Image_1_Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum.JPEG

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) is a cosmopolitan fungus that has been reported from soil, herbivore dung, and as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. Taking advantage of the fact that this species produces prolific numbers of perithecia in culture, the genome of F. neocosmosporiellum was sequenced and transcriptomic analysis across five stages of perithecium development was performed to better understand the metabolic potential for sexual development and gain insight into its life history. Perithecium morphology together with the genome and transcriptome were compared with those of the plant pathogen F. graminearum, a model for studying perithecium development. Larger ascospores of F. neocosmosporiellum and their tendency to discharge as a cluster demonstrated a duality of dispersal: the majority are passively dispersed through the formation of cirrhi, while a minority of spores are shot longer distances than those of F. graminearum. The predicted gene number in the F. neocosmosporiellum genome was similar to that in F. graminearum, but F. neocosmosporiellum had more carbohydrate metabolism-related and transmembrane transport genes. Many transporter genes were differentially expressed during perithecium development in F. neocosmosporiellum, which may account for its larger perithecia. Comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during later stages of perithecium development. Deletion of a polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype, suggesting an important role of the corresponding metabolite, which has yet to be identified, in perithecium development. Results of this study have provided novel insights into the genomic underpinning of development in F. neocosmosporiellum, which may help elucidate its ability to occupy diverse ecological niches.</p

Table_1_Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum.XLSX

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) is a cosmopolitan fungus that has been reported from soil, herbivore dung, and as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. Taking advantage of the fact that this species produces prolific numbers of perithecia in culture, the genome of F. neocosmosporiellum was sequenced and transcriptomic analysis across five stages of perithecium development was performed to better understand the metabolic potential for sexual development and gain insight into its life history. Perithecium morphology together with the genome and transcriptome were compared with those of the plant pathogen F. graminearum, a model for studying perithecium development. Larger ascospores of F. neocosmosporiellum and their tendency to discharge as a cluster demonstrated a duality of dispersal: the majority are passively dispersed through the formation of cirrhi, while a minority of spores are shot longer distances than those of F. graminearum. The predicted gene number in the F. neocosmosporiellum genome was similar to that in F. graminearum, but F. neocosmosporiellum had more carbohydrate metabolism-related and transmembrane transport genes. Many transporter genes were differentially expressed during perithecium development in F. neocosmosporiellum, which may account for its larger perithecia. Comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during later stages of perithecium development. Deletion of a polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype, suggesting an important role of the corresponding metabolite, which has yet to be identified, in perithecium development. Results of this study have provided novel insights into the genomic underpinning of development in F. neocosmosporiellum, which may help elucidate its ability to occupy diverse ecological niches.</p

Image_3_Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum.JPEG

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) is a cosmopolitan fungus that has been reported from soil, herbivore dung, and as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. Taking advantage of the fact that this species produces prolific numbers of perithecia in culture, the genome of F. neocosmosporiellum was sequenced and transcriptomic analysis across five stages of perithecium development was performed to better understand the metabolic potential for sexual development and gain insight into its life history. Perithecium morphology together with the genome and transcriptome were compared with those of the plant pathogen F. graminearum, a model for studying perithecium development. Larger ascospores of F. neocosmosporiellum and their tendency to discharge as a cluster demonstrated a duality of dispersal: the majority are passively dispersed through the formation of cirrhi, while a minority of spores are shot longer distances than those of F. graminearum. The predicted gene number in the F. neocosmosporiellum genome was similar to that in F. graminearum, but F. neocosmosporiellum had more carbohydrate metabolism-related and transmembrane transport genes. Many transporter genes were differentially expressed during perithecium development in F. neocosmosporiellum, which may account for its larger perithecia. Comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during later stages of perithecium development. Deletion of a polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype, suggesting an important role of the corresponding metabolite, which has yet to be identified, in perithecium development. Results of this study have provided novel insights into the genomic underpinning of development in F. neocosmosporiellum, which may help elucidate its ability to occupy diverse ecological niches.</p

Table_2_Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum.xlsx

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) is a cosmopolitan fungus that has been reported from soil, herbivore dung, and as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. Taking advantage of the fact that this species produces prolific numbers of perithecia in culture, the genome of F. neocosmosporiellum was sequenced and transcriptomic analysis across five stages of perithecium development was performed to better understand the metabolic potential for sexual development and gain insight into its life history. Perithecium morphology together with the genome and transcriptome were compared with those of the plant pathogen F. graminearum, a model for studying perithecium development. Larger ascospores of F. neocosmosporiellum and their tendency to discharge as a cluster demonstrated a duality of dispersal: the majority are passively dispersed through the formation of cirrhi, while a minority of spores are shot longer distances than those of F. graminearum. The predicted gene number in the F. neocosmosporiellum genome was similar to that in F. graminearum, but F. neocosmosporiellum had more carbohydrate metabolism-related and transmembrane transport genes. Many transporter genes were differentially expressed during perithecium development in F. neocosmosporiellum, which may account for its larger perithecia. Comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during later stages of perithecium development. Deletion of a polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype, suggesting an important role of the corresponding metabolite, which has yet to be identified, in perithecium development. Results of this study have provided novel insights into the genomic underpinning of development in F. neocosmosporiellum, which may help elucidate its ability to occupy diverse ecological niches.</p

Image_2_Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum.JPEG

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) is a cosmopolitan fungus that has been reported from soil, herbivore dung, and as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. Taking advantage of the fact that this species produces prolific numbers of perithecia in culture, the genome of F. neocosmosporiellum was sequenced and transcriptomic analysis across five stages of perithecium development was performed to better understand the metabolic potential for sexual development and gain insight into its life history. Perithecium morphology together with the genome and transcriptome were compared with those of the plant pathogen F. graminearum, a model for studying perithecium development. Larger ascospores of F. neocosmosporiellum and their tendency to discharge as a cluster demonstrated a duality of dispersal: the majority are passively dispersed through the formation of cirrhi, while a minority of spores are shot longer distances than those of F. graminearum. The predicted gene number in the F. neocosmosporiellum genome was similar to that in F. graminearum, but F. neocosmosporiellum had more carbohydrate metabolism-related and transmembrane transport genes. Many transporter genes were differentially expressed during perithecium development in F. neocosmosporiellum, which may account for its larger perithecia. Comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during later stages of perithecium development. Deletion of a polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype, suggesting an important role of the corresponding metabolite, which has yet to be identified, in perithecium development. Results of this study have provided novel insights into the genomic underpinning of development in F. neocosmosporiellum, which may help elucidate its ability to occupy diverse ecological niches.</p

FigS2_nop1_phenotypes

Triplet crossing plates between the wild type strains (A and B) and between the nop-1 knockout and the wild type strains (C and D) when cultured under constant light with sealed (A and C) and unsealed plates (B and D). Wild type crosses produced perithecia earlier when cultured under constant white light on sealed plates (A) than when cultured under constant white light on unsealed plates (B). matA ∆nop-1 cross with mata wild type exhibited wild type perithecial development when cultured under constant white light on sealed plates (C), but exhibited earlier and more abundant production of perithecia for ∆nop-1 when cultured under constant white light on unsealed plates (D). Conidiation (visible as orange pigment) is much more abundant on unsealed plates in all comparison

TableS4_Bagel_Dunlap_MBE_new

Results of BAGEL analyses for microarray data GSE8932. Relative gene expression analysis of 10 microarrays from Chen et al. (2009). Abbreviations: WT: wild type, nop: nop-1 knockout, Ref: pooled RNA reference, D: dark (DD), S: short light exposure (15–30 minutes, LL15, LL30), and L: long light exposure (60–120 minutes, LL60 and LL120)

Fungal opsin sequences analyzed

Sequences used in the evolutionary analyse

Key morphological characters of <i>N. crassa, N. tetrasperma</i> and <i>N. discreta</i> 144 h after crossing.

<p>Scanning electron micrographs, in which arrowheads indicate the perithecial beaks, of A) <i>N. crassa</i> (bar: 134 µm), B) <i>N. tetrasperma</i> (bar: 98 µm) and C) <i>N. discreta</i> (bar: 98 µm), and light micrographs of squash mounts of (D) <i>N. crassa</i> (a: ascus), (E) <i>N. tetrasperma</i>, and (F) <i>N. discreta</i> (with conidia). At 144 h, some spores are not fully mature.</p

Comparative analysis of meiosis-related genes, exhibiting differences in gene expression between <i>N. tetrasperma</i> (red dashed line), <i>N. crassa</i> (blue solid line) and <i>N. discreta</i> (green dash-dotted line).

<p>A) Expression of the <i>N. crassa</i> gene encoding chromosome segregation protein 3 was up-regulated during early sexual development in both <i>N. crassa</i> and in the orthologous gene in <i>N. discreta</i>, but the <i>N. tetrasperma</i> ortholog was down-regulated across sexual development, B) Expression of the gene encoding translation factor pelota in <i>N. crassa</i> and expression of its ortholog in <i>N. discreta</i> was consistent, but the ortholog in <i>N. tetrasperma</i> was dramatically and dynamically differentially expressed. C) Expression of meiosis specific gene <i>spo-11</i> and its orthologs was up-regulated for all three species from 96 h after crossing, but the up-regulation started early for the <i>N. tetrasperma</i> ortholog. D) Expression of <i>asm-1</i> (ascus maturation) in <i>N. crassa</i> and its orthologin <i>N. discreta</i> exhibited the same two-peaked pattern, featuring a peak of expression during early development of the perithecium and a second peak at a later stage of perithecial development, but the ortholog in <i>N. tetrasperma</i> exhibited only one peak 72 h after crossing. E) Expression of <i>N. crassa rsp</i> (round spore) and its ortholog in <i>N. discreta</i> exhibited up-regulation preceding 48 h, but upregulation in <i>N. tetrasperma</i> preceded 72 h. F). Expression of <i>N. crassa asd-3</i> (ascospore development) peaked at 72 h in <i>N. crassa,</i> as did its ortholog in <i>N. discreta</i>, but expression of the ortholog in <i>N. tetrasperma</i> peaked at 48 h. Error bars indicate the inferred 95% credible interval.</p