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RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements Abstract The fungal pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a prominent pathogen of wheat. The reference genome of the isolate IPO323 is one of the best-assembled eukaryotic genomes and encodes more than 10,000 predicted genes. However, a large proportion of the previously annotated gene models are incomplete, with either no start or no stop codons. The availability of RNA-seq data allows better predictions of gene structure. We here used two different RNA-seq datasets, de novo transcriptome assemblies, homology-based comparisons, and trained ab initio gene callers to generate a new gene annotation of Z. tritici IPO323. The annotation pipeline was also applied to re-sequenced genomes of three closely related species of Z. tritici: Z. pseudotritici, Z. ardabiliae, and Z. brevis. Comparative analyses of the predicted gene models using the four Zymoseptoria species revealed sets of species-specific orphan genes enriched with putative pathogenicity-related genes encoding small secreted proteins that may play essential roles in virulence and host specificity. De novo repeat identification allowed us to show that few families of transposable elements are shared between Zymoseptoria species while we observe many species-specific invasions and expansions. The annotation data presented here provide a high-quality resource for future studies of Z. tritici and its sister species and provide detailed insight into gene and genome evolution of fungal plant pathogens. The genus Zymoseptoria (class Dothideomycetes, order Capnodiales) comprises a group of plant pathogens that infect a variety of Poaceae species. The four pathogen species Z. tritici, Z. pseudotritici, Z. ardabiliae, and Z. brevis originated in the Middle East and have diverged recently (within the past ∼22,000 years) (Stukenbrock et al. 2007). Speciation in the genus Zymoseptoria has been associated with specialization and adaptation to different hosts in different environments (Quaedvlieg et al. 2011; Stukenbrock et al. 2011). Most notably, Z. tritici co-evolved and spread with domesticated Triticum species and is today a prominent pathogen of wheat worldwide (Banke and McDonald 2005). The poorly described Z. brevis species (Quaedvlieg et al. 2011) was isolated in Iran like Z. pseudotritici and Z. ardabiliae, but from another grass host, Phalaris minor. Phylogenetic analyses based on information from six DNA loci place Z. brevis next to Z. pseudotritici, suggesting that this species also shares recent common ancestry with the wheat pathogen (Stukenbrock et al. 2012). The close relatedness of the four Zymoseptoria species makes this a unique model system to study host specialization and speciation of fungal plant pathogens. The genome of Z. tritici (isolate IPO323) was sequenced and annotated by the Joint Genome Institute (JGI) and provides one of the best-assembled eukaryotic genomes with 21 complete chromosomes sequenced from telomere to telomere (Goodwin et al. 2011). Of the 21 chromosomes, eight are considered accessory chromosomes because they can be lost during meiosis without any apparent effect on fitness in sexual progenies (Wittenberg et al. 2009). The functional relevance of these accessory chromosomes is so far not known. They contain a higher proportion of repetitive DNA, encode fewer genes (Goodwin et al. 2011), and show a dramatically lower level of transcription compared to the core chromosomes (Kellner et al. 2014). The previously generated annotation predicted more than 10,000 genes in the genome of IPO323. The pipeline applied for the annotation used several gene predictors including putative full-length genes from EST cluster consensus sequences (Goodwin et al. 2011). Nevertheless, this gene annotation comprises many incomplete gene models (14%) without start and/or stop codons. Different aspects of genome evolution in Z. tritici have been studied using comparative analyses of different Zymoseptoria genomes (Stukenbrock et al. 2010, 2011). A comparative genome study of the reference isolate IPO323 and an isolate of Z. pseudotritici allowed a detailed analysis of genome divergence in coding and noncoding sequences and a comparison of chromosome content and synteny in the two species (Stukenbrock et al. 2010). Multiple genomes were analyzed in a comparative population genomic analysis including Z. tritici, Z. pseudotritici, and Z. ardabiliae to further assess signatures of positive selection and the speciation history of the three species (Stukenbrock et al. 2011). Both studies relied on the previously generated annotation of the Z. tritici reference isolate IPO323, and thereby only described evolution of gene content shared between species. Repeats have also been identified in the reference genome of Z. tritici (Dhillon et al. 2010; Goodwin et al. 2011; Ohm et al. 2012), but they were only exhaustively classified into transposable element (TE) families recently (Dhillon et al. 2014). In fungal genomes, as in many eukaryotic genomes, TEs can constitute a large fraction of the genome, e.g., 40% of the Pseudocercospora fijiensis genome (Ohm et al. 2012) and 64% of the Blumeria graminis genome (Spanu et al. 2010). TEs play an important role in the evolution of genomes, and in fungi they are shown to be responsible for large genomic rearrangements (Croll et al. 2013; de Jonge et al. 2013; Grandaubert et al. 2014) and for the creation of highly dynamic regions that provide accelerated diversification and chromatin-based regulation for genes within or near these regions (Rouxel et al. 2011; Soyer et al. 2014). An in-depth characterization of the complete TE repertoire of the four known Zymoseptoria species would allow detailed insights into the impact of repetitive DNA on the evolution of core as well as accessory chromosomes in these pathogens. We set out to conduct a thorough annotation of protein-encoding genes and repetitive sequences in all four Zymoseptoria species. Our goal was to improve the existing annotation of Z. tritici and to generate a complete set of gene models and repeat families for the four Zymoseptoria species for comparative genome analyses. All predicted gene models were in silico functionally annotated. We particularly focused on the presence and distribution of small proteins with signal peptides because these could be effector proteins produced to overcome host immune defenses (de Jonge et al. 2011). To characterize a set of core Zymoseptoria genes and to identify species-specific orphan genes, we conducted a detailed analyses of gene homologies. Furthermore, we addressed the distribution of TEs in the Zymoseptoria genomes with a particular focus on TE content of core and accessory chromosomes of Z. tritici and the distribution of TE families between the four Zymoseptoria species. The dataset presented here provides not only a new high-quality annotation of Z. tritici but also a detailed characterization of gene families among Z. tritici, Z. pseudotritici, Z. ardabiliae, and Z. brevis. Materials and Methods Genome data For the gene annotation, the genomes of Z. tritici (isolate IPO323) (Goodwin et al. 2011), Z. pseudotritici (isolate ST04IR_2.2.1), and Z. ardabiliae (isolate ST04IR_1.1.1) (Stukenbrock et al. 2011) were used. For the annotation of Z. brevis, the genome of the isolate Zb18110 was sequenced. Genomic DNA was isolated using a standard phenol-chloroform protocol (Sambrook and Russell 2001), and sequencing of 100-bp paired-end reads was performed using a HiSeq2000 Illumina platform (AROS Applied Biotechnology, Denmark). A de novo assembly of the Z. brevis Illumina reads was generated using the CLC Genomics Workbench version 5 (CLC, Aarhus, Denmark) with standard settings for paired-end read assembly. This assembly is available under the NCBI BioProject (PRJNA273516) on Genbank. The assembled genomes of Z. pseudotritici, Z. ardabiliae (Stukenbrock et al. 2011), and Z. brevis used for the gene annotation contained a very low number of repetitive DNA. Therefore, new assemblies better representing the repeat content of these species genomes were constructed using Illumina sequences obtained from the isolates Z. pseudotritici ST04IR_5.5, Z. ardabiliae ST11IR_6.1.1, and Z. brevis Zb163. Assemblies of these new Illumina genomes were generated using SOAPdenovo2 (Luo et al. 2012) with optimized k-mer values allowing the inclusion of repeats in the assemblies. These three assemblies are available under the NCBI BioProject (PRJNA274679) on Genbank. RNA-seq data Two previously published RNA-seq datasets were used for de novo transcript assembly of Z. tritici IPO323 including one dataset obtained from RNA extracted from infected Triticum aestivum (cultivar Obelisk) seedlings and one dataset obtained from axenically grown fungal cells (Kellner et al. 2014). For Z. pseudotritici, Z. ardabiliae, and Z. brevis, RNA-seq data were obtained from axenically grown cultures. Total RNA was extracted from fungal cells grown in YMS (4 g yeast extract, 4 g malt extract, 4 g sucrose, 20 g bacto agar, 1 liter H2O) agar in a shaking incubator at 200 rpm at 18° using the TRIZOL reagent (Invitrogen, Darmstadt, Germany) following the protocol of the manufacturer. Illumina RNA-seq libraries for two axenic culture replicates per species were prepared from an input of 10 µg total purified polyA RNA (Palma-Guerrero et al. 2013). Libraries were quantified by fluorometry, immobilized, and processed onto a flow cell with a cBot (Illumina), followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq2000 at the Max Planck Genome Center (Cologne, Germany). RNA-seq data for Z. pseudotritici, Z. ardabiliae, and Z. brevis are respectively available in the NCBI BioProjects (PRJNA277173, PRJNA277174, PRJNA277175). For data processing, the sequence read quality was first evaluated using FASTQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Subsequently, reads were filtered using tools from the Galaxy server, including grooming, trimming, filtering, and masking steps (Giardine et al. 2005). Reads with an overall quality score less than 20 were removed. For the remaining reads, all nucleotides with a quality score less than 20 were masked with Ns. For Z. tritici, reads from the host (T. aestivum) transcriptome were initially filtered out using fastq_screen v0.4.1 (www.bioinformatics.babraham.ac.uk/projects/fastq_screen) as described by Kellner et al. (2014). Gene annotation Protein-coding genes were identified using the Fungal Genome Annotation pipeline described by Haas et al. (2011). The individual steps of the pipeline are described below. Transcript reconstruction: Transcript reconstruction using Trinity (Grabherr et al. 2011; Haas et al. 2013) was carried using de novo and genome-guided methods. By the de novo method, RNA-seq reads were first assembled into unique sequences of transcripts (contigs) using the Inchworm module within Trinity. Contigs were clustered by the Chrysalis module, and corresponding De Bruijn graphs that represent the possible different isoforms were constructed. In the final step, De Bruijn graphs were processed by the Butterfly module to produce full-length transcripts. In the genome-guided method, RNA-seq reads were first aligned to the genome using GMAP (Wu and Watanabe 2005). Based on these aligned-read clusters, the Chrysalis and Butterfly modules were consecutively executed to produce the final reconstructed transcripts. Transcripts generated by these two methods were combined using the “Program to Assemble Spliced Alignments” (PASA) (Haas et al. 2003) pipeline to build a complete set of unique transcripts corresponding to gene models. Training: First, GeneMark-ES (Ter-Hovhannisyan et al. 2008) was used for ab initio predictions, because its self-training algorithm allowed the identification of high-quality gene models. Next, evidence from homology searches using tBLASTn (e-value cut-off of 1e-10) (Altschul et al. 1990) against a nonredundant protein database (UniRef90) (Suzek et al. 2007) and from reconstructed transcripts were used to filter the ab initio predicted gene models. Only the complete gene models predicted by GeneMark-ES with a support from the homology-based comparison (100% of coverage for each exon) and with the exact same exon–intron boundaries as in the reconstructed transcripts were selected for the training and testing of ab initio gene predictors. The 2693 selected gene models were divided into two sets: one for the training (training set) containing 1611 sequences (60%) and one for assessing prediction accuracy (test set) containing 1082 sequences (40%). The evaluation of the training process was performed using Augustus (Stanke and Waack 2003). For all species, better performance was obtained using datasets of Z. tritici. We used the Z. tritici training set to train the ab initio gene callers for all the species. Gene prediction and annotation: The trained GeneMark.hmm (Lukashin and Borodovsky 1998) and Augustus programs were used to predict gene models. For Z. tritici, Fgenesh (Salamov and Solovyev 2000) gene models obtained from the first annotation by JGI (Goodwin et al. 2011) were also included. Gene models obtained from the trained gene predictors were evaluated and combined using the EVidenceModeler (EVM) software (Haas et al. 2008) to create a weighted consensus of the gene structures. Weights of 3, 5, and 7 were used for ab initio predictions, homology-based predictions, and transcript evidence, respectively. Homology-based gene models obtained from GeneWise (Birney et al. 2004) were only used for Z. tritici as reliable gene models; they could not be obtained in the much more fragmented genomes of Z. pseudotritici, Z. ardabiliae, and Z. brevis. Based on transcript alignments, the PASA pipeline was used to correct the consensus gene model structure and to resolve conflicts between different isoforms. Gene comparison Based on the four predicted proteomes of the Zymoseptoria species, sequence comparisons were performed with BLASTp (e-value cut-off of 1e-5). Obtained pairwise protein alignments were processed using the software SiLiX to build families of homologous proteins (Miele et al. 2011). Proteins were clustered together into families if they shared at least 55% of sequence identity over at least 60% of sequence coverage. The building of these families was divided in two steps. First, only complete protein sequences were used to create families. Second, using a semi-bipartite graph, partial protein sequences were added to the existing families. Secretome prediction Plant pathogens secrete proteins to interfere with host immune defenses. Genes encoding secreted proteins are therefore of particular interest due to their potential role in infection and host–pathogen interaction. We screened predicted proteins for the presence of signal peptides and categorized proteins as secreted under the following conditions: (i) if a signal peptide was predicted by both Neural-Network and HMM methods by the software SignalP 3.0 (Emanuelsson et al. 2007); (ii) if zero or one transmembrane domain was present in the protein (the domain having at least 30% overlap with the signal peptide) using the software TMHMM 2.0 (Krogh et al. 2001); and (iii) if the protein was predicted to be targeted to the secretory pathway by the software TargetP 1.1 (Emanuelsson et al. 2007). Secreted proteins with a size of 300 amino acids or less were considered as small secreted proteins (SSPs). Functional annotation Automated functional annotations of the predicted proteins of Z. tritici, Z. pseudotritici, Z. ardabiliae, and Z. brevis were performed as previously described by Grandaubert et al. (2014). Using a combination of BLAST and InterProScan (Quevillon et al. 2005), predicted proteins of each of the four species were categorized into three classes. The first class included proteins with no significant BLAST hit and with no known protein domain identified by InterProScan. These proteins were classified as “predicted proteins,” i.e., predictions with no functional support. This class contained an excess of species-specific genes. The second class, termed “hypothetical proteins,” included proteins with at least one domain identified by InterProScan in the InterPro or Pfam databases (Hunter et al. 2012; Coggill et al. 2008) or that fulfilled the BLAST result criteria defined by Grandaubert et al. (2014) and for which the description indicated “hypothetical protein” in more than 90% of the BLAST hits. Globally, this class contained predictions with poor functional evidence likely corresponding to conserved proteins among several organisms but with no defined functions. The third class included predictions that fulfilled the BLAST result conditions with at least one domain from the InterPro or Pfam database corroborating by the consensus BLAST description. This class was termed the “similar to function” and included well-conserved proteins with defined functions in many organisms. Repeats and transposable elements identification Repetitive DNA was identified and annotated in SOAP assembled genomes of the four isolates described above to create a repertoire of repeats specific to the Zymoseptoria genus using the REPET pipeline (Flutre et al. 2011). To obtain more complete elements, repeat families in each species were clustered using Blastclust from the NCBI-BLAST package (Altschul et al. 1990), aligned using Mafft (Katoh and Standley 2013), and new consensuses were then created. These steps were iterated with decreasing values of identity percentage (from 100% to 75%) and coverage (from 100% to 30%) until there was no more clustering of the sequences. Next, the sequences were classified (TEclassifier.py script from REPET) using tBLASTx and BLASTx against the Repbase Update database (Jurka et al. 2005) and by the identification of structural features such as long terminal repeats (LTRs) or terminal inverted repeats (TIRs). The sequences were additionally translated into the six reading frames to perform a protein domain search on the conserved domain database (CDD) (Marchler-Bauer et al. 2011) using RPS-BLAST. Transposable element (TE) families of each strain were classified and named according to the nomenclature defined by Wicker et al. (2007). The 497 repeat families identified in this study are available in FASTA format in Supporting Information, File 1. Results Improved gene annotation of Z. tritici RNA-seq data and detailed homology searches allowed us to generate an improved annotation of gene models in the IPO323 Z. tritici reference genome. Read data obtained from in planta and in vitro experiments were filtered (Table S1) and used for transcriptome assembly. Assemblies were based on two different but complementary approaches: (i) de novo, where the reads were assembled without a reference sequence and (ii) genome-guided, where the IPO323 reference genome was used as a template for transcript assemblies. In total, 68,653 transcripts were generated by the de novo method and 73,127 transcripts by the genome-guided method (Table 1). These transcripts were used to create a final database containing 13,847 putative gene models next used for the generation of a training set for ab initio predictors and for the correction of predicted gene models. We generated a final training set of 1611 gene models that was used to train two ab initio gene predictors: Augustus (Stanke and Waack 2003) and GeneMark-hmm (Lukashin and Borodovsky 1998). The outputs of these software were combined with 10,893 predicted gene models of another ab initio predictor, Fgenesh (Salamov and Solovyev 2000), obtained from the JGI annotation. We thereby obtained a total of 36,423 different gene models combining models from Augustus, GeneMark-hmm, and Fgenesh. These gene models were processed by EVidence Modeler (EVM) (Haas et al. 2008) to identify a consensus model for each gene. Finally, corrections were applied to the gene models using PASA (Haas et al. 2003) and the previously reconstructed RNA-seq-based transcripts. Table 1 Annotation features for the four members of the Zymoseptoria species complex Z. tritici Z. pseudotritici Z. ardabiliae Z. brevis Assembly Assembly size (Mb) 39.7 32.7 31.5 31.9 No. of scaffolds 21 1164 868 6116 Previous annotation New
annotation Transcriptome reconstruction No. of transcripts (de novo) — 68,653 16,056 16,353 17,870 No. of transcripts (genome-guided) — 73,127 19,076 20,193 15,331 No. of gene models — 13,847 12,027 12,719 10,649 Gene annotation No. of predicted gene models 10,952 11,839 11,044 10,787 10,557 No. of complete gene models 9397 11,795 10,957 10,686 10,342 No. of partial gene models 1555 44 87 101 215 No. of gene models with RNA-seq supporta 9423 10,048 7618 8297 9939 Average gene length (bp) 1599.8 1620.9 1594.3 1584.9 1592.8 Average transcript length (bp) 1388.8 1462.1 1459.4 1440.9 1462.5 Average protein length (aa) 436.6 487.8 488.0 482.0 487.5 No. of exons 28,309 30,068 26,699 26,231 25,367 Average exon length (bp) 505.7 575.2 604.7 593.7 608.1 Average no. of exons per gene 2.59 2.54 2.42 2.43 2.40 No. of introns 17,357 18,226 15,653 15,445 14,809 Average intron length (bp) 124.1 91.6 90.9 98.4 94.6 Average no. of introns per gene 2.27 2.27 2.16 2.16 2.16 No. of genes with introns 7654 8044 7234 7165 6883 Gene density (genes/Mb) 276.0 298.3 338.2 330.3 331.1 Functional annotation % of predicted proteins — 22.9 18.8 19.2 18.1 % of hypothetical proteins — 31.3 31.2 31.4 32.8 % of similar to proteins — 45.8 50 49.4 49.1 No. of secreted proteins 970b 874 838 965 700 No. of small secreted proteins (<300 aa) 441b 441 399 540 331 a Based on alignment with reconstructed transcripts (e-value < 1e-5). b Extracted from Morais do Amaral et al. 2012. The final gene annotation of IPO323 consists of 11,839 gene models (Table 1). Distributions of the number of gene models along the chromosomes of the annotation presented here and the previous JGI annotation are shown in Figure S1. In our new annotation, only 44 gene models were incomplete (i.e., without start and/or stop codon) compared to 1555 incomplete genes in the previous annotation (Table 1). To identify shared and unique gene models, we used a BLAST search (e-value cut-off of 1e-10). We found 4707 identical gene models between the two annotations. Furthermore, we found 442 gene models uniquely predicted by the JGI pipeline and 1200 models uniquely predicted by the pipeline used here. Gene models of our annotation have an average length of 1621 bp and exhibit longer exons (mean exon length 575 vs. 505 bp) and encode longer proteins (488 vs. 437 amino acids) when compared to the annotation generated by the JGI pipeline (Table 1). A BLAST comparison at the nucleotide level of our final gene models against the reconstructed transcripts showed that 10,048 out of the 11,839 predicted genes have support based on the RNA sequencing. In the previous annotation, 9423 predicted genes had support compared to the transcripts reconstructed in this study, which underlines the efficiency of this new annotation to predict biologically relevant gene models. In silico functional annotation based on protein signatures and homologies allowed us to assign a function to 43% of the 11,839 predicted proteins. A total of 2714 sequences (22.9%) had no homologies within the NCBI nonredundant protein database and did not include any known protein domain. These represent either species-specific genes of Z. tritici or incorrectly predicted genes. Given the fact that 55% of these have RNA-seq support, we considered that the majority of these novel genes must be correctly predicted. Characterization of the Z. tritici secretome yielded comparable results to the previously reported Z. tritici secretome (Morais Do Amaral et al. 2012), representing 874 secreted proteins including 441 small, secreted proteins (SSPs), i.e., with a size inferior to 300 amino acids (Table 1). SSPs of Z. tritici have, on average, 2.8-times more cysteine residues compared to the whole proteome (data not shown supporting an extracellular role) (Fass 2012). Gene annotation using re-sequenced genomes and RNA-seq data from Z. pseudotritici, Z. ardabiliae, and Z. brevis RNA-sequencing data obtained from axenic cultures of Z. pseudotritici, Z. ardabiliae, and Z. brevis were filtered (Table S1) and assembled. The resulting transcriptomes include 35,132, 36,546, and 33,201 transcripts clustered into 12,027, 12,719, and 11,542 putative gene models for Z. pseudotritici, Z. ardabiliae, and Z. brevis, respectively (Table 1). The training set established for Z. tritici was also for the annotation of the three other Zymoseptoria species. For each species, EVM created a weighted consensus of the gene models, which after PASA corrections resulted in 11,044, 10,787, and 10,557 gene models for Z. pseudotritici, Z. ardabiliae, and Z. brevis, respectively (Table 1). The total number of predicted gene models in the re-sequenced Zymoseptoria species was similar; however, due to the fragmented genome assemblies of Z. pseudotritici, Z. ardabiliae, and Z. brevis, more partial gene models were predicted compared to models in Z. tritici (Table 1). Overall, the gene characteristics of these four species are very similar in accordance with the close phylogenetic relationships. Compared to Z. tritici, the functional annotation of the predicted gene models in Z. pseudotritici, Z. ardabiliae, and Z. brevis showed a larger proportion of sequences with an attributed function and a smaller proportion of sequences with no functional evidences. The four annotations are available from http://fungi.ensembl.org/Zymoseptoria_tritici/Info/Index (Z. tritici), http://genome.jgi.doe.gov/Zymps1/Zymps1.home.html (Z. pseudotritici), http://genome.jgi.doe.gov/Zymar1/Zymar1.home.html (Z.ardabiliae), and http://www.uniprot.org/taxonomy/1047168 (Z. brevis). Gene distribution in Zymoseptoria species Homology relationships among the four Zymoseptoria species including orthology (interspecies) and paralogy (intraspecies) were analyzed by a comparison of the predicted proteomes using the software package SiLiX (Miele et al. 2011). Of the total 44,227 proteins predicted in the four Zymoseptoria species, 39,177 (88.6%) were clustered into 10,612 families. These families belong to three categories. First, there are 10,361 families of orthologous sequences present in at least two species. The different distributions of these families across the Zymoseptoria species are shown in Figure 1. Second, there are 236 families of orthologous sequences that also included species-specific paralogous sequences, i.e., independent duplication of a conserved gene occurred in one or more species. Third, there are 15 families of paralogous sequences, i.e., duplication of species-specific genes. The remaining 5050 sequences that could not be classified into a gene family were considered as proteins encoded by orphan genes. Figure 1 Venn diagram showing the distribution of predicted models in Z. tritici: Z. pseudotritici, Z. ardabiliae, and Z. brevis. The categorizations of core Zymoseptoria genes, orphan genes, and genes shared by three or two species were performed using a detailed characterization of gene orthology. Orphan genes: The genome of Z. tritici encodes 1798 orphan genes (15.1% of all the predicted genes), of which 1221 are localized on core chromosomes and 577 on accessory chromosomes. However, accessory chromosomes are significantly enriched in orphan genes because they constitute 79.3% of the genes on these chromosomes compared to 10.9% on core chromosomes (χ2 test, P < 2.2e-16). A large majority of the orphan genes (95.5%) have no in silico attributed function. In general, we could not link species-specific genes to any biological or pathogenicity-related function; however, this uniqueness supports the species-specific nature of the genes that have no homology with known proteins from organisms outside the Zymoseptoria species complex. Among the orphan sequences that could be assigned a function, we found predicted functions relating to molecule transport (drugs, proteins, amino acids), primary and secondary metabolism (oxydoreductase activity, nonribosomal peptide synthase), and organic compounds degradation (chitinase, glycoside hydrolase). Small secreted proteins (SSPs) of plant pathogens particularly play an important role as putative effectors during the host infection (Stergiopoulos and De Wit 2009), and we found in Z. tritici that SSP-encoding genes were significantly enriched in the orphan gene set compared to the whole proteome: 8% vs. 3.7% (χ2 test, P < 2.2e-16). Orphan genes representing 9–11% of the predicted genes in Z. pseudotritici, Z. ardabiliae, and Z. brevis were likewise significantly enriched in SSP-encoding genes and genes that could not be assigned a function. Paralogous genes: Families of paralogous genes were only found in Z. tritici (eight families) and Z. ardabiliae (seven families) and included 23 and 14 genes, respectively. In Z. ardabiliae, 57% of these duplicated sequences are SSP-encoding genes, whereas there were no SSP paralogs in Z. tritici. In Z. ardabiliae, only one family could be associated with a gene function (kinase), whereas in Z. tritici several families contained sequences with known protein domains of transposable elements. Orthologous genes: Families of orthologous genes within the four Zymoseptoria species were divided into three categories. The first category comprised the core set of Zymoseptoria genes and included 7786 families containing one gene per species (Figure 1). A large proportion of these genes (59.5%) could be associated with a predicted function, whereas 8.3% of them had no homology to genes in other organisms and thereby potentially represented a set of Zymoseptoria-specific genes. The second category comprised genes present in three out of the four species and included 1294 families. Genes in this second category appeared to be less conserved because only 33% of them could be associated with function information. Finally, the third category included 1281 families comprising genes only found in two of the four species. Compared to the two other categories, genes with a function represented a smaller fraction (18%). Orthologous genes with paralogy: A particular category of families was also identified where orthologous sequences were conserved in two or more species with independent duplications in one or more species. This category contained 236 families with 1552 sequences. Most of the families (87%) comprised genes present in the four species. The largest family included 15 genes all encoding an alcohol dehydrogenase with four copies found in Z. tritici, Z. pseudotritici, and Z. brevis and three copies in Z. ardabiliae. Transposable element annotation TEs in Z. tritici: Of the 39.7-Mb genome assembly of Z. tritici IPO323, 7.4 Mb (18.6%) (Table 2) were found to be repetitive DNA, in agreement with the recently reported repeat content of IPO323 (>17%) in Dhillon et al. (2014). Repeats were classified into TE families based on features such as terminal repeats, protein domains, and homology with known TE available in the Repbase Update database (Jurka et al. 2005). The fact that the assembled genome of Z. tritici consists of complete chromosomes allowed a high-quality repeat annotation with only few uncategorized families. TEs of class I (retrotransposons) are the most abundant in the IPO323 genome and represent 13.1% of the total genome size (5.2 Mb), whereas TEs of class II (DNA transposons) represent 4.2% (1.6 Mb) (Table 2). The remaining repetitive sequences represent 0.5 Mb and could not be associated with classified TEs. From the 111 consensus sequences obtained by our procedure (see Materials and Methods), we identified 101 families of TEs. The majority of these families belong to the class II (62 families), mainly represented by TIRs (44 families), MITEs (11 families), and Helitron (4 families). Although present in a lower number (32 families), class I elements represent 71% of the repetitive fraction of the genome. The most abundant group of class I elements is the LTR elements from the Gypsy superfamily (14 families), followed by those of the Copia superfamily (12 families) and LINEs (7 families) (Table 2). Interestingly, we also identified one family of a complete tyrosine-recombinase retrotransposon that belongs to the Ngaro superfamily and that otherwise has been described to be absent in Ascomycota (Muszewska et al. 2013). Distinguishing core and accessory chromosomes of Z. tritici, we find that repetitive DNA represents 16.6% of the core chromosomes and 33.6% of the accessory chromosomes (Figure 2A). However, the relative distribution of the major TE families on core and accessory chromosomes does not differ significantly (Wilcoxon test, P = 0.3692) (Figure 2B). Table 2 Transposable element content in genomes of the Zymoseptoria species complex Z. tritici Z. pseudotritici Z. ardabiliae Z. brevis Family No. DNA Amount (kb) % of Genome Family No. DNA Amount (kb) % of Genome Family No. DNA Amount (kb) % of Genome Family No. DNA Amount (kb) % of Genome Class I (retrotransposons) LTR RLC 12 1017 2.56 6 90 0.23 5 232 0.62 7 827 2.08 RLG 14 2649 6.67 17 2906 7.50 16 1074 2.88 18 3616 9.09 LINE RII 4 737 1.86 0 0 0.00 3 76 0.20 4 547 1.38 RIL 2 747 1.88 0 0 0.00 1 32 0.09 0 0 0.00 RIX 1 5 0.01 1 83 0.22 1 67 0.18 1 193 0.48 DIRS RYN 1 23 0.06 0 0 0.00 0 0 0.00 0 0 0.00 SINE RSX 1 1 0.00 0 0 0.00 0 0 0.00 0 0 0.00 TRIM RLX-TRIM 4 35 0.09 0 0 0.00 0 0 0.00 1 4 0.01 Sub-total class I 39 5214 13.14 24 3080 7.94 26 1481 3.97 31 5186 13.04 Class II (DNA transposons) TIR DTT 14 246 0.62 3 51 0.13 4 29 0.08 9 254 0.64 DTA 7 150 0.38 1 35 0.09 1 4 0.01 5 175 0.44 DTH 10 184 0.46 0 0 0.00 0 0 0.00 11 292 0.74 DTM 7 145 0.36 1 44 0.11 0 0 0.00 4 213 0.54 DTX 6 364 0.92 6 432 1.11 5 76 0.20 3 315 0.79 Unknown DXX 2 40 0.10 0 0 0.00 0 0 0.00 0 0 0.00 Crypton DYX 1 6 0.02 0 0 0.00 0 0 0.00 0 0 0.00 Helitron DHH 4 470 1.18 7 357 0.92 1 39 0.10 5 391 0.98 Maverick DMM 0 0 0.00 2 476 1.23 0 0 0.00 0 0 0.00 MITE DTX-MITE 11 48 0.12 1 2 0.01 1 5 0.01 3 11 0.03 Sub-total class II 62 1653 4.17 21 1399 3.61 12 153 0.41 40 1652 4.15 Uncategorized repeats NoCat NoCat 10 516 1.30 60 1518 3.92 79 1303 3.49 93 2634 6.62 Total 111 7383 18.60 105 5997 15.47 117 2937 7.87 164 9472 23.87 Figure 2 Transposable elements (TEs) characteristics along the 21 chromosomes of Zymoseptoria tritici. (A) Proportions of TEs in the chromosomes of Z. tritici. The red dashed lines show the mean values of TEs on core (1–13) and accessory chromosomes (14–21). (B) The distribution of five major TE classes across core and accessory chromosomes in Z. tritici show a more or less similar distribution and frequency on the two types of chromosomes. As already described by Goodwin et al. (2011), repetitive sequences are highly affected by the fungal-specific repeat inactivation mechanism known as repeat-induced point mutations (RIP) (Galagan and Selker 2004). Multiple alignments of several family copies analyzed by RIPCAL (Hane and Oliver 2008) showed an excess of CpA→TpA and TpG→TpA mutations. As hypothesized by Goodwin et al. (2011), these mutations should prevent TEs from expressing their own machinery. However, it appears that 98 predicted gene models overlap TE sequences with at least 50% of their length, including 75 genes models that are completely embedded in repetitive DNA. Of the 98 corresponding proteins, 33 harbor domains associated with TEs such as reverse-transcriptase, transposase, or integrase (Table 3). These domains belong to 22 distinct TE families, including 12 TIR, eight LTR, one LINE, and one uncategorized element. Comparison of these gene models with the reconstructed transcripts showed that 48% have RNA-seq support; this suggests that TE families (mainly class II DNA transposons) are still active in the Z. tritici genome despite the RIP machinery. Table 3 Gene models with protein domains associated with transposable elements Protein ID Length (aa) Domain Name Domain Description Interpro or Pfam Accession No. Overlapping Repeat Family RNA-seq Support Zt09_chr_1_00001 143 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 — Zt09_chr_1_00017 272 DDE_Tnp_4 DDE superfamily endonuclease PF13359 DTH_element5_ZTIPO323 — Zt09_chr_1_01076 477 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 Yes Zt09_chr_2_00093 477 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 — Zt09_chr_2_00258 409 DDE_Tnp_1_7 Transposase IS4 PF13843 DTX_element1_ZPST04IR55 Yes Zt09_chr_2_00383 648 DDE_1 DDE superfamily endonuclease PF03184 DTT_element1_ZTIPO323 Yes Zt09_chr_2_00481 532 Chromo Chromo (CHRromatin Organization MOdifier) domain PF00385 RLG_element5_ZPST04IR55 — Zt09_chr_2_00619 272 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element3_ZTIPO323 — Zt09_chr_2_00906 219 DDE_1 DDE superfamily endonuclease PF03184 DTT_element5_ZTIPO323 Yes Zt09_chr_2_00907 269 DDE_1 DDE superfamily endonuclease PF03184 DTT_element5_ZTIPO323 Yes Zt09_chr_3_00204 734 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element2_ZTIPO323 Yes Zt09_chr_3_00229 349 DDE_3 DDE superfamily endonuclease PF13358 DTT_element14_ZTIPO323 Yes Zt09_chr_4_00051 195 DDE_3 DDE superfamily endonuclease PF13358 DTT_element4_ZB163 — Zt09_chr_4_00288 371 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element3_ZTIPO323 Yes Zt09_chr_5_00137 477 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 Yes Zt09_chr_7_00478 338 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element6_ZTIPO323 Yes Zt09_chr_7_00479 108 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element6_ZTIPO323 Yes Zt09_chr_9_00003 1506 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 — Zt09_chr_9_00154 621 DDE_1 DDE superfamily endonuclease PF03184 DTT_element1_ZTIPO323 Yes Zt09_chr_9_00557 1061 rve Integrase core domain PF00665 RLC_element7_ZTIPO323 Yes Zt09_chr_9_00615 458 DDE_Tnp_1_7 Transposase IS4 PF13843 DTX_element1_ZAST11IR611 Yes Zt09_chr_10_00001 218 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element7_ZTIPO323 — Zt09_chr_11_00364 162 Chromo Chromo (CHRromatin Organization MOdifier) domain PF00385 RLG_element7_ZPST04IR55 — Zt09_chr_13_00054 869 DDE_3 DDE superfamily endonuclease PF13358 DTT_element10_ZTIPO323 Yes Zt09_chr_13_00057 150 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element2_ZTIPO323 — Zt09_chr_13_00271 480 RNaseH-like_dom Ribonuclease H-like domain IPR012337 DTA_element1_ZTIPO323 Yes Zt09_chr_17_00004 876 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 — Zt09_chr_17_00088 523 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RIL_element2_ZTIPO323 — Zt09_chr_18_00008 750 RNaseH-like_dom Ribonuclease H-like domain IPR012337 NoCat_element60_ZAST11IR611 — Zt09_chr_19_00003 169 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element5_ZTIPO323 — Zt09_chr_19_00040 947 RVT_2 Reverse-transcriptase (RNA-dependent DNA polymerase) PF07727 RLC_element9_ZTIPO323 — Zt09_chr_19_00041 107 UBN2_3 gag-polypeptide of LTR copia-type PF14244 RLC_element9_ZTIPO323 — Zt09_chr_21_00003 1609 RVT_1 Reverse-transcriptase (RNA-dependent DNA polymerase) PF00078 RLG_element9_ZTIPO323 — TEs in Z. pseudotritici, Z. ardabiliae, and Z. brevis: To improve the repeat annotation of Z. pseudotritici, Z. ardabiliae, and Z. brevis, we generated improved assemblies of Illumina-sequenced genomes of the isolates: ST04IR55 of Z. pseudotritici, ST11IR611 of Z. ardabiliae, and Zb163 of Z. brevis. The assembly sizes were 38.8 Mb, 37.3 Mb, and 39.8 Mb, respectively, compared to the 39.7 Mb genome assembly of Z. tritici. The three genomes reflect different extents of repeat invasion: repetitive DNA comprises 7.9% of the Z. ardabiliae genome, 15.5% of the Z. pseudotritici genome, and 23.9% of the Z. brevis genome, including a total of 117, 105, and 164 repeat families identified in the genomes, respectively (Table 2). As a result of the fragmented assemblies, the number of uncategorized repeat families in the Z. pseudotritici, Z. ardabiliae, and Z. brevis genomes represent more than 50% of all the families and between 25% and 44% of the repetitive fraction. In contrast, the number of uncategorized families in the Z. tritici genome represents only 9% of the families and 7% of the repetitive fraction. Nevertheless, it was possible to classify some TE families of Z. pseudotritici, Z. ardabiliae, and Z. brevis and to record general patterns of TE distribution among the three genomes. As in the Z. tritici genome, class I TEs that are mainly represented by LTR-Gypsy elements are most abundant and account for 51–55% of the total repetitive fraction (Table 2). LINE elements are hardly represented in the Z. pseudotritici, Z. ardabiliae, and Z. brevis assemblies; however, this may be an artifact of the fragmented assemblies. In Z. pseudotritici and Z. brevis, class II TEs are mainly composed of TIRs that represent approximately 20% of the repetitive fraction similar to class II TEs in Z. tritici. Helitron elements were also identified in Z. pseudotritici, Z. ardabiliae, and Z. brevis; however, they accounted for only 1–6% of the repetitive fraction compared to 6.4% in Z. tritici. Maverick elements (Pritham et al. 2007) were only identified in Z. pseudotritici and were the third most represented TE family in the genome (Table 2). The unique presence and distribution of Maverick elements in Z. pseudotritici could result from a recent invasion of the genome followed by massive waves of transposition of these elements. The complete repertoire of repeats in Zymoseptoria spp: In total, we found 497 repeat families in the four Zymoseptoria species, including 120 families of class I TEs (24.1%), 135 families of class II TEs (27.2%), and 242 uncategorized families (48.7%). We could improve the TE annotation using the complete Zymoseptoria TE library generated here. We found 19.9% of repeats (+1.3%) in the genome of Z. tritici, 17.6% (+2.2%) in the genome of Z. pseudotritici, 12.7% (+4.8%) in the genome of Z. ardabiliae, and 25.2% (+1.3%) in the genome of Z. brevis. Addressing TE evolution in the Zymoseptoria genomes, we found that some families identified independently in each species were derived from a common ancestral TE family. An analysis of the 497 families was performed using Blastclust (Altschul et al. 1990) with a coverage cut-off of 50% and an identity percentage cut-off of 80%; this resulted in the clustering of 76 families into 34 larger groups (Table S2). Fourteen of these groups were composed of TIR elements, eight groups of LTR-Gypsy elements, six groups of uncategorized elements, three groups of LTR-Copia elements, two groups of Helitrons, and one group of LINE elements. Only one of these groups included TE families present in each of the four species; this suggests that this element, an LTR-Gypsy element, was present in the genome of the common ancestor of the four species (Table S2). Interestingly, this element may have expanded prior to the divergence of species because we observed a comparable size expansion in the four species comprising between 120 and 180 kb in each genome. Given the phylogenetic tree of the four Zymoseptoria species, as shown in Stukenbrock et al. (2012), the other TE groups were distributed in either two or three species with eight different ancestral relationships (Table S2). This analysis mainly showed that these species have undergone events of invasion and expansion of distinct TEs after their divergence. Discussion “Omics” analyses such as comparative and evolutionary genomics, transcriptomics, epigenomics, or proteomics mainly rely on the accuracy of predicted gene models. The Zymoseptoria species complex provides a unique model system for the application of “omics” data to study the underlying genetics of pathogenicity and host specificity of plant pathogens (Stukenbrock et al. 2010, 2011, 2012). However, updated and comparable annotations of gene and TE content in species of Zymoseptoria have so far been missing. Here, we present a new gene and repeat annotation of the prominent fungal wheat pathogen Z. tritici and its three close relatives: Z. pseudotritici, Z. ardabiliae, and Z. brevis; therefore, we provide a valuable resource for future functional, experimental, and evolutionary studies. We conducted the re-annotation of the IPO323 genome using a pipeline that identifies the most probable gene models based on information from transcript assemblies, homology searches, and ab initio gene predictors (Haas et al. 2011). This allowed us to identify 11,839 gene models, including 1200 models that were not predicted previously by the JGI. The support of RNA-seq data for most of these genes underlines the potential of our pipeline for identifying novel genes. We applied the same annotation pipeline to re-sequenced genomes of the three close relatives of Z. tritici, Z. pseudotritici, Z. ardabiliae, and Z. brevis, and could call comparable numbers of genes in these species (∼10,500 models). Of these, 7786 represent core Zymoseptoria genes shared among the four species. Our exhaustive search for gene orthology also identified genes shared by two or three species and suggested recent gains or losses of genes among the Zymoseptoria species. Notably, we also identified 1798 orphan genes in Z. tritici enriched in putative pathogenicity-related factors. Species-specific orphan genes in Z. tritici and in the three other species may include key determinants of virulence in wheat and other grass hosts. Further functional studies will allow this hypothesis to be tested. Recently, a new identification and classification of repeats and TEs in Z. tritici was conducted (Dhillon et al. 2014). In the present study we found very similar patterns in terms of repeat and TE distribution, number of families, and evidence of TE activity. However, we could further improve the assignment of repeat families to known TE families; 39.8% of the 93 repeat families identified by Dhillon et al. were not categorized into known TE classes. We were able to improve the TE classification, leaving only 9% of the 111 repeat families unclassified. The TE annotation pipeline used here contains a number of supplementary steps of clustering of the REPET outputs and allowed us to identify more complete elements. These were all manually checked to avoid the generation of false or chimera elements. The gene and TE annotation of the four Zymoseptoria species genomes coupled with preliminary comparative analysis allowed us to highlight interesting features relevant to the biological life traits of these organisms. Establishment of homologous sequence families across the four species showed that a large part of genes are shared between two or more species and that the major difference of gene content relies on orphan genes. These orphan genes, in all four species, are significantly enriched in putative pathogenicity-related genes and potentially play a role in the determination of host specificity. Similar presence–absence patterns of pathogenicity-related genes were shown to be strong determinants of host range in plant pathogens, e.g., between lineages of the rice blast pathogen Magnaporthe oryzae, the wilt pathogen Verticillium dahliae, and lineages of the Leptosphaeria maculans–Leptosphaeria biglobosa species complex (Couch et al. 2005; de Jonge et al. 2012; Grandaubert et al. 2014). Similarly, comparison of TE families showed a majority of species-specific sequences; this underlies the fact that each species genome has been widely invaded after the species divergence. We speculate that TEs may have played a role in host specialization by the acquisition or modification of pathogenicity-related traits. Also, large TE-rich regions could have played a role in speciation through the suppression of homologous recombination in chromosomal regions with inversions or translocations as proposed for the Leptosphaeria maculans–Leptosphaeria biglobosa species complex (Grandaubert et al. 2014). In Dhillon et al. (2014), the authors stated that several genes with putative pathogenicity-related functions were found to be associated with TEs. Preliminary analyses of genes and TEs tend to show that orphan genes are located significantly closer to TEs than other nonorphan genes (J. Grandaubert, unpublished data). TEs thus may play a role in the origin and evolution of these genes. The annotation data presented here will greatly improve our understanding of gene evolution, adaptation, and the role of TEs in pathogen evolution. The predicted gene models will furthermore greatly support future studies of gene expression in Z. tritici and its related species and provide a strong basis to understand the underlying genetics and molecular biology of host–pathogen interactions in Zymoseptoria spp. Acknowledgments This work was supported by intramural funding from the Max Planck Society (to E.H.S.). Supporting information is available online at www.g3journal.org/lookup/suppl/doi:10.1534/g3.115.017731/-/DC1 Communicating editor: J. D. Faris

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