De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways

Morphology of Saro-13 isolate used for whole genome sequencing. (PDF 13621 kb

WAG model of ML tree

Based on orthoMCL clustering, 100 single copy ortholog gene groups from five fungal species were selected randomly and aligned separately using MUSCLE version 3.8.31 with default parameters. All hundred Multiple Sequence Alignments (MSA) were concatenated. Then, 1000 bootstrap replicates were performed using SEQBOOT program in Phylip package version 3.696. The maximum-likelihood tree was constructed by PhyML V3.1 (--datatype aa --model WAG --bootstrap 1000) with 1000 bootstrap replicates to infer phylogenetic relationship of Sarocladium oryzae in relation to other Ascomycetes fungi (Magnaporthe oryzae, Fusarium graminearum, Acremonium chrysogenum, and Fusarium oxysporum). The consensus tree constructed using CONSENSE in Phylip package

Additional file 10: of De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways

Protein sequences of putative gene clusters involved in Helvolic acid biosynthesis. (DOCX 134 kb

Genome-Wide In Silico Identification, Structural Analysis, Promoter Analysis, and Expression Profiling of <i>PHT</i> Gene Family in Sugarcane Root under Salinity Stress

The phosphate transporter (PHT) family of proteins plays an imperative role in regulating phosphorus (P) acquisition as well as in translocation from the soil into cells and organs. Phosphorus is an essential macronutrient required for plant life that is not readily available to crops, and resources are diminishing rapidly because of the huge needs of global agriculture. In this study, 23 ShPHT genes were identified in the sugarcane (Saccharum spp.) genome through a comprehensive genome-wide in silico analysis. Phylogeny, gene structure, and conserved motif analysis of PHT genes in sugarcane (ShPHTs) indicated five subfamilies (PHT1-4 and PHO1 subfamily). Gene ontology (GO) analysis revealed that the ShPHT genes were largely involved in phosphate ion transport, phosphate starvation, stimulus response, stress response, and symporter activity. Gene expression analysis under salinity stress confirmed strong induction of PHT genes in wild genotype sugarcane (IND99-907). PHT1-1, PHT1-2, and PHT1-3 members were notably up-regulated in roots under salt stress. The upstream region of PHT genes contained PHR1-binding sites (P1BS), MYB-type, and WRKY- type binding elements. Overall, the present study paves the way for a deeper understanding of the evolution of sugarcane PHT genes and their role in salinity and Pi stress tolerance in sugarcane

Genome-Wide In Silico Identification, Structural Analysis, Promoter Analysis, and Expression Profiling of PHT Gene Family in Sugarcane Root under Salinity Stress

The phosphate transporter (PHT) family of proteins plays an imperative role in regulating phosphorus (P) acquisition as well as in translocation from the soil into cells and organs. Phosphorus is an essential macronutrient required for plant life that is not readily available to crops, and resources are diminishing rapidly because of the huge needs of global agriculture. In this study, 23 ShPHT genes were identified in the sugarcane (Saccharum spp.) genome through a comprehensive genome-wide in silico analysis. Phylogeny, gene structure, and conserved motif analysis of PHT genes in sugarcane (ShPHTs) indicated five subfamilies (PHT1-4 and PHO1 subfamily). Gene ontology (GO) analysis revealed that the ShPHT genes were largely involved in phosphate ion transport, phosphate starvation, stimulus response, stress response, and symporter activity. Gene expression analysis under salinity stress confirmed strong induction of PHT genes in wild genotype sugarcane (IND99-907). PHT1-1, PHT1-2, and PHT1-3 members were notably up-regulated in roots under salt stress. The upstream region of PHT genes contained PHR1-binding sites (P1BS), MYB-type, and WRKY- type binding elements. Overall, the present study paves the way for a deeper understanding of the evolution of sugarcane PHT genes and their role in salinity and Pi stress tolerance in sugarcane