journal.pone.0121893.g001

There were 452, 382 and 265 Citrus NBS genes in CC1, CC2 and TIR groups, respectively. S2 Table lists the group classification of 1,099 Citrus NBS genes. For each sub-group, we constructed a new ML phylogenetic tree rooted by Streptomyces coelicolor protein P25941 (S2 Fig.). The NBS domains in CC groups, especially in the CC1 group, were relatively more diverged in sequence versus those in TIR group. The average Poisson corrected distances between sequence pairs within each group were 0.947, 0.827 and 0.663 for CC1, CC2 and TIR groups, respectively. We aligned the NBS domains sequences in each group using mafft with default parameters (—auto). The average percentages of identities for NBS domain sequences were 40%, 44% and 52% for CC1, CC2 and TIR groups, respectively.

The number of LRR domains varied amongst the three classes of Citrus NBS genes. The number of LRR domains in the TIR group is significantly higher than the numbers of LRR domains in the CC1 and CC2 groups (S3 Fig.). The majority of CC1 NBS genes have only one LRR domain. On other hand, the TIR NBS genes have 2.4 LRR domains on average. The most frequent type of LRR domain in the CC1 group is LRR_8 (PF13855), but LRR_1 (PF00560) is the most frequent domain in both the CC2 group and the TIR group (S3 Table).

NBS genes in the three Citrus genomes are polyphyletic amongst branches of phylogenetic tree as shown in the Fig. 1. We partitioned the NBS gene tree into clades based on NBS domain sequence distance using PhyloPart with distance threshold of 0.025. This resulted in 114 clades (with at least two genes) and eight orphan genes (S2 Table). The numbers of clades in each NBS gene group are similar. There are 39, 42, 32 clades in CC1, CC2 and TIR groups, respectively. We calculated average sequence similarities between NBS domains in each clade using alistat in SQUID (http://selab.janelia.org/software.html). The minimum average sequence similarity of NBS domains in each clade was 70%. The largest clade included 90 NBS genes. On average, there were 9.56 genes per clade. There were seven clades with more than 40 genes. Among these clades, four clades were in CC1; two clades were in CC2 and one clade was in the TIR group. Most of the clades contain NBS genes from the three Citrus genomes (Fig. 1, Table 2). There are 89 clades with at least three NBS genes and 87 of these clades contain members from each of the three Citrus genomes. Together, these results imply that three Citrus genomes may have similar types of NBS genes.

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Table 2. Types of Citrus NBS gene clades.

https://doi.org/10.1371/journal.pone.0121893.t002

To understand the evolutionary dynamics maintaining functional constraint while maintaining so many gene family members, we tested for evidence of accelerated sequence evolution (positive selection) by searching for positively-selected sites within each clade. We detected positively selected sites in 53.5% (61) of clades. There were 18, 24 and 19 clades with sites under positive selection in CC1, CC2 and TIR groups, respectively. In total, we detected 541 positively selected sites. Consistent with previous reports [6], there are more positively selected sites in the C-terminal region of NBS genes (LRR domains) than those in the N-terminal and NBS domains (S4 Table). Approximately 56.4% (305 out of 541) of the positively selected sites were located in the C-terminal region (LRR domain). While most clades have positively selected sites in the LRR domain, there were clades with a greater number of positively selected sites within the NBS domain. For example, there were 46 positively selected sites in Clade_1260 that are located in NBS domain while there are only two positively selected sites in LRR domain (S4 Fig.).

Mapping Re-sequencing Reads Showed the Conservation of NBS Genes in Citrus Genomes

To verify that C. sinensis (sweet orange) is a backcross hybrid of C. maxima (pomelo) and C. reticulata (mandarin) [19], Xu et al. previously re-sequenced three pomelo cultivars and three mandarin cultivars and showed that SSR and SNP markers in the C. sinensis genome derive from the pomelo and mandarin genomes at an approximately ratio of 1:3 [19]. Since our comparison of C. sinensis and C. clementina genomes showed that most of their NBS genes are very similar in sequence, we investigated the relationships amongst the NBS genes of C. sinensis (sweet orange), C. maxima (pomelo), and C. reticulata (mandarin) to compare and contrast how mutations accumulated and determine if there are differences in sequence, and hence potentially functional, constraints amongst NBS gene types in Citrus genomes.

We mapped the re-sequenced reads of three C. maxima (pomelo) genomes and three C. reticulata (mandarin) genomes to hybridized genome of C. sinensis (sweet orange) China using BWA with mem method [41] and calculated the coverage of each NBS gene in C. sinensis China. We detected 524 of 650 C. sinensis China NBS genes with more than 50% coverage in all of the six re-sequenced genomes. Additionally, 249 of 650 C. sinensis China NBS genes with more than 85% coverage in all six resequenced genomes and 592 (91%) of C. sinensis China NBS genes with coverage over 85% in at least one of the re-sequenced Citrus genomes. Using a cutoff of 15% coverage as missing calls over the entire length of the gene, only 25 (<4%) of C. sinensis China NBS genes seem to be deleted in at least one of the six re-sequenced genomes. No NBS genes were lost amongst all of the six re-sequenced genomes.

Re-sequenced reads tended to map to exons rather than to introns (S5 Table). For example, the entire coding region of NBS gene Cs9g13310 was 3,693 bp in length and covered by all reads from the re-sequenced samples. However, the 16 kb introns were not consistently present in all of the re-sequenced reads. When we used exon presence instead of whole gene coverage, 403 out of 650 (62%) C. sinensis China NBS genes have more than 85% coverage in all six re-sequenced Citrus genomes and 645 (99%) C. sinensis China NBS genes have more than 85% coverage in at least one of the resequenced Citrus genomes. Most C. sinensis China NBS genes have high exon coverage on both the C. maxima (pomelo) and C. reticulata (mandarin) genomes (S5 Fig.). There were only three C. sinensis China NBS genes, Cs1g02140.1, Cs6g02120.1 and Cs7g02220.1, with low (<40%) exon coverage in all three C. maxima genomes, but high coverage was achieved in at least two of the three C. reticulata genomes (S5 Fig.). Our mapping results showed that most NBS genes of C. sinensis (sweet orange) have a corresponding copy in the re-sequenced C. maxima (pomelo) and C. reticulata (mandarin) genomes.

Motif Patterns in Citrus NBS Genes

To further examine the gene structures of three Citrus NBS gene groups, we searched the motifs in the sequences of each group using MEME. Fig. 2 lists consensus sequences of the top 20 motifs identified by MEME from the CC1, CC2 and TIR Citrus NBS gene groups.

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Fig 2. Architecture of NBS gene motifs in Citrus.

The consensus sequences of the top 20 motifs identified by MEME for each group of Citrus NBS genes are listed (A: CC1 group, B: CC2 group, C: TIR group). The motifs in blue are identified from N-terminal (CC or TIR domain). The motifs in red are identified from NBS domain. The motifs in green are identified from C-terminal (LRR domain). The motifs in black are identified from other region of NBS genes. The bold letters highlight the conserved motifs in Arabidopsis. The motifs underlined in green were repeated in C-terminal (LRR domain).

https://doi.org/10.1371/journal.pone.0121893.g002

The motifs in the N-terminal of CC1 and CC2 groups showed little similarity to each other. The MEME found two motifs from CC1 group. One of them, EEQQQMRRLNQVQGWLSRVEA, was present in 356 of 452 CC1 NBS genes. The other motif, GSQEIDKLCLGGYCSKNCKSSYKFGKKVA, was present in 189 of 452 CC1 NBS genes. Both motifs have high level of sequence similarities with the CC NBS genes of Arabidopsis (S6 Fig. A). The MEME found three motifs from CC2 group. Two of the motifs, KKLTNMLEMIKAVLDDAEEKQ and AVKLWLGKLKDAAYDVEDVLDEFQTEALR were identified in 325 and 340 of 382 CC2 NBS genes, respectively. The motif AVKLWLGKLKDAAYDVEDVLDEFQTEALR has high levels of similarity with the motif identified from the CC NBS genes of Oryza sativa japonica (Japonica rice) [45] (S6 Fig. B). The different motifs in CC1 and CC2 NBS genes implied that they may be from different evolutionary origins.

For the TIR group, the MEME identified five motifs in the N-terminal. They can be found in 76% to 90% of 265 TIR Citrus NBS genes. The first four motifs YDVFLSFRGEDTRDNFTSHLY, AIEASAISVIIFSEGYASSRWCLDELVKI, GQIVIPVFYRVDPSDVRKQTG, and ENPEKVQKWRDALKEA were very similar to the TIR1-4 motifs identified from TIR NBS genes in Arabidopsis [6] and Populus trichocarpa [44] (S6 Fig. C).

The MEME algorithm identified nine motifs from NBS domains of CC2 and TIR groups, which are similar to the motif structures of NBS domains in Arabidopsis thaliana [6] and Populus trichocarpa NBS genes [44]. MEME results also showed that the motif structure of NBS domain of CC1 groups is slightly different from those of CC2 and TIR groups. Eleven motifs were identified from NBS domains of CC1 group with two extra RNBS motifs (RNBS-F, RNBS-G) between GLPL and MHDV motifs. Five motifs: P-loop, Kinase-2, RNBS-B, GLPL and MHDV, showed high levels of sequence similarity amongst NBS genes of three groups, which were also similar to those motifs from Arabidopsis [6] and Populus trichocarpa NBS genes [44]. The MHDV motif in Citrus was often slightly modified to MHDL, as found in Arabidopsis and Populus previously. Meanwhile, the motifs RNBS-A, RNBS-C, and RNBS-D were quite dissimilar to each other amongst three groups.

The LRR domains in the C-terminal of NBS genes usually have high sequence diversity as they play a role in recognizing pathogen virulence proteins. The MEME algorithm identified five, six, and four motifs from LRR domains of CC1, CC2 and TIR NBS genes, respectively. Most of the motifs contained LxxL repeats. The LRR motifs from different groups were highly variable in sequence, which implied that the three groups of NBS genes play different roles in the Citrus immune system. Some LRR motifs had repeated several times in the same gene. Examples include: motif APNLKSLEVSSCxxMEEIISV found in 367 of 452 CC1 group with an average 4.8 motifs per gene; motif IKTLPESVCELYNLQTLDLEGCRRLKKLP found in 332 of 382 CC2 group with an average 2.8 times per gene and motifs CKRLKSLPSSLCKLKSLGxLNLSGCSNLE and GNISELFLDGTAIEELPSSIE found in 208 and 209 of 265 TIR group with 2.5 and 2.1 times per gene, respectively.

Analysis of NBS Gene Clusters in Citrus Genomes

The majority of Citrus NBS genes were physically clustered in genome (Table 3). 525 of 618 NBS genes in C. clementina were found in 108 clusters and 500 of 650 NBS genes in C. sinensis China were found in 126 clusters (S2 Table). Although the assembly of C. sinensis USA is more fragmented, there still are 207 of 508 NBS genes present in 72 clusters. The largest number of gene clusters in C. clementina, C. sinensis China and C. sinensis USA contain 55, 37 and 13 NBS genes, respectively.

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Table 3. Citrus NBS genes in clusters.

https://doi.org/10.1371/journal.pone.0121893.t003

Most clusters contain NBS genes from the same group. In C. clementina, there were 38 clusters with NBS genes of CC1 group, 40 clusters with NBS genes of CC2 group and 23 clusters with NBS genes of TIR group. Only seven out of 108 clusters contain the NBS genes from two or three groups. In C. sinensis China, there were 41 clusters with NBS genes of CC1 group, 44 clusters with NBS genes of CC2 group and 26 clusters with NBS genes of TIR group. There were 15 clusters containing NBS genes from two or three groups in C. sinensis China. In C. sinensis USA, there were 27 clusters with NBS genes of CC1 group, 25 clusters with NBS genes of CC2 group and 15 clusters with NBS genes of TIR group. Only five clusters contain NBS genes from different groups in C. sinensis USA. The lower number of clusters in C. sinensis USA may due to its fragmented assembly.

The sequences of NBS genes within clusters are much more similar to each other than those between clusters (T-test p value < 2.2e-16). The mean identities between genes within and between clusters were 0.628 and 0.393 respectively (Fig. 3). Furthermore, NBS genes in the same cluster tend to be in the same strand, which indicates that the NBS genes in the clusters are due to tandem duplication. We detected 204 pairs of tandem duplications in C. clementina and 217 pairs of tandem duplications in C. sinensis China using MCScanX [39]. The numbers of tandem duplications within CC1 and CC2 groups are much greater than that within the TIR group. Among 204 pairs in C. clementina, 90 and 85 pairs were present in the CC1 and CC2 groups and only 29 pairs from TIR group. Among 217 tandem gene pairs in C. sinensis China, 88 and 87 pairs were present in the CC1 and CC2 groups and only 42 pairs in the TIR group. The fewer tandem duplications of NBS genes in the TIR group may be the reason that there are fewer clusters of TIR groups in Citrus genomes.

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Fig 3. Percentage identity distribution of NBS-encoding genes in C. clementina (Cc) and C. sinensis China (Csc).

Green lines indicate pairwise identity distribution of inter-cluster NBS-encoding genes. Orange lines indicate intro-cluster NBS-encoding genes.

https://doi.org/10.1371/journal.pone.0121893.g003

We identified 254 and 246 gene conversion events from 116 NBS gene clusters in C. clementina and 144 NBS gene clusters in C. sinensis China, respectively (Table 4). The gene conversion events in C. sinensis USA is much less due to fragmented assembly. It is interesting that most of the conversion events (483 out of 520) were identified from the relatively small clusters with less than 10 NBS genes. Among these conversions, 119 events located in N-terminal, 178 in NBS domains and 223 in C-terminal, which indicating that there was no significantly bias in the location of conversion. Most gene conversions were between genes from the same group. We identified 101, 184 and 229 conversion events from NBS genes in TIR, CC1 and CC2 groups respectively and only four conversion events were identified between NBS genes of TIR and CC2 groups. While we could identify similar total numbers of conversion events in C. clementina and C. sinensis China, we found almost double such events in C. sinensis China TIR clusters versus in C. clementina TIR clusters. Meanwhile, we also found many more conversion events in C. clementina CC2 clusters than that in C. sinensis China CC2 clusters (Table 4).

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Table 4. Gene conversion events found in C. clementina and C. sinensis China.

https://doi.org/10.1371/journal.pone.0121893.t004

Analysis of NBS Orthologs

We identified 719 Citrus NBS gene pairs of orthologs amongst C. clementina, C. sinensis China and C. sinensis USA. 270 orthologs were shared between C. clementina and C. sinensis China (S7 Fig.); 227 orthologous gene pairs were shared between C. clementina and C. sinensis USA and 222 orthologous gene pairs were shared between C. sinensis China and C. sinensis USA. The percentages of identities between orthologous genes range from 53.8% to 100% (mean of 93.6%, median of 96.8%). The percentages of identities between orthologous genes from TIR group (TNL and TN, 88.42 ± 10.04) were significantly (T-test: P<2.6e-6) lower than those from CC groups (CNL and CN, 92.92 ± 7.03). The nonsynonymous divergence (dN) values of the 719 orthologs ranged from 1.46e-6 to 0.31 (mean of 0.03, median of 0.08) and the synonymous divergence (dS) values ranged from 1.14e-5 to 0.75 (mean of 0.05, median of 0.019) (Fig. 4A, B). The dN/dS rate ratios ranged from 0.001 to 50 with a median of 0.62. Similar to Arabidopsis, the dN and dS of orthologs from TIR group (TNL and TN) were higher than those from CC groups (CNL and CN). The dN values of orthologs from TIR group ranged from 0.001 to 0.24 (mean of 0.038, median of 0.017) while those of orthologs from CC group ranged from 1.4e-6 to 0.23 (mean of 0.025, median of 0.007). The dS rate of orthologs from TIR group ranged from 3.27e-5 to 0.76 (mean of 0.078, median of 0.029) while those of orthologs from CC group ranged from 1e-5 to 0.67 (mean of 0.04, median of 0.016). However, the dN/dS rate ratios of orthologs from TIR group were relatively lower than that of orthologs from CC group (Fig. 4C).

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Fig 4. Divergence of orthologous NBS-encoding genes amongst Citrus species.

A-C. Divergence of different classes. D-F. Divergence of singletons and cluster members. dN indicates the nonsynonymous mutation rate (rate of nonsynonymous mutations per nonsynonymous site). dS indicates the synonymous mutation rate. CNL, CN, TNL, TN, NL and N indicate orthologs between two proteins belonging to same cluster with CC-NBS-LRR domains (CNL), CC-NBS domains (CN), TIR-NBS-LRR domains (TNL), TIR-NBS domains (TN), NBS-LRR domains (NL), NBS domain (N), respectively. The others indicate orthologs between different clusters.

https://doi.org/10.1371/journal.pone.0121893.g004

The dN and dS rates as well as dN/dS rate ratios of ortholog residues in clusters are generally greater than those of orthologous singletons (Fig. 4D-F). The median dN/dS rate ratio of 148 orthologous singletons was 0.55 while that of 361 orthologs in clusters was 0.63. There were 124 orthologs with dN/dS rate ratios above 1. Variation in these orthologs may be shaped by positive selection pressure. Most of the positive selected orthologs (87.9%, 109 out of 124) belonged to CC groups (49 orthologs from CC1 group and 50 from CC2 group).

We also detected 38 NBS gene syntenic blocks between C. clementina and C. sinensis China using MCScanX [39]. Totally, there are 416 syntenic orthologs of NBS genes between C. clementina and C. sinensis China (S8 Fig.). On average, there are 11 genes per block. The biggest block contains 45 NBS genes and was located in scaffold_5 of C. clementina and chromosome 3 of C. sinensis China. There were 80, 77 and 71 syntenic NBS genes in scaffold_5 of C. clementina/chromosome 5 of C. sinensis China, scaffold_3 of C. clementina/chromosome 5 of C. sinensis China and scaffold_7 of C. clementina/chromosome 1 of C. sinensis China. Furthermore, there were 68, 66 and 8 syntenic NBS genes in the unknown chromosome of C. sinensis China corresponding to NBS genes in scaffold_3, _5 and _7 of C. clementina, respectively.

Analysis of Conserved NBS Gene Clusters

We identified 118 pairs of conserved NBS gene clusters between C. clementina and C. sinensis China (S9 Fig.). There were 19 NBS gene clusters completely conserved in C. clementina and C. sinensis China. For example, all 14 NBS genes in cluster CL225 of C. sinensis China have orthologs in the cluster CL168 C. clementina which contains nine NBS genes and vice versa. Some clusters (in both C. clementina and C. sinensis China) have several corresponding conserved clusters. This may due to either the genome arrangement or the incomplete assembly of genomes. Furthermore, there were 19 clusters of C. clementina with no conserved clusters in C. sinensis China and 18 clusters of C. sinensis China with no conserved clusters in C. clementina.

The conserved clusters provided additional insights into NBS gene evolution within and between Citrus genomes. For example, cluster CL142 (9 NBS genes) in C. clementina and cluster CL282 (7 NBS genes) in C. sinensis China were highly conserved. The phylogenetic tree of these 16 genes suggested division into two subgroups (depicted in blue and orange color in Fig. 5A). This division suggests two ancestral genes for this conserved cluster. Using the phylogenetic tree as a framework, we reconstructed the evolutionary history of these two clusters. There were several tandem duplication events in the evolutionary history of the conserved clusters, and extra tandem duplication was observed in C. clementina after it separated from C. sinensis (Fig. 5B). Two NBS genes were lost in C. sinensis and one NBS gene was lost in C. clementina. Furthermore, there was a recombination event within C. clementina.

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Fig 5. Duplication histories of one of the conserved NBS-encoding genes cluster in C. clementina and C. sinensis.

A. Phylogenetic tree of the NBS-encoding genes; B. Orthologs in the conserved cluster of C. clementina and C. sinensis. Black connectors indicate tandem duplications and red dotted connectors indicate gene loss. A gene recombination event occurred in the ancestor of C. clementina, as indicated with an orange connector.

https://doi.org/10.1371/journal.pone.0121893.g005

Mutations and Transposons in Citrus NBS Genes

Plant NBS genes are continuously evolving. Sequence variation and structural constraints are shaped by gene birth-and-death processes [46]. Besides possible interallelic recombination and gene conversion, gene mutations and transposable elements appear to play important roles in NBS gene evolution.

We compared the DNA sequences of NBS genes from different Citrus genomes to identify mutations. Approximately half of Citrus NBS genes have mutations maintained amongst corresponding orthologs. When a mutation took place in an exon and resulted in stop-codon gaining or frame-shift, the target gene often became a pseudogene. For example, Cs1g18610.1_cc_32, Cs1g18610.1 and orange1.1g003367m are orthologs of C. clementina, C. sinensis China and C. sinensis USA. There were 2 stop-codon gaining mutations in Cs1g18610.1 (S10 Fig. A), which means that Cs1g18610.1 might become a pseudo (nonfunctional) gene after gaining these mutations.

LTR retrotransposons are widespread in eukaryotic genomes, especially plant genomes. We predicted 19014, 6296 and 1479 LTR retrotransponsons with typical LTR characters in the draft genomes of C. clementina, C. sinensis China and C. sinensis USA, respectively. Then, we filtered out LTR retrotransponsons with low similarity with known TE proteins using BLASTX with e-value greater than 1e-5. Finally, 4920, 3726 and 1240 LTR retrotransponsons remained in C. clementina, C. sinensis China and C. sinensis USA, respectively. We identified 33, 32 and 4 NBS genes that were inserted with LTR retrotransposons in C. clementina, C. sinensis China and C. sinensis USA respectively (S6 Table). Most of these genes will likely become pseudogenes due to these insertions. For an instance, orange1.1g043039m, orange1.1g043039m_cc_116 and orange1.1g043039m_csc_123 were orthologs of C. sinensis USA, C. clementina and C. sinensis China respectively (S10 Fig. B). The results of gene structure analysis showed that structure in orange1.1g043039m in C. sinensis USA seems relatively well maintained. But there is an about 10 kb fragment of LTR-retrotransposons in the corresponding homologous gene in C. clementina and C. sinensis China (S10 Fig. B). We identified both orange1.1g043039m_cc_116 and orange1.1g043039m_csc_123 as pseudogenes using PseudoPipe [37].

Experimental Validation of One NBS Gene in Citrus Genomes

We validated the orthologs of a conserved NB gene, Cs1g09350.1, in a wide range of Citrus species. Cs1g09350.1 conserved in the 3 sequenced Citrus genomes. It is a CNL NBS gene and has 5 exons with about 4 kb in length. We designed the primers targeting about 3.5 kb fragment and could amplify a 3.5 kb fragment using PCR in different Citrus species, including C. sinensis (sweet orange), C. clementina (clementine), C. japonica (kumquat), C. sinensis Navelina (navel orange), C. maxima (pomelo), C. aurantiifolia (lime), and C. aurantium (sour orange). The orthologs from C. sinensis and C. clementina were identical as expected. There are a few mutations in the orthologs of C. japonica, C. sinensis Navelina, and C. maxima, but the orthologs of C. aurantiifolia and C. aurantium should be undergoing a pseudogenization process. There was a deletion plus several mutations in the NBS domain in C. aurantiifolia. There was an eight-base deletion in the LRR domain in C. aurantiifolia and C. aurantium. Most C. aurantiifolia mutations were shared with C. aurantium (S11 Fig.), and these mutations were not shared with other species. The results suggest that in C. aurantiifolia and C. aurantium, this gene is likely derived from the same common ancestor and was inherited as a pseudogene.

Similar NBS Genes in Hybrid Citrus sinensis and Original Citrus clementina Genome

After carefully reannotating the Citrus genome sequences, we found similar numbers of NBS genes in C. clementina and C. sinensis China. There are slightly fewer NBS genes in C. sinensis USA, possibly due to the more fragmented assembly of this genome. In phylogenetic tree using NBS domains, the NBS genes from three different Citrus genomes are spread across clades. After partitioning NBS genes on the tree into clades, we found that 97.7% of the clades containing at least three genes had members from each of three Citrus genomes. This pattern suggests that these three Citrus genomes have similar types of NBS genes derived from common ancestors. Because C. sinensis is the hybrid of C. reticulata (mandarin) and C. maxima (pomelo), it should be heterozygous and some of NBS genes in C. sinensis are expected have different genetic distances from NBS genes in C. clementina. This would support previous observations of NBS genes in F1 progeny of Poncirus trifoliata (trifoliate orange) and Citrus reticulata (tangerine). However, this is clearly not the case.

Furthermore, we mapped the re-sequenced reads of three C. maxima (pomelo) genomes and three C. reticulata (Mandarin orange) genomes onto the genome of C. sinensis China. In this case, 62% of C. sinensis China NBS genes have a copy present in all six resequenced genomes and 99% of C. sinensis China NBS genes have a copy in at least one of the re-sequenced genomes. The mapping results confirmed that a significant percentage of NBS genes of hybrid C. sinensis genomes have corresponding homologous genes in both the C. maxima and the C. reticulata genomes. Because the reference genome sequence of C. maxima is not yet available, the total number of NBS genes in C. maxima genomes is still unknown. However, we can at least conclude from the mapping of re-sequenced genomes that the C. maxima genome has homologous copies of NBS genes in C. reticulata and C. sinensis genomes. The homologous NBS genes in C. maxima and C. reticulata may be the reason that NBS genes in their hybrid C. sinensis are similar to those in C. clementina in this study.

Three Groups of Citrus NBS Genes

We identified 442, 393 and 264 genes with full length NBS domains from C. clementina, C. sinensis China and C. sinensis USA reference genomes, respectively. There are also many genes with short NBS domains in three Citrus genomes. The Citrus NBS genes can be divided into three groups according to the phylogenetic tree of NBS domains: two of them without TIR domain (CC1 and CC2 groups) and the other group with TIR domain (TIR group). The number of non-TIR NBS genes is three times of the number of TIR NBS genes. In most of the TIR NBS genes, we can find the LRR domains defined in Pfam database [47]. We only can identify LRR domains in small part of non-TIR NBS genes using Pfam LRR domain definition. However, we can find the LxxLs repeats in most of the non-TIR NBS genes as shown in motifs from MEME. This implied that there may be other types of LRR domain in Citrus non-TIR NBS genes.

Our motif analyses also showed that motifs of TIR domains in Citrus TIR NBS genes are similar to those of TIR domains in Arabidopsis [6] and Populus trichocarpa [44] TIR NBS genes. Furthermore, the motifs of Citrus CC domains in CC1 NBS genes are similar to those motifs of CC domains in Arabidopsis CC NBS genes and the motifs of Citrus CC domains in Citrus CC2 NBS genes are similar to those motifs of CC domains in japonica rice CC NBS genes [45]. The different structure of motifs in NBS domain and CC domain between Citrus CC1 NBS genes and Citrus CC2 NBS genes suggested that they are likely from separate evolutionary origins.

To further confirm the three groups of NBS genes, we identified the NBS genes from Arabidopsis, Populus, Oryza sativa and grape. We used the same criteria to select the NBS domains from NBS genes of these genomes. Finally, we selected 152, 216, 209, 126 NBS domains from Arabidopsis, Populus, Oryza sativa and grape, respectively. Then, together with 442 NBS domains selected from C. clementina, we constructed a phylogenetic tree of those 1145 NBS domain sequences from five genomes. As shown in Fig. 6, the un-rooted phylogenetic tree was divided into three main branches. The Populus, grape and Citrus genomes have significant amount of NBS genes in all three branches. However, the NBS genes of Oryza sativa dominated in CC2 branch and most of Arabidopsis NBS genes located in CC1 and TIR branches. Our study showed that the NBS genes can be divided into three major groups as the non-TIR NBS genes are separated into two groups. The three groups of NBS genes underwent divergent evolution in different genomes. Further comparison of NBS genes of more genomes may help to understand the evolution of NBS genes and will help elucidate how plants maintain and adapt their defense system against pathogens.

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Fig 6. The maximum likelihood phylogenetic tree of NBS genes of C. clementina, Arabidopsis thaliana, Populus trichocarpa, Oryza sativa and V. vinifera (grape).

Species are indicated by the color of the outer circle and branches. Nodes with bootstrap support of 100 are indicated with grey circles on the tree.

https://doi.org/10.1371/journal.pone.0121893.g006

Highly Clustering of Citrus NBS Genes

The Citrus NBS genes are highly clustered in the genome. 84.9% of NBS genes in C. clementina and 76.9% of NBS genes in C. sinensis China were found in clusters. Previous studies showed 76% of rice [48], 64% of A. lyrata and 71% A. thaliana [13], 83.2% of grapevine and 67.5% of poplar [9] NBS genes are found in clusters. The percentage of Citrus NBS genes in clusters is in the high level comparing to other genomes. The average number of genes per clusters is 4.86 in C. clementina and 3.97 in C. sinensis China. These numbers are similar to those in other genomes [9]. Furthermore, most Citrus NBS genes in the same cluster belong to the same phylogenetic group, suggesting that tandem duplication is the primary mechanism for the expansion of NBS genes in the Citrus genus.

Molecular Evolution of Citrus NBS Genes

Similar to NBS genes in other genomes, Citrus NBS genes are highly dynamic and are shaped by several evolutionary processes leading to several differences amongst NBS genes, including domain presence and mutation constraints and genome organization. Our results revealed multiple molecular evolution events amongst Citrus NBS genes including gene duplications, gene conversions, mutation constraint changes, recombination and transposable element insertions. Likely these events support a birth-and-death process leading to the origins of new NBS genes as well as nonfunctionalization and total loss of other NBS genes [12]. We found more than 200 tandem duplications in both C. clementina and C. sinensis China genomes alone. We also found that NBS genes become pseudogenes following original frame-shift mutations leading to mutation accumulations plus disruption of gene constraint leading to loss of function through transposable element insertions.

Most molecular evolutionary events occurred within NBS gene groups, suggesting that gene birth-death processes have been occurring since divergence from a common ancestral gene copy. Interestingly, the molecular evolution processes occurred differently amongst NBS gene groups and differently within each Citrus genome. For example, the number of gene conversion events in C. sinensis China TIR clusters is almost double than that in C. clementina TIR clusters, while there are many more conversion events in C. clementina CC2 clusters than in C. sinensis China CC2 clusters (Table 4). Numbers of tandem duplications in CC1 and CC2 groups are much greater than that from the TIR group.