Global Genome and Transcriptome Analyses of Magnaporthe oryzae Epidemic Isolate 98-06 Uncover Novel Effectors and Pathogenicity-Related Genes, Revealing Gene Gain and Lose Dynamics in Genome Evolution
[['Rice ( Oryza sativa ) is one of the most important staple food crops for more than half of the global human population [1] .', 'However , the rice production is severely impacted by the blast disease caused by the fungus Magnaporthe oryzae , despite the cultivation of various disease-resistance cultivars [2 , 3 , 4] .', 'One of the reasons is that new cultivars often lose their resistance within a few years of introduction .', 'It is thought that genetic variability occurs rapidly within pathogen populations , especially in regions with high genome plasticity , and that the pathogenic traits such as secreted pathogen avirulence ( AVR ) /effectors evolve rapidly to counteract plant defense [5 , 6 , 7 , 8] .', 'M . oryzae primarily infects rice but can also infects wheat or other small grains [9] .', 'Recent advances in genetic and genomic technology have allowed M . oryzae to be a tractable model for studying the plant-microbe interaction [10] .', 'Jantasuriyarat and colleagues used large-scale expressed sequence tag ( EST ) sequencing to profile gene expression at the early stage of the M . oryzae-rice interaction and identified four genes to be involved in the interaction out of 13 , 570 uniESTs [11] .', 'Approximately 100 pathogenesis-related protein genes specific to infection were identified in other studies using EST analysis [10] , and four biotrophy-associated secreted ( BAS ) proteins were also found in M . oryzae using microarray [4] .', 'More recently , several studies have identified the presence of an infection structure , known as the biotrophic interfacial complex ( BIC ) , that is involved in mediating the delivery of pathogen effectors into the rice host cytoplasm [4 , 12] .', 'Interestingly , studies have also revealed that genome plasticity is closely linked to host-pathogen interaction specificities .', 'Using genome-wide DNA polymorphism existed between M . oryzae field isolate Ina168 and isolate 70–15 , one of the progenies from a cross between a weeping lovegrass isolate and the archetypical rice isolate Guy11 [13 , 14 , 15] , three novel AVR genes were identified [16] .', 'The presence of these AVRs correlates to a 1 . 68 Mb sequence in Ina168 that is absent from the assembled genome sequence of 70–15 [16] .', 'Studies of two other field isolates , P131 and Y34 , also revealed slightly larger genome contents with more genes .', 'It is suggested that the presence of these isolate-specific genes play diverse roles , including conidiation , vegetative growth , or virulence [17] .', 'Genome studies of additional M . oryzae field isolates and identification of novel AVR effectors will help us to further address the mechanism of pathogen and host coevolution .', 'Here , we characterized the genome of the dominant blast isolate 98–06 on several different rice cultivars cultivated in Southeast China ( S1 Table ) .', 'We found that 98–06 contains seven known AVRs , corresponding to its wide field adaptability .', 'AVR PWL1 , PWL2 , Avr-Pita , Avr1-CO39 , and ACE1 are highly polymorphic due to point mutations while AVR Avr-Pia and Avr-Pii are also polymorphic , but with complete deletions .', 'AvrPiz-t and Avr-Pik allele ( D ) were also found and conserved .', 'In addition , we found that isolate 98–06 contains 1 . 43 Mb of isolate-specific sequences encoding 238 isolate-specific genes , in comparison to isolate 70–15 .', 'In addition , genome-wide expression profiling revealed the presence of a defense network in rice and major expression patterns of pathogenesis-related genes during the M . oryzae-rice interaction .', 'Moreover , we predicted 134 candidate effectors from 1 , 732 putative secreted proteins and provided evidence to demonstrate that IUG6 and IUG9 are novel effectors .'], ['The genome of the M . oryzae isolate 98–06 was sequenced using Illumina high-throughput sequencing technology .', 'Four different insert-size libraries ( 500 , 350 , 5 , 000 , and 10 , 000 bp ) were generated , which represent 36 . 8- , 38 . 2- , 31 . 9- , and 27 . 6-fold coverage assemblies spanning 1 , 560 , 1 , 618 , 1 , 350 , and 1 , 167 Mb , respectively .', 'The sequence coverage that was approximately six-fold greater than that of P131 and Y34 [17] , provided a near perfect assembly .', 'The sequence reads were assembled into 1 , 161 contigs and placed into 284 scaffolds with a combined length of 42 . 1 Mb using SOAPdenovo [18 , 19] .', 'The N50 and maximum lengths of scaffolds were 1 , 530 and 3 , 511 kb , respectively ( Table 1 ) .', 'The sequences have been deposited at GenBank under the submission number of JRBC00000000 .', 'When the scaffolds of isolate 98–06 were aligned with the assembled genome of isolate 70–15 , 98 . 83% of the genome was conserved .', 'However , 98–06 contains 1 . 4 Mb isolate-specific sequences that are dispersed throughout the genome ( Fig 1 , S2 Table ) .', 'Interestingly , blocks of the reverse-alignment sequences and chromosomal breakpoints were found at regions near the telomeres ( S1 Fig ) .', 'A total of 14 , 019 genes including 1 , 732 secreted protein genes were identified from the annotated isolate 98–06 genome ( Table 1 ) .', 'The average length of predicted proteins is ~470 amino acids , and the predicted genes comprise 46% of the assembly genome .', 'In all , the 98–06 genome possesses more genes than isolates 70–15 [15] , P131 , Y34 [17] , FJ , or HN [20] .', 'Further analysis revealed that 238 genes are unique when compared with 70–15 ( 49 genes if compared with P131 and Y34 ) , and of these 238 genes , 10% encode secreted proteins while 69% have no significant homologs in GenBank ( S3 Table ) .', 'We conducted a Clusters of Orthologous Groups ( COG ) study and found that some of these specific genes are associated with general biological functions , including secondary metabolism and energy generation processes ( S2 Fig ) .', 'Intriguingly , isolate-specific genes appear to be mainly located at some of the chromosomal ends .', 'To identify possible gene families , we clustered the predicted proteins of isolates 98–06 , 70–15 , P131 , and Y34 using the OrthoMCL algorithm .', 'A total of 52 , 177 proteins were grouped into 13 , 236 clusters , with each cluster containing at least two putative protein orthologs/paralogs ( S3 Fig , S4 Table ) .', 'The mean gene number of each cluster for 98–06 , 70–15 , P131 , and Y34 was 1 . 11 , 1 . 04 , 1 . 02 , and 1 . 02 , respectively .', 'Among these clusters , 12 . 86% of all 14 , 019 genes in 98–06 had at least one paralog , while 6 . 28% , 3 . 27% , and 3 . 08% of all genes for 70–15 , P131 , and Y34 respectively ( S4 Table ) .', 'These results suggested that there are more paralogs in 98–06 than in the other isolates .', 'Meanwhile , there are 455 , 310 , 165 , and 150 gene families with at least two paralogs in 98–06 , 70–15 , P131 , and Y34 , respectively .', 'Comparative analysis indicated that 227 gene families are expanded in 98–06 ( S4 Table ) , which is consistent with its larger genome content .', 'Repeated sequences and transposable elements ( TEs ) often account for a large portion of genomes and therefore are important in genome annotation .', 'Using multiple approaches , we found that 9 . 3% of the 98–06 genome consists of repetitive sequences .', 'This is consistent with other fungi in which repetitive sequences comprise ≤ 10% proportion of the genomes [21] .', 'However , transposable elements predicted by RepeatMasker [22] are more abundant in isolate 98–06 ( 2 , 776 ) than in isolates 70–15 ( 2 , 297 ) , P131 ( 2 , 055 ) , or Y34 ( 2 , 322 ) ( S5 Table ) .', 'In a follow-up examination of the larger number of genes ( up to 1 , 732 ) that encode putative secreted proteins in 98–06 , 132 genes containing putative signal peptide sequences were disrupted by TEs ( S6 Table ) .', 'Proteins secreted by fungal pathogens during host colonization are generally referred to as effectors [23 , 24] , which are often less than 200 amino acids in length and cysteine-rich .', 'Therefore , we principally focused on small secreted proteins less than 200 amino acids in length , and identified 645 effector candidates out of 1 , 732 secreted proteins in 98–06 ( S7 Table ) .', 'These candidates , including known AVR genes Avr-Pik ( allele D ) and AvrPiz-t , have an average cysteine content of 3 . 11% in comparison to 1 . 26% of all 1 , 732 putative secreted proteins .', 'Isolate 98–06 is known to exhibit an incompatible interaction with various rice cultivars harboring 12 known resistance ( R- ) genes: Pi7 , Pi1 , Pik , Pik-m , Pi20 , Pi9 , Pita2 , Piz-t , Pik-p , Pish , Piz5 , and Pik-h ( S1 Table ) , and the Pi7 , Pi1 , Pik , Pik-m , Pi-kp , and Pik-h are alleles that could all recognize Avr-Pik ( allele D ) .', 'We focused on the remaining 643 ( 645–2 = 643 ) secreted proteins that provide a rich repertoire for the identification of novel effectors .', 'Despite that conserved motifs such as the RxLR domain of oomycetes [25] were not found in some M . oryzae effectors , the M . oryzae effectors are often planta-specific and secreted proteins [4] .', 'To study the host-pathogen interaction , we performed RNA sequencing ( RNA-Seq ) for six stages: mycelium ( MY ) and conidial infection at 0 h , 8 h , 24 h , 48 h , and 72 h post inoculation ( CO-0h to CO-72h ) .', 'After discarding low-quality raw reads , we obtained 12 . 8~13 . 7 million clean reads from each of the six samples , and aligned these reads against the reference genes and genomes ( S8 Table ) .', 'Almost all of the genes in isolate 98–06 and rice ( O . sativa ) were transcribed ( 11 , 075 and 26 , 452 , respectively , S9 Table ) .', 'The majority of the differentially expressed genes ( log2Ratio ≥1 and GFOLD ( 0 . 01 ) >1 ) in M . oryzae were up-regulated during host-pathogen interaction in comparison to conidial infection at 0 h , suggesting a strong interaction between M . oryzae and rice ( S4 Fig ) .', 'To confirm the RNA-Seq profiles , qRT-PCR was conducted on nine randomly selected M . oryzae and rice genes that were either induced or repressed .', 'The average match between RNA-Seq and qRT-PCR data of the original sequenced samples was 30 of 41 ( 73% ) ( S5 Fig ) , indicating basic consistency between the two approaches .', 'In addition , the average match between qRT-PCR of another independent sampling and the original sampling , or the RNA-Seq , was 76% and 63% , respectively ( S5 Fig ) .', 'There also appear certain correlations among the sequencing data of samples belonging to different stages , as distinct from the comparative RNA-Seq between wild type and mutant .', 'Moreover , the expression patterns of several previously characterized genes , such as MoACTIN; MoAP1 , MoVAM7 , and MoBAS1 [4 , 26 , 27] , in the transcriptome ( see S10 Table ) were similar to previous studies .', 'These validation tests rectified to certain degree the potential limitation resulting from lack of sample duplication in RNA-Seq analyses .', 'Since plant hormone responses play an important role in the host defense network during the rice-pathogen interaction [28] , we examined the expression of genes involved in salicylic acid ( SA ) , jasmonic acid ( JA ) , ethylene ( ET ) , and mitogen-activated protein kinase ( MAPK ) signaling cascades .', 'Most of the genes in the SA and ET signaling pathways were up-regulated , meanwhile , JAZ genes that act as transcriptional repressors of JA [29] were induced after 48 hpi .', 'A comparison of aggregate expression levels at 0 hpi versus 8 , 24 , 48 and 72 hpi in planta is shown in Fig 2 .', 'Transcription for the most of the MAPK genes was increased during infection .', 'In addition , several WRKY transcription factors and pattern recognition receptors ( PRRs ) FLS2 [30] and EFR were also significantly induced at 48 hpi ( Fig 2 ) .', 'These findings revealed that multiple host defense signaling pathways were involved in the response to the infection of isolate 98–06 .', 'Finally , to investigate how the M . oryzae genetic program is deployed during infection , we explored 64 known genes relevant to pathogenicity and 10 known effectors of M . oryzae in our interaction transcriptome ( S10 Table ) , and determined their expression patterns by the clustering affinity search technique ( CAST ) assay through MultiExperiment Viewer 4 . 6 software package [31] .', 'The distance metric is the default Pearson correlation , and the threshold affinity value is 0 . 8 .', 'Fourteen clusters were generated , and the cluster-a with the most members ( 23 genes ) was illustrated , which provided the major expression pattern of pathogenesis-related genes ( Fig 3A , a; S10 Table ) .', 'The expression pattern-a represents high expression throughout the infection process , with the exception of sharp reduction at 24 hpi .', 'In general , the virulence factors were up-regulated with different waves of expression during infection ( Fig 3A ) .', 'Interestingly , another expression pattern-b for effectors was also distinguished ( Fig 3A and 3B; S10 Table ) .', 'In transcriptome analysis described above , two genes MoVAM7 and MoSSO1 encoding soluble N-ethylmaleimide-sensitive factor attachment protein receptor ( SNARE ) were also identified .', 'SNARE proteins mediate intracellular transport that is an essential biological process in fungi [32] .', 'Consistent with this , MoVam7 and MoSso1 were found to be important in effector secretion and pathogenesis [27 , 33] .', 'We gathered 21 SNARE genes and 35 other endocytosis-related ( ER ) genes through bioinformatics analysis , and found five expression patterns of SNARE genes and eight patterns of ER genes using the CAST method ( S6 Fig; S11 and S12 Tables ) .', 'It is surprising that the key expression patterns of SNARE and ER genes are similar to the pathogenicity pattern-a , suggesting that this typical pathogen–host interaction pattern could be used to explore novel pathogenicity genes .', 'In a broader definition , effectors are specific types of proteins secreted into the plant by pathogens to interfere with plant defenses , and they most likely play other roles in promoting infection as well [34] .', 'To date , 15 effectors were identified that include nine Avr effectors , six newly identified effectors including four BAS proteins , Slp1 , and MC69 .', 'In this analysis , AvrPiz-t , BAS1 , BAS3 , BAS4 , and SLP1 genes were clustered into expression pattern-b ( Fig 3A ) , indicating that the expression is highly inducible during the biotrophic invasion .', 'Hierarchical clustering ( HCL ) analysis also showed two distinct expression patterns that are similar to pattern-a and pattern-b , respectively ( Fig 3B ) .', 'Since Avr-Pik and AvrPiz-t genes are highly expressed during infection , and studies of two M . oryzae isolate-specific sequences and Verticillium dahliae indicated that lineage-specific genomic regions are enriched in genes encoding new effectors [35] , we explored the expression patterns of 645 small candidate effectors in 98–06 through CAST assay .', '134 candidate effectors were found to be co-regulated with Avr-Pik and AvrPiz-t ( Fig 4; S13 Table ) .', 'Six known effectors BAS1 , BAS2 , BAS3 , BAS4 , SLP1 , and PWL1 were among these candidates , providing a compelling argument for the presence of additional effectors among these candidates .', 'Many bacterial and fungal pathogen effectors can suppress innate plant immunity , particularly that triggered by pathogen-associated molecular patterns [34 , 36 , 37] .', 'For example , M . oryzae AvrPiz-t suppresses the BAX-mediated programmed cell death in tobacco leaves [38] .', 'Among 134 putative secreted proteins identified , most have no predicted functions , including several 98–06 isolate-unique genes ( IUG ) that were not found in 70–15 .', 'We queried the nucleic acid sequences against the genomic sequences of P131 and Y34 and found that IUG6 ( Mo_GLEAN_10000617 ) and IUG9 ( Mo_GLEAN_10000765 ) are specific to 98–06 .', 'To identify Iug6 and Iug9 functions , we used a PVX-based high-throughput transient plant expression system in Nicotiana benthamiana .', 'We also included three randomly selected non-specific proteins Nup1 , Nup2 , and Nup3 ( MGG_07900 , MGG_08024 , and MGG_04546 ) for controls .', 'We first removed the signal peptides of IUG6 , IUG9 , NUP1 , NUP2 , and NUP3 to enable the genes to be expressed stably in plant cells before cloning into the PVX vector pGR106 .', 'Infiltration of N . benthamiana leaves with Agrobacterium tumefaciens cells carrying pGR106:IUG6 , pGR106:IUG9 , pGR106:NUP1 , pGR106:NUP2 , pGR106:NUP3 , and the negative control pGR106:GFP did not cause any obvious cell-death symptoms ( S7 Fig ) , whereas obvious cell death was observed in N . benthamiana leaves infiltrated with A . tumefaciens cells carrying pGR106:BAX .', 'N . benthamiana leaves infiltrated with A . tumefaciens cells harboring IUG6 , IUG9 , NUP1 , NUP2 , and NUP3 genes 24 h prior to infiltration with the pGR106:BAX-harboring cells did not produce symptoms ( Fig 5A ) .', 'The expression of BAX was detected at 48 h after infiltration ( Fig 5B ) , which ruled out the possibility that BAX failed to express .', 'Iug6 , Iug9 , Nup1 , Nup2 , and Nup3 all conferred BAX cell-death suppression activity .', 'By analogy , additional effectors may also present in these 134 candidate effectors .', 'Presence or absence polymorphisms of these 127 candidate effectors ( minus six known effectors and one failed to be amplified by PCR ) were tested by PCR using 29 M . oryzae field isolates collected from China ( Fig 5C ) .', 'The candidate effectors showed different segregation patterns .', 'Among them , IUG6 , IUG9 , and NUP2 have varied presence in 29 field stains , whereas NUP1 and NUP3 are detected in all isolates ( Fig 5C ) .', 'A recent report indicates that the presence or absence of putative secreted proteins shows a good correlation with AVR genes in M . oryzae [16] .', 'Since half of the characterized blast AVR effector genes are not present in the isolate 70–15 genome , it may suggest that gene gain or loss events could be a major factor in the evolution of AVR effectors [39] .', 'Functional characterization of IUGs may reveal novel effectors or other factors significant in the host-pathogen interaction .', 'We thus further characterized the functions of IUG6 and IUG9 , along with IUG17 , IUG18 , IUG34 , and IUG37 .', 'We found that IUG6 and IUG9 are located near the chromosomal ends ( S14 Table ) , which is consistent with the hypothetic rapid development of novel effectors in plastic regions [40] .', 'IUG17 ( Mo_GLEAN_10000632 ) and IUG18 ( Mo_GLEAN_10001404 ) are predicted to each contain the aminoglycoside phosphotransferase ( APH ) domain ( 145–223 amino acids ) and the RelA_SpoT domain ( 96–234 amino acids ) , while IUG34 ( Mo_GLEAN_10000877 ) and IUG37 ( Mo_GLEAN_10002374 ) are predicted to be associated with pathogenicity-related expression pattern through CAST assays .', 'We also generated respective deletion mutants in 98–06 using the hygromycin-resistance marker gene and complemented the mutants with the respective wild type gene alleles including the endogenous promoter of approximately 1-kb ( S8 Fig ) .', 'Disruption of IUG6 and IUG9 , as well as IUG18 , resulted in defects in vegetative hyphal growth and virulence , whereas disruption of IUG17 , IUG34 , and IUG37 had no obvious effects on colony morphology , conidiation , or virulence ( S9 Fig ) .', 'Iug6 is relatively specific to M . oryzae , since only one homolog was identified in the fungus Gaeumannomyces graminis ( GL385397 . 1 , 53% identity , E = 4e-17 ) .', 'Iug9 homologs can be found in Colletotrichum higginsianum ( CCF43986 . 1 , 63% identity , E = 7e-29 ) and C . graminicola ( EFQ33033 . 1 , 63% identity , E = 4e-26 ) .', 'In contrast , Iug18 contain the RelA_SpoT domain that is well conserved among other filamentous fungi .', 'Microsynteny analysis revealed that all three genes are located at the genomic inserted regions comparable to 70–15 ( S10A Fig ) .', 'However , the parallel result was unfavorable , probably because the laboratory strain 70–15 was generated from a cross between rice and weeping lovegrass isolates [13 , 14] .', 'To exclude the possibility that this was an assembly gap leading to gene deletion in the other three isolates , we amplified the genes by PCR from isolates 70–15 , Guy11 , P131 , and Y34 and performed a Southern blotting analysis ( S10B Fig ) .', 'Expression of these three genes was validated by qRT-PCR , which also showed that IUG6 and IUG9 exhibit high expression levels during the pathogen-host interaction ( S11 Fig ) .', 'The Δiug6 , Δiug9 , and Δiug18 mutants were examined for phenotypes including conidiogenesis .', 'Conidiation in 10-d-old cultures of the iug6 mutant was reduced dramatically , by ~17-fold , compared with WT ( Fig 6B ) .', 'The Δiug9 and Δiug18 mutants showed approximately 14% and 32% reduction in conidiation on SDC medium ( Fig 6B ) .', 'Microscopic observations showed that Δiug6 , Δiug9 , and Δiug18 mutants produced significantly fewer conidia than the WT strain ( Fig 6A ) .', 'To determine whether IUG6 , IUG9 , and IUG18 affect the expression of conidiation-related genes including MoCOM1 , MoHOX2 , MoCON7 , MoCOS1 , and MoSTUA [41 , 42 , 43 , 44 , 45] , we measured and found that their expression was decreased ( Fig 6C ) .', 'To determine whether Δiug6 , Δiug9 , and Δiug18 have defects in pathogenicity , conidial suspensions ( 5 x 104 spores /ml ) were sprayed onto 2-wk-old susceptible rice seedlings ( CO-39 & LTH ) .', 'Only small , necrotic-like dark brown spots were observed in Δiug6-infected rice leaves in comparison to controls ( Fig 7A and 7B ) .', 'When the lesions were excised , surface sterilized with 70% ethanol for 1 min , and incubated with light and humidity on 4% water agar for 2 days , as described in a previous study [46] , no fungal growth or conidia occurred .', 'The Δiug9 and Δiug18 mutants also resulted in a reduction in disease symptoms on rice 7 days after inoculation ( Fig 8A ) .', 'The mean lesion density per unit area of the mutants was significantly lower than that of WT ( Fig 8B ) .', 'Disease symptoms of three approximately 6 cm long rice blades from the same parts of plants infected by Δiug9 mutant or WT were also quantified using a ‘lesion-type’ scoring assay [9] , which showed that lesion types 4 and 5 ( severe , coalescing ) were rarely produced by the Δiug9 mutant ( Fig 8C ) .', 'In addition , fungal DNA in rice was significantly lower in infection by Δiug9 and Δiug18 mutants than that by the WT as determined by M . oryzae 28S rDNA quantitation [47] ( Fig 8D ) .', 'Finally , we performed a detailed phenotypic analysis to investigate the infectious hyphae within the host cells .', 'At 24 hpi in barley epidermal cells and 48 hpi in rice leaf sheaths , both the WT and the Δiug6 mutant strain formed normal appressoria , but the invasive hyphae ( IH ) of the WT strain freely expanded into host cells .', 'On the other hand , appressoria of Δiug6 failed to develop any penetration structures among 50 examined infection sites in rice and barley , respectively ( Fig 7C and 7D ) .', 'We also analyzed invasive hyphal growth of Δiug9 and Δiug18 mutants at 100 appressorial penetration sites in barley tissues by rating the hyphal growth into four types ( type I , no penetration; type II , with penetration peg; type III , with a single invasive hypha; type IV , with extensive hyphal growth ) after inoculation with the spore suspensions for 30 hours ( Fig 8E ) .', '75% of penetration sites of WT showed III or IV invasive growth type , by contrast 42% of cells were limited in type I invasive hyphal growth in the Δiug9 mutant , and 77% penetration sites of the Δiug18 mutant showed type II or III hyphal growth .', 'A similar result was also observed in rice leaf sheaths , with the WT and complemented strains displaying faster hyphal growth extension to neighboring cells while the Δiug9 and Δiug18 mutants showing lower hyphal growth limited to one cell ( Fig 8F ) .', 'To further characterize these Iug proteins , we expressed IUG6:GFP , IUG9:GFP , and IUG18:GFP fusion genes under the control of their native promoters in Guy11 , respectively .', 'GFP fluorescence was observed in the conidial septum expressing Iug6:GFP and Iug9:GFP , while faint fluorescence was seem in the cytoplasm of conidia expressing Iug18:GFP ( S12 Fig ) .', 'We next detected whether any GFP signals can be detected in the biotrophic interfacial complex ( BIC ) .', 'To suppress host immunity during biotrophic intracellular growth , fungal effectors of M . oryzae are secreted and accumulated at the BIC or more generally within the Extra-Invasive Hyphal Membrane ( EIHM ) [4] .', 'When transformants invaded rice sheath cells at ~27 hpi , the fluorescence of Iug6 can be observed in BIC ( Fig 9A ) .', 'Microscopy of the secreted Iug9:GFP protein showed fluorescence that outlines the primary hyphae and BICs at ~27 hpi ( Fig 9B ) , similar to the BIC localization control ( Fig 9C ) , AvrPiz-t:GFP [48] .', 'Both findings suggested that Iug6 and Iug9 could be delivered into the rice cytoplasm and accumulated in BICs to facilitate biotrophic invasion .', 'To validate the signal peptide prediction of Iug6 and Iug9 , we used an assay based on the method previously described by Oh et al . [49] .', 'The constructs with the signal peptides of Iug6 and Iug9 allowed the invertase secretion-deficient yeast strain YTK12 to grow on YPRAA medium , and this invertase activity was confirmed by inclusion of the triphenyl tetrazolium chloride dye ( S13 Fig ) .', 'These results showed that the signal peptides of IUG6 and IUG9 are indeed functional .', 'We further transformed the IUG6 gene into the virulent isolate Guy11 and used the Δiug9 mutant for pathogenicity comparison tests in four resistant rice cultivars: IRBLz5-CA ( Pi-z5 ) , IRBLsh-S ( Pi-sh ) , IRBL20-IR24 ( Pi-20 ) , IRBLta2-Re ( Pi-ta2 ) , and susceptible cultivar LTH .', 'All of the transformants showed disease symptoms ( S14 Fig ) , excluding the possibility that IUG6 and IUG9 are conventional AVR genes corresponding to these specific resistance genes .', 'However , further studies are underway to address whether or not IUG6 and IUG9 are unknown avirulence genes that are involved in the evolutionary host-pathogen arms race .', 'As Iug6 and Iug9 can suppress the BAX-mediated programmed cell death in tobacco leaves , we investigated whether their expression affects the transcription of the rice defense-related genes .', 'When infected with Guy11 over-expressing IUG6 and IUG9 , the pathogenicity of these transformants is not obviously improved , but the expression of PR1a and Cht1 in rice was significantly less than that caused by Guy11 following qRT-PCR analysis ( Fig 10B ) .', 'Similarly , the expression levels of PR1a and Cht1 in rice by infection with isolate 98–06 were also significantly lower than that infected with Guy11 at 24 hpi or 8 hpi , with delayed peak expression .', 'The expression patterns of PR1a and Cht1 in rice when infected with isolates over-expressing IUG6 or IUG9 is similar to that by isolate 98–06 , with somewhat lowered peak expression .', 'PR1a and Cht1 are respective SA and ET signaling marker genes .', 'SA is involved in establishing basal defenses , effector-triggered immunity , and systemic acquired resistance in many dicotyledonous species [50 , 51] , as well as in modulating redox balance and protecting rice plants from the oxidative stress caused by M . oryzae [52] .', 'Our above interaction transcriptome analysis also suggested that SA and ET signaling pathways might function positively on rice basal defense against M . oryzae .', 'We hypothesized that Iug6 and Iug9 might target unknown factors in rice , leading to suppression of the SA and ET signaling and promotion of biotrophy .'], ['M . oryzae is known for its natural genetic variation in the field , resulting in emergence of new epidemics threatening world food supply .', 'Comparative analyses of multiple new epidemics not only steadily improved the assembly and annotation and the identification of variations in the M . oryzae genome , but also open a door to explore new virulence mechanism of the pathogen for effective blast control [2 , 9] .', 'In this study , we reported the genome and interactive transcriptome analyses of isolate 98–06 that is known to be one dominant field isolate containing as many as seven AVR genes ( Avr-Pik/km/kp , AvrPiz-t , Avr-Piz5 , Avr-Pita2 , Avr-Pish , Avr-Pi20 , and Avr-Pi9 ) .', 'Among them , Avr-Pik/km/kp [16] , AvrPiz-t [38] , and Avr-Pi9 [53] were characterized .', 'Avr-Pik/km/kp ( allele D ) and AvrPiz-t were also identified in our study .', 'Our analysis indicated that isolate 98–06 contains an extra 1 . 4 Mb of genomic sequences not present in 70–15 , while a whole-genome dot-plot alignment of 98–06 and P131 suggested good genome synteny ( S15 Fig ) .', 'To examine whether the extra genomic region is present in other isolates , we searched the genomes of isolates P131 and Y34 that found that 49 genes remain unique to isolate 98–06 .', 'COG classification revealed that , while the functions for most of these genes were unknown , those identified exhibit functions relevant to general characteristics , secondary metabolites , and energy metabolism ( S2 Fig ) .', 'Yoshida et al . [16] observed that presence or absence of effector gene polymorphisms are often associated with unstable genomic regions near the chromosome ends .', 'It is therefore hypothesized that isolate-specific regions located at the chromosomal ends supply new effectors and pathogenicity-related factors to drive genome evolution .', 'The dynamic adaptation of M . oryzae may be primarily achieved by deletion or recovery of AVR genes [54] .', 'Such hypotheses indicate that further genome sequencing of multiple M . oryzae isolates is warranted for characterizing rice pathogenic strains , as key information can be discovered only by exploring beyond the “core” genomes [16] .', 'One good example is that the extensive chromosomal rearrangement in asexual fungus V . dahliae establishes dynamic , lineage-specific regions that provide new effectors as a general mechanism of adaptation [35] .', 'Although sexual reproduction can occur in M . oryzae under laboratory conditions , it has not been observed in nature .', 'Such asexual organisms are often considered to be less flexible than sexual organisms [55 , 56] , so that the expanded genome is likely to represent examples of evolutionary tradeoffs , as the cost of maintaining the extra DNA is counterbalanced by the functional advantages it confers [57] .', 'Since horizontal gene transfer ( HGT ) enables the acquisition of new genes and functions [57] , we hypothesize that some of these isolate-specific genes might also be acquired by HGT to drive the evolutionary process .', 'Based on the genome data of isolate 98–06 , our transcriptome analysis provides a further molecular view of M . oryzae and rice gene expression during infection .', 'The major expression patterns of M . oryzae genes relevant to pathogenicity remain high throughout the infection process , with the exception of a sharp decline at 24 hpi ( Fig 3A ) .', 'The decreased expression pattern might due to low levels of transcript detection at 24 hpi , with only 2 , 426 genes ( M . oryzae ) compared with at least 5 , 161 genes for other infection stages .', 'This is consistent with the previous discovery that expression of known pathogenicity genes was unchanged or down-regulated at 36 hpi [4] .', 'We should point out that our RNA-Seq analyses were carried out without sample duplication that could result in potentially biased interpretation of the transcriptome data .', 'Nevertheless , the result is agreeable with that from validation of several selected genes through qRT-PCR .', 'Effectors are known key pathogenicity determinants that modulate plant innate immunity and enable disease development in plant-pathogen interactions [58] .', 'Several AVR genes have been previously isolated by map-based cloning , genetic association analysis , or loss-of-function approaches [7 , 16 , 59 , 60 , 61 , 62] .', 'Most of these effectors are small secreted proteins lacking homology to known proteins [63 , 64 , 65] .', 'In characterizing the isolate 98–06 genome , we found 645 small candidate effectors with an average 3 . 11% cysteine content from 1 , 732 putative secreted proteins .', 'Biotrophic invasive-specific expression is one of the best indicators for identifying new blast effectors [65] .', 'Based on the gene expression data , we found that BAS1
['Introduction', 'Results', 'Discussion', 'Materials and Methods']
['Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution , in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates .', 'This same principle applies to the rice blast pathogen Magnaporthe oryzae and the rice host; however , genetic variations among different isolates of M . oryzae remain largely unknown , particularly at genome and transcriptome levels .', 'Here , we applied genomic and transcriptomic analytical tools to investigate M . oryzae isolate 98-06 that is the most aggressive in infection of susceptible rice cultivars .', 'A unique 1 . 4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15 .', 'Genome-wide expression profiling revealed the presence of two critical expression patterns of M . oryzae based on 64 known pathogenicity-related ( PaR ) genes .', 'In addition , 134 candidate effectors with various segregation patterns were identified .', 'Five tested proteins could suppress BAX-mediated programmed cell death in Nicotiana benthamiana leaves .', 'Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity .', 'Moreover , Iug6 and Iug9 are located exclusively in the biotrophic interfacial complex ( BIC ) and their overexpression leads to suppression of defense-related gene expression in rice , suggesting that they might participate in biotrophy by inhibiting the SA and ET pathways within the host .', 'Thus , our studies identify novel effector and PaR proteins involved in pathogenicity of the highly aggressive M . oryzae field isolate 98-06 , and reveal molecular and genomic dynamics in the evolution of M . oryzae and rice host interactions .']
['Genetic variations in pathogens , such as the causal agent of rice blast Magnaporthe oryzae , often lead to circumvention of disease-resistance cultivars .', 'Previous genome-wide analyses of model organisms suggest that pathogen effectors are also rapidly evolving , especially in regions with high genome plasticity .', 'However , genetic variations among different isolates remain largely unknown in M . oryzae , particularly at the genome and transcriptome levels .', 'In this study , we provided a systematic genomic and interaction transcriptome profile for a dominant rice blast field isolate , resulting in identification of 134 candidate effectors .', 'Two effectors , Iug6 and Iug9 , and one pathogenicity-related ( PaR ) gene product , Iug18 , were subjected to functional characterization .', 'We found that Iug6 and Iug9 are located in the biotrophic interfacial complex ( BIC ) and their overexpression leads to suppression of defense-related gene expression in rice , while Iug18 appears to be a novel PaR protein .', 'Our studies support the hypothesis that isolate-unique genes may serve as a source of genetic variability in the M . oryzae population encountering different environments .', 'Our studies also facilitate further understanding of effectors and genomic variations in pathogenicity of M . oryzae .']
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