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Background:
The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface-dwelling extremophile, based on long-read DNA sequencing technology, to assess possible mechanisms associated with genome co...
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... [16]. A relatively small number of protein-coding genes was annotated in P. fructicola (8072) (average size = 500 aa) (Fig. S1), compared with the fungal phytopathogens Sphaerulina populicola (9739) and Passalora fulva (14,127). P. fructicola has higher gene density than other characterized Dothideomycetes species, except for B. compniacensis (Fig. 3). The genomic size of P. fructicola is similar to that of the basidiomycete Ustilago maydis (19.66 Mb) [17], but P. fructicola has higher gene density (425 per Mb vs. 345 per Mb) and shorter average intron ( Fig. 2c and Fig. S2) and intergenic length (Fig. 2d). There is little difference in gene density between P. fructicola and compact ...
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... fructicola, 8057 were supported by at least one FPKM (Fragments per kilobase of exon per million reads mapped), and 7658 models were supported by at least 10 FPKM. Among the predicted genes, 6010 genes had matches to entries in the PFAM database, 7575 genes had matches in the non-redundant database and 5723 were mapped to Gene Ontology (GO) terms (Fig. S3). We re-predicted a previous draft genome of P. fructicola [12] using the pipeline developed in this study (see methods section) and obtained 7604 gene models. To compare gene content between the current and former annotations of P. fructicola, we used BUSCO v.1.2 to search for a set of 1438 fungi universal single-copy orthologous genes ...
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... [16]. A relatively small number of protein-coding genes was annotated in P. fructicola (8072) (average size = 500 aa) (Fig. S1), compared with the fungal phytopathogens Sphaerulina populicola (9739) and Passalora fulva (14,127). P. fructicola has higher gene density than other characterized Dothideomycetes species, except for B. compniacensis (Fig. 3). The genomic size of P. fructicola is similar to that of the basidiomycete Ustilago maydis (19.66 Mb) [17], but P. fructicola has higher gene density (425 per Mb vs. 345 per Mb) and shorter average intron ( Fig. 2c and Fig. S2) and intergenic length (Fig. 2d). There is little difference in gene density between P. fructicola and compact ...
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... fructicola, 8057 were supported by at least one FPKM (Fragments per kilobase of exon per million reads mapped), and 7658 models were supported by at least 10 FPKM. Among the predicted genes, 6010 genes had matches to entries in the PFAM database, 7575 genes had matches in the non-redundant database and 5723 were mapped to Gene Ontology (GO) terms (Fig. S3). We re-predicted a previous draft genome of P. fructicola [12] using the pipeline developed in this study (see methods section) and obtained 7604 gene models. To compare gene content between the current and former annotations of P. fructicola, we used BUSCO v.1.2 to search for a set of 1438 fungi universal single-copy orthologous genes ...
Citations
... The high error rate inherent to this system is then accounted for by using its long-read output in conjunction with short-read data to assemble highly accurate and exceedingly long contiguous sequences [20]. In fungi, this approach has allowed for the assembly of chromosome-scale sequences, often spanning from telomere to telomere [22][23][24][25]. Such complete or near-complete assemblies thus allow for investigations into the structural and architectural properties of genomes, and the role these play in the biology of fungi, as well as their overall genome evolution [22,26]. ...
The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome’s distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.
... The high error rate inherent to this system is then accounted by using its long-read output in conjunction with short-read data to assemble highly accurate and exceedingly long, contiguous sequences [27]. In fungi, this approach has allowed for the assembly of chromosome-scale sequences, often spanning from telomere to telomere [29][30][31][32]. Such complete or near complete assemblies thus allow for investigations into the structural and architectural properties of genomes, and the role these play in the biology of fungi, as well as their overall genome evolution [29,33]. ...
The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threads to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness, and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome-level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome's distal and proximal regions. These regions, characterized by a lower gene density and G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. Comparison of overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggested a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.
... In the Basmati 334 rice genome, using Nanopore long reads, Choi et al. assembled the Basmati 334 genome to the chromosome level [88]. For the fungus Peltaster fructicola, the Nanopore long reads are sufficient to assemble a complete genome [102]. LTH has already been used to clone>10 Pi genes and other R genes. ...
The widely used rice variety Lijiangxintuanheigu (LTH) shows a universal susceptibility to thousands of Magnaporthe oryzae isolates, the causal agent of devastating rice blast, making LTH an ideal line in resistance (R) gene cloning. However, the underlying genetic mechanism of the universal susceptibility has not been fully revealed because of the lack of a high-quality genome. Here, we took a genomic approach together with experimental assays to investigate LTH’s universal susceptibility to rice blast. Using Nanopore long reads, we assembled a chromosome-level genome. Millions of genomic variants were detected by comparing LTH with 10 other rice varieties, of which large-effect variants could affect plant immunity. Gene family analyses show that the number of R genes and leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding genes decrease significantly in LTH. Rice blast resistance genes called Pi genes are either absent or disrupted by genomic variations. Additionally, residual R genes of LTH are likely under weak pathogen selection pressure, and other plant defense-related genes are weakly induced by rice blast. In contrast, the pattern-triggered immunity (PTI) of LTH is normal, as demonstrated by experimental assays. Therefore, we conclude that weak effector-trigger immunity (ETI)-mediated primarily by Pi genes but not PTI results in the universal susceptibility of LTH to rice blast. The attenuated ETI of LTH may be also associated with reduced numbers of R genes and LRR-RLKs, and minimally functional residual defense-related genes. Finally, we demonstrate the use of the LTH genome by rapid cloning of the Pi gene Piak from a resistant variety.
... The removal of deleterious TEs can be very efficient [66][67][68]. In plant pathogens, closely related Box 2. Genome size expansions in filamentous pathogens Genome size can differ among closely related fungal species [77,78] and even within a single species [49,50,79]. A striking example of genome size expansion comes from rust fungi that have massively expanded genomes. ...
Transposable elements (TEs) spread in genomes through self-copying mechanisms and are a major cause of genome expansions. Plant pathogens have finely tuned the expression of virulence factors to rely on epigenetic control targeted at nearby TEs. Stress experienced during the plant infection process leads to derepression of TEs and concurrently allows the expression of virulence factors. We argue that the derepression of TEs elements causes an evolutionary conflict by favoring TEs that can be reactivated. Active TEs and recent genome size expansions indicate that plant pathogens could face long-term consequences from the short-term benefit of fine-tuning the infection process. Hence, encoding key virulence factors close to TEs under epigenetic control constitutes a devil’s bargain for pathogens.
... Counterintuitively, T. adhaerens is one of the simplest free-living multicellular animals (Srivastava et al. 2008) . The large variability of intron densities owes to remarkable differences in rates of intron loss through eukaryotic evolution (Roy and Gilbert 2005; al. microsporidia as well as saccharomycetous yeasts (Byrne and Wolfe 2005;Neuvéglise et al. 2011;Hooks et al. 2014;Corradi 2015;Han and Weiss 2017;Whelan et al. 2019;Priest et al. 2020;Wang et al. 2020) . For instance, only 4% of S. cerevisiae genes have introns. ...
Current evolutionary reconstructions predict that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. However, some extant eukaryotes have few introns, raising the question as to why these few introns are retained. Here we have used recently available fungal genomes to address this question. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species support the idea that massive intron loss has occurred in multiple clades. The intron densities estimated in the fungal ancestral states differ from zero to 8.28 introns per one kbp of protein-coding gene. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts (0.01 and 0.05 introns/kbp on average, respectively), but also in diverse smuts and allies (e.g. Ustilago maydis , Meira miltonrushii and Malassezia globosa have 0.06, 0.10 and 0.20 introns/kbp, respectively). To investigate the roles of introns, we searched for their special characteristics using 1302 orthologous genes from eight intron-poor fungi. Notably, most of these introns are found close to the translation initiation codons. Our transcriptome and translatome data analyses showed that these introns are from genes with both higher mRNA expression and translation efficiency. Furthermore, these introns are common in specific classes of genes (e.g. genes involved in translation and Golgi vesicle transport), and rare in others (e.g. base-excision repair genes). Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
Microsporidia and Apicomplexa are eukaryotic, single‐celled, intracellular parasites with huge public health and economic importance. Typically, these parasites are studied separately, emphasizing their uniqueness and diversity. In this review, we explore the huge amount of genomic data that has recently become available for the two groups. We compare and contrast their genome evolution and discuss how their transitions to intracellular life may have shaped it. In particular, we explore genome reduction and compaction, genome expansion and ploidy, gene shuffling and rearrangements, and the evolution of centromeres and telomeres.
Complete chromosomal-level assemblies of fungal genomes are rare. The intimate ecological symbioses and complex reproduction strategies utilized by fungi make highly contiguous, gapless genome assemblies particularly difficult. Here, we use long-read sequencing on the Oxford Nanopore Technology MinION platform to sequence and assemble the genome of Lepraria neglecta ( Ascomycota , Lecanorales ). In addition to eight contigs ascribable to chromosomes, six of which are assembled telomere-to-telomere, we discovered the presence of a complete MAT locus with two conserved MAT1-2 genes and a putative MAT1-1 pseudogene. The full genome assembly of a widespread, common species presents an opportunity for new insights into lichen reproduction while the presence of the mating-type locus in the genome of an asexual lichen raises fundamental questions about reproductive biology in fungi generally.
Pneumocystis species colonize mammalian lungs and cause deadly pneumonia if the immune system of the host weakens. Each species presents a specificity for a single mammalian host species. Pneumocystis jirovecii infects humans and provokes pneumonia, which is among the most frequent invasive fungal infections. The lack of in vitro culture methods for these fungi complicates their study. Recently, high-throughput sequencing technologies followed by comparative genomics have allowed a better understanding of the mechanisms involved in the sexuality of Pneumocystis organisms. The structure of their mating-type locus corresponding to a fusion of two loci, Plus and Minus, and the concomitant expression of the three mating-type genes revealed that their mode of sexual reproduction is primarily homothallism. This mode is favored by microbial pathogens and involves a single self-compatible mating type that can enter into the sexual cycle on its own. Pneumocystis sexuality is obligatory within the host's lungs during pneumonia in adults, primary infection in children, and possibly colonization. This sexuality participates in cell proliferation, airborne transmission to new hosts, and probably antigenic variation, processes that are crucial to ensure the survival of the fungus. Thus, sexuality is central in the Pneumocystis life cycle. The obligate biotrophic parasitism with obligate sexuality of Pneumocystis is unique among fungi pathogenic to humans. Pneumocystis organisms are similar to the plant fungal obligate biotrophs that complete their entire life cycle within their hosts, including sex, and that are also difficult to grow in vitro.
Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron-exon structures, and raising the question as to why these few introns are retained. Here we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per one kbp of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and non-coding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
