In total, 12,815 repeat elements were identified in the genome (Table S2 in Additional file 2). In general, the relatively low repeat content of the P. ultimum genome (approximately 7% by length) is similar to what would be expected for small, rapidly reproducing eukaryotic organisms 4243. While the repeat content is much lower than that of the oomycete Ph. infestans 28, the difference is likely due to the presence of DNA methylases identified by protein domain analyses in the P. ultimum genome, which have been shown to inhibit repeat expansion 44. Interestingly, the oomycete Ph. infestans lacks DNA methylase genes, the absence of which is believed to contribute to repeat element expansion within that organism, with repeats making up > 50% of the genome 272845.

The P. ultimum DAOM BR144 mitochondrial genome is 59,689 bp and contains a large inverted repeat (21,950 bp) that is separated by small (2,711 bp) and large (13,078 bp) unique regions (Figure S1 in Additional file 3). The P. ultimum DAOM BR144 mitochondrion encodes the same suite of protein coding (35), rRNA (2), and tRNA (encoding 19 amino acids) genes present in other oomycetes such as Phytophthora and Saprolegnia 464748. However, the number of copies is different due to the large inverted repeat as well as some putative ORFs that are unique to P. ultimum (Additional file 1). No insertions of the mitochondrial genome into the nuclear genome were identified.

Several families involved in proteolysis were over-represented in P. ultimum compared to Phytophthora spp. (Table 1). This is primarily due to a massive expansion of subtilisin-related proteases (PTHR10795) in P. ultimum following the divergence from ancestors of Phytophthora. With regard to the total complement of serine proteases, the subtilisin family expansion in P. ultimum is somewhat counterbalanced by the trypsin-related serine protease family, which has undergone more gene duplication events in the Phytophthora lineage than the Pythium lineage. The metalloprotease M12 (neprolysin-related) family has also undergone multiple expansions, from one copy in the stramenopile most recent common ancestor, to three in the oomycete most recent common ancestor (and extant Phytophthora), then up to 12 in P. ultimum (data not shown).

E3 ligases are responsible for substrate specificity of ubiquitination and subsequent proteolysis, and secreted E3 ligases have been shown to act as effectors for pathogens by targeting host response proteins for degradation 5152. The HECT E3 family of ubiquitin-protein ligases (PTHR11254) apparently underwent at least two major expansions, one in the oomycete lineage after the divergence from diatoms and another in the P. ultimum lineage (Figure S2 in Additional file 3; Table 1). Most of the expansion in the P. ultimum lineage appears to be derived from repeated duplication of only two genes that were present in the Pythium-Phytophthora common ancestor. This expanded subfamily is apparently orthologous to the UPL1 and UPL2 genes from A. thaliana. Of the 56 predicted HECT E3 ligases in the P. ultimum genome (that had long enough sequences for phylogenetic analysis), 16 are predicted by SignalP 53 to have bona fide signal peptides, and another 10 have predicted signal anchors, a substantially larger number than reported for other oomycete genomes 54.

Several gene families are significantly under-represented in the P. ultimum genome compared to Phytophthora (Table 1) and it appears that these are mostly due to expansions in the Phytophthora lineage rather than losses in the Pythium lineage, though the relatively long distance to the diatom outgroup makes this somewhat uncertain. These include the aquaporin family (PTHR19139), the phospholipase D family (PTHR18896; Additional file 1), four families/subfamilies of intracellular serine-threonine protein kinases, and three families involved in sulfur metabolism (sulfatases (PTHR10342), cysteine desulfurylases (PTHR11601) and sulfate transporters (PTHR11814)).

As oomycete plant pathogens secrete a variety of proteins to manipulate plant processes 3055, we predicted and characterized in detail the soluble secreted proteins of P. ultimum. The secretome of P. ultimum was identified by predicting secreted proteins using the PexFinder algorithm 56 in conjunction with the TribeMCL protein family clustering algorithm. The P. ultimum secretome is composed of 747 proteins (4.9% of the proteome) that can be clustered into 195 families (each family contains at least 2 sequences) and 127 singletons (Table S3 in Additional file 2; selected families are shown in Figure S3 in Additional file 3). Of these, two families and one singleton encode transposable-element-related proteins that were missed in the repeat masking process. The largest family contains 77 members, mostly ankyrin repeat containing proteins, of which only 3 were predicted to have a signal peptide. Notable families of secreted proteins include protease inhibitors (serine and cysteine), NPP1-like proteins (toxins), cellulose-binding elicitor lectin (CBEL)-like proteins with carbohydrate binding domains, elicitins and elicitin-like proteins, secreted E3 ubiquitin ligases (candidate effectors), cell-wall degrading enzymes, lipases, phospholipases, potential adhesion proteins, highly expanded families of proteases and cytochrome P450 (Table 2), and several families of 'unknown' function. A subset (88 proteins) of the secretome showed exclusive similarity to fungal sequences yet are absent in other eukaryotes (Table S4 in Additional file 2; see Table S1 in 57 for a list of organisms). These may represent shared pathogenicity proteins for filamentous plant pathogens, such as peroxidases (Family 68), CBEL-like proteins (Family 8), and various cell wall degrading enzymes and other hydrolases.

Many plant pathogens, especially biotrophic and hemi-biotrophic ones, produce effector proteins that either enter into host cells or are predicted to do so 275859. The genomes of Ph. sojae, Ph. ramorum and Ph. infestans encode large numbers (370 to 550) of potential effector proteins that contain an amino-terminal cell-entry domain with the motifs RXLR and dEER 2829, which mediate entry of these proteins into host cells in the absence of pathogen-encoded machinery 6061. RXLR-dEER effectors are thought, and in a few cases shown, to suppress host defense responses, but a subset of these effectors can be recognized by plant immune receptors resulting in programmed cell death and disease resistance. To search for RXLR effectors in the genome of P. ultimum, we translated all six frames of the genome sequence to identify all possible small proteins, exclusive of splicing. Among these, a total of 7,128 translations were found to contain an amino-terminal signal peptide based on SignalP prediction. We then used the RXLR-dEER Hidden Markov Model (HMM) 29 to search the translations for candidate effectors and, as a control, the same set of translations following permutation of their sequences downstream of the signal peptide (Figure 1a). Only 35 sequences with significant scores were found in the non-permuted set while an average of 5 were found in 100 different permuted sets. In comparison to the Ph. ramorum secretome, 300 hits were found without permutation. Examination of the 35 significant sequences revealed that most were members of a secreted proteinase family 62 in which the RXLR motif was part of a conserved subtilisin-like serine protease domain of 300 amino acids in length, and thus unlikely to be acting as a cell entry motif. A string search was then performed for the RXLR motif within the amino terminus of each translation, 30 to 150 residues from the signal peptide. In this case, the number of hits was not significantly different between the real sequences and the permuted sequences. The same result was obtained with the strings RXLX and RX[LMFY][HKR] (Figure 1b). HMMs have been defined to identify carboxy-terminal motifs conserved in about 60% of RXLR-dEER effectors 2963. Searching the secretome and the permutated secretome with this HMM also identified no significant numbers of candidate effectors (data not shown). Blast searches with the most conserved Phytophthora effectors likewise produced no hits.

Based on synteny analysis of surrounding genes, a small number of Phytophthora effectors share conserved genomic positions 27. Synteny analysis (see below) was used to identify the corresponding positions in the P. ultimum genome, but no predicted secreted proteins were found in those positions in the P. ultimum genome. A paucity of predicted RXLR effector sequences was reported previously in the transcriptome of P. ultimum 31; the one candidate noted in the transcriptome sequence dataset has proven to be a false positive, matching the negative strand of a conserved transporter gene in the genome sequence. Therefore, we conclude that the P. ultimum genome lacks RXLR effectors that are abundant in other oomycetes, although this analysis does not rule out the possible presence of other kinds of effectors (see below). Nonetheless, the lack of RXLR effectors in P. ultimum is consistent with the absence of gene-for-gene interactions, all known instances of which in Phytophthora spp. involve RXLR effectors with avirulence activities.

In Phytophthora spp. the Crinkler (crn) gene family encodes a large class of secreted proteins that share a conserved amino-terminal LFLAK domain, which has been suggested to mediate host translocation and is followed by a major recombination site that forms the junction between the conserved amino terminus and diverse carboxy-terminal effector domains 28. In sharp contrast to the RXLR effectors, the CRN protein family appears conserved in all plant pathogenic oomycete genomes sequenced to date. BLASTP searches of 16 well-defined amino-terminal domains from Ph. infestans against the P. ultimum predicted proteome identified 18 predicted proteins within P. ultimum (BLAST cutoff of 1 × 10^-10; Table S5 in Additional file 2). Examination of protein alignments revealed considerable conservation of the P. ultimum LFLAK domain. We used P. ultimum CRN sequence alignments to build an HMM and through HMM searches identified two additional predicted proteins with putative LFLAK-like domains. We assessed the distribution of candidate CRN proteins within P. ultimum families and identified six additional candidates in Family 64. Further examination of candidates confirmed the presence of LFLAK-like domains (Table S5 in Additional file 2). Surprisingly, only 2 (approximately 7.5%) of the 26 predicted CRN proteins were annotated as having signal peptides (Table S5 in Additional file 2). Two additional CRNs (PYU1_T003336 and PYU1_T002270) have SignalP v2.0 HMM scores of 0.89 and 0.76, respectively, which although below our stringent cutoff of 0.9 may still suggest potential signal peptides. Several of the remaining genes have incomplete ORFs and gene models, suggesting a high frequency of CRN pseudogenes as previously noted in Ph. infestans 28. All 26 amino-terminal regions were aligned to generate a sequence logo. These analyses revealed a conserved LxLYLAR/K motif that is shared amongst P. ultimum CRN proteins (Figure S4 in Additional file 3) and is followed by a conserved WL motif. The LxLYLAR/K motif is closely related to the F/LxLYLALK motif found in Aphanomyces euteiches 64. Consistent with results obtained in other oomycete genomes, we found that the LxLYLAR/K motif was located between 46 and 64 amino acids after the methionine, followed by a variable domain that ended with a conserved motif at the proposed recombination site (HVLVxxP), reflecting the modular design of CRN proteins in the oomycetes (Figure S4 in Additional file 3). This recombination site, which is characteristic for the DWL domain, was found highly conserved in 11 of the putative P. ultimum CRN genes, consisting of an aliphatic amino acid followed by a conserved histidine, another three aliphatic amino acids, two variable amino acids and a conserved proline. In a phylogenetic analysis, these 11 genes were predominantly placed basal to the validated CRNs from Phytophthora (Figure S5 in Additional file 3). Although the CRN-like genes in Pythium are more divergent than the validated CRNs of Phytophthora (Figure S5 in Additional file 3), both the recombination site and the LxLYLAR/K-motif, which is a modification of the prominent LxLFLAK-motif present in most Phytophthora CRNs, show a significant degree of conservation, highlighting that the CRN family, greatly expanded in Phytophthora 28, had already evolved in the last common ancestor of P. ultimum and Phytophthora.

In the absence of obvious proteins with an amino-terminal RXLR motif, we used other known features of effectors to identify candidate effector families in P. ultimum. Ph. infestans RXLR effectors are not only characterized by a conserved amino-terminal translocation domain but also by their occurrence in gene-sparse regions that are enriched in repetitive DNA 28. Based on the length of the flanking non-coding regions, the distribution of P. ultimum genes is not multimodal as was observed in Ph. infestans (Figure S6 in Additional file 3). However, relative to the rest of the genes, P. ultimum secretome genes more frequently have long flanking non-coding regions (Figure S7 in Additional file 3). In addition, the secretome genes show a higher proportion of closely related paralogs, suggesting recent duplications in P. ultimum (Figure S7 in Additional file 3) and indicating that the secretome genes may have distinct genome organization and evolution as noted in Phytophthora spp. 2857. Using genome organization properties to identify families of secreted proteins in P. ultimum that could correspond to novel effector candidates, we sorted the 194 secretome families based on highest rate of gene duplication, longest flanking non-coding region, and lowest similarity to Ph. infestans proteins (see Figure S8 in Additional file 3 for examples). One relatively large family of secreted proteins, Family 3, stood out because it fulfilled the three criteria and included proteins of unknown function. BlastP similarity searches identified similar sequences only in oomycete species (Phytophthora spp. and A. euteiches). Furthermore, of the 44 family members in P. ultimum for which transcripts could be detected, 32 (73%) were induced more than 2-fold during Arabidopsis infection compared to mycelia, with 5 members induced more than 40-fold. In total, we identified a set of 91 predicted secreted proteins with similarity to Family 3 proteins from the various oomycete species (Additional file 4). Multiple alignments of these proteins, along with motif searches, identified a YxSL[RK] amino acid motif (Figure 1c). This motif is at least two-fold enriched in secreted proteins compared to non-secreted proteins in four oomycete species (Figure 1d). In addition, the YxSL[RK] motif is positionally constrained between positions 61 and 80 in secreted oomycete proteins only (Figure 1d). The 91 YxSL[RK] proteins show a modular organization with a conserved amino-terminal region, containing four conserved motifs, followed by a highly variable carboxy-terminal region (Figure 1c; Figure S9 in Additional file 3) as reported for other oomycete effectors 30. Phylogenetic analyses of the YxSL[RK] family revealed four main clades and suggest an expansion of this family in Phytophthora spp. (Figure 1e).

The YxSL[RK] motif appears to be a signature for a novel family of secreted oomycete proteins that may function as effectors. It is intriguing that the YxSL[RK] motif shares some similarity in sequence and position with the canonical RXLR motif, a resemblance increased by the fact that the variable amino acid is a basic amino acid (lysine) in 28 out of the 91 family members. Whether the YxSL[RK] motif defines a host-translocation domain as noted for RXLR effectors remains to be determined.

Detection of pathogens through the perception of PAMPs/MAMPs leads to the induction of plant immune responses (for review, see 50). Oomycetes produce various and specific molecules able to induce defense responses like elicitins (for review, see 65), but only two oomycete cell-surface proteins containing a MAMP have been characterized: a transglutaminase 66 and a protein named CBEL 67. Genes encoding both of these cell-surface proteins were detected in P. ultimum (Additional file 1), suggesting that P. ultimum produces typical oomycete MAMPs, which can be efficiently perceived by a wide range of plant species. The occurrence of PAMPs/MAMPs in P. ultimum suggests that this pathogen must have evolved mechanisms to evade PAMP-triggered immunity. This could occur through a necrotrophic mechanism of infection or using the candidate effector proteins described above.

A total of 180 candidate glycoside hydrolases (GHs) were identified in P. ultimum using the CAZy annotation pipeline 68. This number is apparently similar to those reported previously for Ph. ramorum (173), Ph. sojae (190), and Ph. infestans (157) 2728. However, when the CAZy annotation pipeline was applied to Ph. sojae, Ph. ramorum and Ph. infestans, 301, 258 and 277 GHs were found, respectively, nearly twice the number present in P. ultimum (Table 2). Among these we identified putative cellulases belonging to families GH5, GH6 and GH7. All six GH6 candidate cellulases harbor secretion signals. Only one GH6 protein contains a CBEL domain at the carboxyl terminus. Three contain a transmembrane domain and one contains a glycosylphosphatidylinisotol anchor, features suggesting that these proteins may be targeting the oomycete cell wall rather than plant cell walls. The P. ultimum strain studied here could not grow when cellulose was the sole carbon source (Table 3; Figure S10 in Additional file 3).

Cutinases are a particular set of esterases (CAZy family CE5) that cleave cutin, a polyester composed of hydroxy and hydroxyepoxy fatty acids that protects aerial plant organs. No candidate cutinases could be found in the P. ultimum genome. Cutinase activity was reported in culture filtrates of P. ultimum, but its growth was not supported on apple cutin 69 and low levels of fatty acid esterase were detected in P. ultimum only in 21-day-old culture 70. The absence of recognizable cutinases suggests these enzymes are not critical for penetration and infection by P. ultimum, which attacks young, non-suberized roots and penetrates tissues indirectly through wounds. This contrasts with the number of putative cutinases identified in several Phytophthora spp. 27717273, which presumably promote penetration of leaf and stem tissues that are protected by a thick cuticle or colonization of heavily suberized root and bark tissue.

The xylan degrading capacity of P. ultimum appears to be limited, if not totally absent. No members of the GH10 and GH11 families encoding endoxylanases essential for xylan degradation could be found. Furthermore, families involved in the removal of xylan side chains or modifications such as GH67, CE3, and CE5 are absent while families CE1 and CE2 contain only a limited number of members. The lack of significant xylan digestion was confirmed by the absence of growth when xylan was used as a carbon source (Table 3; Figure S10 in Additional file 3), consistent with previous work on P. ultimum and other Pythium spp. 70.

Pectinases play a key role in infection by Pythium spp. 74. Twenty-nine candidate pectin/pectate lyases (PL1, PL3 and PL4 families) are present in P. ultimum while the genomes of Phytophthora spp. 2728 encode even larger PL families (Table 2). In P. ultimum, the set of pectin lyases is complemented by 11 pectin hydrolases from family GH28, several of which having been functionally characterized in various Phytophthora spp. 75767778. P. ultimum lacks pectin methylesterases as well as genes encoding family GH88 and GH105 enzymes and therefore cannot fully saccharify the products of pectin/pectate lyases, consistent with previous reports of incomplete pectin degradation and little or no galacturonic acid production during P. ultimum infection of bentgrass 79. The data from the carbon source utilization experiment (Table 3; Figure S10 in Additional file 3) show only limited growth on medium with citrus pectin as the sole carbon source.

We also observed that the P. ultimum genome encodes candidate GH13 α-amylases, GH15 glucoamylase and a GH32 invertase, suggesting that plant starch and sucrose are targeted. The growth data confirm these observations, with excellent growth on soluble starch and sucrose (Figure S10 in Additional file 3).

The CAZy database also contains enzymes involved in fungal cell wall synthesis and remodeling. Cell walls of oomycetes differ markedly from cell walls of Fungi and consist mainly of glucans containing β-1,3 and β-1,6 linkages and cellulose 808182. The P. ultimum genome encodes four cellulose synthases closely related to their orthologs described for Ph. infestans 82. The genome also specifies a large number of enzyme activities that may be involved in the metabolism of β-1,3- and β-1,6-glucans (Additional file 1), as well as a large set of candidate β-1,3-glucan synthases likely involved in synthesis of cell wall β-glucans and in the metabolism of mycolaminaran, the main carbon storage compound in Phytophthora and Pythium spp. 818384.

P. ultimum does not typically exhibit release of zoospores from sporangia in culture 12 but zoospore release directly from aged oospores has been reported 95. Comparative genomics with well studied whiplash flagellar proteins from the green algae Chlamydomonas reinhardtii and other model organisms indicates that indeed P. ultimum does have the necessary genetic complement for flagella. Orthologs of tinsel flagellar mastigoneme proteins have also been identified in P. ultimum through comparison to those studied in Ochromonas danica, a unicellular member of the Straminipila kingdom. Overall, approximately 100 putative whiplash and tinsel flagellum gene orthologs were identified in P. ultimum (Table S7 in Additional file 2) with corresponding orthologs present in Ph. infestans, Ph. sojae, and Ph. ramorum. Expression of flagellar orthologs was observed in 8 growth conditions used in whole transcriptome sequencing, although 14 putative flagellar orthologs for axonemal dynein and kinesin and intraflagellar transport did not show expression in any condition.

Perhaps the most remarkable discovery relative to gene family expansion is that there are four P. ultimum genes that encode cadherins. Previously, members of this gene family have only been found in metazoan genomes (and the one fully sequenced genome from the clade of nearest relatives, the choanoflagellate Monosiga brevicollis). Cadherins are cell adhesion proteins that presumably evolved at the base of the clade containing metazoans and choanoflagellates 96. Cadherin-related proteins are encoded in several bacterial genomes, but these bacterial proteins lack important calcium ion-binding motifs (the LDRE and DxND motifs) found in the extracellular (EC) repeat domains of 'true' cadherins 97. The cadherin genes in P. ultimum do contain these motifs, and this is therefore the first report of true cadherins in a genome outside the metazoans/choanoflagellates. In metazoans, but not in choanoflagellates, some cadherins also contain an intracellular catenin-binding domain (CBD) that connects intercellular binding via EC domains to intracellular responses such as cytoskeletal changes. A search of predicted gene models with the PANTHER HMMs for cadherins (PTHR10596) identified two genes containing cadherin EC domains in the Ph. infestans genome, but none in the Ph. ramorum, Ph. sojae and Phaeodactylum tricornutum genomes. The identification of cadherin EC domains in both P. ultimum and Ph. infestans led us to postulate that such genes may also exist in other Phytophthora genomes that were not found in the original analysis of these genomes. Indeed, a TBLASTN search of genomic DNA using the predicted P. ultimum cadherin domain-containing proteins identified one putative cadherin-containing ORF in the Ph. sojae genome and four in the Ph. ramorum genome. The P. ultimum cadherin genes contain between 2 and 17 full-length cadherin EC domains, as predicted by the Pfam database 98 at the recommended statistical significance threshold, and likely a number of additional cadherin domains that have been truncated and/or have diverged past this similarity threshold. The genes from the Phytophthora genomes each contain between one and seven intact cadherin EC domains, though we did not attempt to construct accurate gene models for the Phytophthora genes. None of the oomycete cadherins appear to have the catenin-binding domain, nor do these genomes appear to encode a β-catenin gene, so like in M. brevicollis, the β-catenin-initiated part of the classical metazoan cadherin pathway appears to be absent from oomycetes.

In order to explore the evolution of these domains in the oomycetes, we performed a phylogenetic analysis. The first (amino-terminal) cadherin EC domain has been used to explore gene phylogeny among the cadherins 9699, and to facilitate comparison we used both neighbor joining 100 and maximum likelihood (using the PhyML program 101102) to estimate a phylogenetic tree for these same sequences together with all of the intact cadherin domains from the P. ultimum and Ph. infestans genomes (Figure 2). To generate a high-quality protein sequence alignment for phylogeny estimation, we used the manual alignment of Nollet et al. 99 as a 'seed' for alignment of other sequences using MAFFT 102. We found that all of the oomycete domains fall within a single clade. However, this clade is broad and also contains several cadherins from the choanoflagellate M. brevicollis, as well as some of the more divergent metazoan cadherins (Cr-2 and Cr-3 subfamilies). In general, the branches in this clade are very long, making phylogenetic reconstruction somewhat unreliable (all branches with bootstrap values > 50% are marked with a circle in Figure 2). Nevertheless, most of the cadherin domains found in P. ultimum are reliably orthologous to domains in one or more Phytophthora species, suggesting descent from a common ancestor by speciation. The most notable example is for the genes PITG_09983 and PYU1_T011030, in which a region spanning three consecutive EC repeats appears to have been inherited by both species from that common ancestor (apparently followed by substantial duplication and rearrangement of individual cadherin domains). These repeats are also apparently orthologous to repeats in both Ph. sojae and Ph. ramorum. The oomycete cadherins may have been initially obtained either vertically (by descent from the common ancestor with metazoans) or horizontally (by transfer of metazoan DNA long after divergence). No cadherins have been found in genomes sequenced from other clades more closely related to either oomycetes (for example, diatoms and alveolates) or the metazoan/choanoflagellates (for example, Fungi and amoebozoa). This means that, if cadherins were present in the most recent common ancestor of oomycetes and metazoans, these genes must have been lost independently in all of these other diverging lineages. Given the data currently available, it is more probable that at least one horizontal cadherin gene transfer event occurred from a choanoflagellate or metazoan to an oomycete ancestor, prior to the divergence of Pythium from Phytophthora. The source of the metazoan DNA may have been a host of the ancestral oomycete, or possibly introduced by a virus. Nevertheless, the subsequent preservation of cadherin domains in at least two lineages of oomycetes over a substantial period of time suggests that the genes are likely to perform an important function, which remains to be explored.

A phylogenetic approach (PHRINGE 103) was used to identify P. ultimum proteins orthologous to proteins encoded in the genomes of Ph. infestans, Ph. sojae, and Ph. ramorum. Of the 15,322 proteins predicted from the P. ultimum genome sequence, 12,230 were identified as orthologous to a protein in at least one Phytophthora genome sequence. A total of 11,331 proteins were identified as orthologs common to all three Phytophthora spp., and of these, 8,504 had identifiable orthologs in P. ultimum. PHRINGE was also used to examine the conservation of gene order (synteny) between the Phytophthora and P. ultimum genomes. As previously described 27, the gene order of orthologs is very highly conserved among Phytophthora spp. In P. ultimum the ortholog content was very similar between broad regions of the P. ultimum and Phytophthora genomes, but the local gene order was greatly rearranged, primarily as a result of inversions. Only short runs of up to 10 orthologs were found to be collinear, whereas runs of more than 100 could be identified between the Phytophthora spp. Figure 3 shows an example spanning a well-assembled region of the Ph. infestans, Ph. ramorum and P. ultimum genome sequences. In Ph. ramorum, the region spans 1.18 Mb and 383 predicted genes and in P. ultimum the region spans 1.15 Mb and 435 predicted genes. Of these genes, 286 are identified as orthologs. In the Ph. ramorum sequence there are an additional 38 genes with orthologs in Ph. infestans but not in P. ultimum. Due to a much larger number of repeat sequences, and expanded gene numbers, the corresponding region in Ph. infestans spans 2.38 Mb and 499 predicted genes, but the order of the orthologous genes is highly conserved with that of Ph. ramorum. The Ph. sojae genome shows similar conservation of gene order in this region but for simplicity is not shown.