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Sugarcane leaf blight (SLB), a major fungal leaf disease of sugarcane (Saccharum spp.), has been attributed to Stagonospora tainanensis. In December 2020 and May 2021, signs of leaf blight were observed on sugarcane in the fields of Chongzuo City, in the Guangxi Province of China. Lesions on the leaves were characterized by yellow or dark red spots in the center. Fungal species were isolated, purified and subjected to pathogenicity evaluation on the sugarcane plants. An isolate that caused symptoms the same as those observed in the field was initially identified as S. tainanensis (Leptosphaeria taiwanensis, perfect state) based on its morphological characteristics both of asexual and sexual stages. Dark brown and nearly spherical pycnidia with conidia of long ellipsoidal, hyaline, one to four cells and 29.27 to 54.39 μm long and 9.03 to 16.12 μm wide were found on corn meal agar medium. Ascomata with asci of cylindrical to clavate, a short stipe and eight spores slightly constricted at the septum, with the size of the spore ranging from 36 to 44 μm long and 8.5 to 12 μm wide, were formed on the sugarcane-leaf-decoction saccharose agar medium. The identity of the species was further confirmed by rDNA ITS and TEF-1α sequencing. The optimal temperature for mycelial growth was 25 °C and the optimal pH was 6.0. The pathogen grew well in a medium with oats as the carbon source and yeast extract as the nitrogen source, but poorly in a medium with urea as the nitrogen source. This study is the first to identify the sugarcane leaf blight pathogen in Guangxi, and the first publication describing the biological characterization of S. tainanensis. The occurrence of sugarcane leaf blight should alert sugarcane breeders and plant pathologists to consider integrating control of this potentially important disease into the agenda of their breeding and disease control programs. [ABSTRACT FROM AUTHOR]

The sexual morph Leptosphaeria taiwanensis Yen and Chi and its asexual morph Stagonospora tainanensis W. H. Hsieh is an important necrotrophic fungal phytopathogen, which causes sugarcane leaf blight, resulting in loss of cane tonnage and sucrose in susceptible sugarcane varieties. Decoding the genome and understanding of the basis of virulence is vitally important for devising effective disease control strategies. Here, we present a 38.25-Mb high-quality genome assembly of S. tainanensis strain StFZ01, denovo assembled with 10.19 Gb Nanopore sequencing long reads (~267×) and 3.82 Gb Illumina short reads (~100×). The genome assembly consists of 12 contigs with N50 of 2.86 Mb of which 5 belong to the telomere to telomere (T2T) chromosome. It contains 13.20% repeat sequences, 12,543 proteins, and 12,206 protein-coding genes with the BUSCO completeness 99.18% at fungi (n = 758) and 99.87% at ascomycota (n = 1706), indicating the high accuracy and completeness of our gene annotations. The virulence analysis in silico revealed the presence of 2379 PHIs, 599 CAZys, 248 membrane transport proteins, 191 cytochrome P450 enzymes, 609 putative secreted proteins, and 333 effectors in the StFZ01 genome. The genomic resources presented here will not only be helpful for development of specific molecular marker and diagnosis technique, population genetics, molecular taxonomy, and disease managements, it can also provide a significant precise genomic reference for investigating the ascomycetous genome, the necrotrophic lifestyle, and pathogenicity in the future. [ABSTRACT FROM AUTHOR]

Sugarcane leaf blight (SLB), a major fungal leaf disease of sugarcane (Saccharum spp.), has been attributed to Stagonospora tainanensis. In December 2020 and May 2021, signs of leaf blight were observed on sugarcane in the fields of Chongzuo City, in the Guangxi Province of China. Lesions on the leaves were characterized by yellow or dark red spots in the center. Fungal species were isolated, purified and subjected to pathogenicity evaluation on the sugarcane plants. An isolate that caused symptoms the same as those observed in the field was initially identified as S. tainanensis (Leptosphaeria taiwanensis, perfect state) based on its morphological characteristics both of asexual and sexual stages. Dark brown and nearly spherical pycnidia with conidia of long ellipsoidal, hyaline, one to four cells and 29.27 to 54.39 μm long and 9.03 to 16.12 μm wide were found on corn meal agar medium. Ascomata with asci of cylindrical to clavate, a short stipe and eight spores slightly constricted at the septum, with the size of the spore ranging from 36 to 44 μm long and 8.5 to 12 μm wide, were formed on the sugarcane-leaf-decoction saccharose agar medium. The identity of the species was further confirmed by rDNA ITS and TEF-1α sequencing. The optimal temperature for mycelial growth was 25 °C and the optimal pH was 6.0. The pathogen grew well in a medium with oats as the carbon source and yeast extract as the nitrogen source, but poorly in a medium with urea as the nitrogen source. This study is the first to identify the sugarcane leaf blight pathogen in Guangxi, and the first publication describing the biological characterization of S. tainanensis. The occurrence of sugarcane leaf blight should alert sugarcane breeders and plant pathologists to consider integrating control of this potentially important disease into the agenda of their breeding and disease control programs.

The sexual morph Leptosphaeria taiwanensis Yen and Chi and its asexual morph Stagonospora tainanensis W. H. Hsieh is an important necrotrophic fungal phytopathogen, which causes sugarcane leaf blight, resulting in loss of cane tonnage and sucrose in susceptible sugarcane varieties. Decoding the genome and understanding of the basis of virulence is vitally important for devising effective disease control strategies. Here, we present a 38.25-Mb high-quality genome assembly of S. tainanensis strain StFZ01, denovo assembled with 10.19 Gb Nanopore sequencing long reads (~267×) and 3.82 Gb Illumina short reads (~100×). The genome assembly consists of 12 contigs with N50 of 2.86 Mb of which 5 belong to the telomere to telomere (T2T) chromosome. It contains 13.20% repeat sequences, 12,543 proteins, and 12,206 protein-coding genes with the BUSCO completeness 99.18% at fungi (n = 758) and 99.87% at ascomycota (n = 1706), indicating the high accuracy and completeness of our gene annotations. The virulence analysis in silico revealed the presence of 2379 PHIs, 599 CAZys, 248 membrane transport proteins, 191 cytochrome P450 enzymes, 609 putative secreted proteins, and 333 effectors in the StFZ01 genome. The genomic resources presented here will not only be helpful for development of specific molecular marker and diagnosis technique, population genetics, molecular taxonomy, and disease managements, it can also provide a significant precise genomic reference for investigating the ascomycetous genome, the necrotrophic lifestyle, and pathogenicity in the future.

Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the characterization of LecRKs and their responses to sugarcane leaf blight (SLB) triggered by Stagonospora tainanensis. A total of 429 allelic and non-allelic LecRKs, which were classified into evolved independently three types according to signal domains and phylogeny, were identified based on the genome. Regarding those closely related LecRKs in the phylogenetic tree, their motifs and exon architectures of representative L- and G-types were similar or identical. LecRKs showed an unequal distribution on chromosomes and more G-type tandem repeats may come from the gene expansion. Comparing the differentially expressed LecRKs (DELs) in response to SLB in sugarcane hybrid and ancestor species S. spontaneum, we found that the DEL number in the shared gene sets was highly variable among each sugarcane accession, which indicated that the expression dynamics of LecRKs in response to SLB were quite different between hybrids and particularly between sugarcane hybrid and S. spontaneum. In addition, C-type LecRKs may participate in metabolic processes of plant–pathogen interaction, mainly including pathogenicity and plant resistance, indicating their putative roles in sugarcane responses to SLB infection. The present study provides a basic reference and global insight into the further study and utilization of LecRKs in plants.

Sugarcane is an important sugar and potential energy crop, and the complexity of its genome has led to stagnant progress in genome decipherment and hindered the genome-wide analysis of the nucleotide binding site leucine-rich repeat (NLR) receptor until the genome of Saccharum spontaneum was published. From the genome of S. spontaneum, 724 allelic and non-allelic NLRs were identified and classified into five types (N, NL, CN, CNL, and P) according to domain architectures and integrity and at least 35 genes encoded non-canonical domains. The phylogenetic analysis indicated NLRs containing the coiled-coil (CC) domain separated from those without CC in six Poaceae species, including S. spontaneum. The motif analysis determined the characteristics and potential functions of the 137 representative non-allelic NLRs, especially the core motifs contained in the NBS and LRR domains, which indicated that motifs were regularly distributed among clades. Through transcription factor binding site (TFBS) profiles, we predicted that the most important transcription regulator of NLRs in sugarcane were ERF, MIKC_MADS, and C2H2. In addition, based on three sets of transcriptome data from two sugarcane hybrids and one S. spontaneum clone infected by the necrotrophic fungal pathogen Stagonospora tainanensis causing sugarcane leaf blight (SLB), the expression dynamics of NLRs responding to the infection in three sugarcane clones were compared. The different genetic background led to the significant difference of NLRs response to SLB in different sugarcane clones, and we got an inference of the potential mechanism of SLB resistance. These results provided a basic reference and new insights to further study and utilize the NLRs.

Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the characterization of LecRKs and their responses to sugarcane leaf blight (SLB) triggered by Stagonospora tainanensis. A total of 429 allelic and non-allelic LecRKs, which were classified into evolved independently three types according to signal domains and phylogeny, were identified based on the genome. Regarding those closely related LecRKs in the phylogenetic tree, their motifs and exon architectures of representative L- and G-types were similar or identical. LecRKs showed an unequal distribution on chromosomes and more G-type tandem repeats may come from the gene expansion. Comparing the differentially expressed LecRKs (DELs) in response to SLB in sugarcane hybrid and ancestor species S. spontaneum, we found that the DEL number in the shared gene sets was highly variable among each sugarcane accession, which indicated that the expression dynamics of LecRKs in response to SLB were quite different between hybrids and particularly between sugarcane hybrid and S. spontaneum. In addition, C-type LecRKs may participate in metabolic processes of plant–pathogen interaction, mainly including pathogenicity and plant resistance, indicating their putative roles in sugarcane responses to SLB infection. The present study provides a basic reference and global insight into the further study and utilization of LecRKs in plants. [ABSTRACT FROM AUTHOR]

Sugarcane is an important sugar and potential energy crop, and the complexity of its genome has led to stagnant progress in genome decipherment and hindered the genome-wide analysis of the nucleotide binding site leucine-rich repeat (NLR) receptor until the genome of Saccharum spontaneum was published. From the genome of S. spontaneum, 724 allelic and non-allelic NLRs were identified and classified into five types (N, NL, CN, CNL, and P) according to domain architectures and integrity and at least 35 genes encoded non-canonical domains. The phylogenetic analysis indicated NLRs containing the coiled-coil (CC) domain separated from those without CC in six Poaceae species, including S. spontaneum. The motif analysis determined the characteristics and potential functions of the 137 representative non-allelic NLRs, especially the core motifs contained in the NBS and LRR domains, which indicated that motifs were regularly distributed among clades. Through transcription factor binding site (TFBS) profiles, we predicted that the most important transcription regulator of NLRs in sugarcane were ERF, MIKC_MADS, and C2H2. In addition, based on three sets of transcriptome data from two sugarcane hybrids and one S. spontaneum clone infected by the necrotrophic fungal pathogen Stagonospora tainanensis causing sugarcane leaf blight (SLB), the expression dynamics of NLRs responding to the infection in three sugarcane clones were compared. The different genetic background led to the significant difference of NLRs response to SLB in different sugarcane clones, and we got an inference of the potential mechanism of SLB resistance. These results provided a basic reference and new insights to further study and utilize the NLRs. [ABSTRACT FROM AUTHOR]