Fig 1.
(A) Developmental stages in the S. scitamineum life cycle: diploid teliospores (2n); haploid yeast-like sporidia (n) after meiosis (R!); hyphal fusion. (B) Scanning electron micrograph of spores adhered to sugarcane bud surface. (C) Germination of spores on bud scale epidermis and tube-like promycelium formation at 6 hai (hours after inoculation); photomicrograph of tube-like promycelium stained with lactophenol-cotton. (D) Photomicrograph of apressorium formation 48 hai stained with lactophenol-cotton blue; (E) Photomicrograph of S. scitamineum growth on parenchyma cells of bud tissue observed at 120 hr stained with lactophenol-cotton blue. (F) Photomicrograph of S. scitamineum intracellular growth on parenchyma cells of white whip portion; stained with lactophenol-cotton blue. (G) Photomicrograph of black whip portion showing the mature spore liberation. Scale bar = 5 μm
Fig 2.
Representation of all chromosomes and contigs assembled of the strain SSC39 genome compared to the strain 2014001 scaffolds.
Regions present in the strain 2014001 are shown in green blocks, delimited by black borders. White regions represent sequences unique to the strain SSC39 assembly. The analysis was performed using MUMmer 3 and parameters = -maxmatch -c -L -b -l 500. Red line above the chromosome 2 indicates the region containing the mating-type loci
Fig 3.
Syntenic view of two chromosomes of S. reilianum that merged as one in S. scitamineum.
Links represents alignment length of more than 1 kbp obtained by BLASTn (e-value < 1 x 10-5). The first outer circle represents the chromosome and scale is coordinates in base pairs. The second indicates the GC content followed by predicted coding regions of the plus and minus strands. Bars display the % of identity to orthologous in S. reilianum. The most inner circle represents the RNAseq coverage of each chromosome region. Red lines are RNAseq data of S. scitamineum growing in planta and blue lines growing in vitro. Circle images of all chromosomes are available in the Supporting Information S3 File.
Fig 4.
Blocks of synteny between chromosome 2 of S. scitamineum and chromosomes 1 and 20 of S. reilianum and schematic representation of the linked mating-type loci in S. scitamineum.
Blue areas correspond to syntenic regions considering BLASTn e-value ≤ 1 x 10-5. Red lines represent the expansion of the region containing the mating type genes in S. scitamineum located at positions 792,295 bp to 863,606 bp of the chromosome 2. The chromosome breakpoint is identified and indicated by a red dot above the sequence. Genes are indicated by gray arrows placed according to transcriptional orientation and the transposons related sequences are highlighted in red. Letters represent functional annotation of encoded proteins: A) c1d1 putative nuclear regulator; B and C) homeodomain transcription factor bE1 and bW1, respectively; D) nat1 putative N-terminal acetyltransferase; E, F, M, N, P, Q and R) Uncharacterized protein; G, J, M and S) Related to transposase; H) sla—cytoskeleton assembly control protein; I) RPN5-26S proteasome regulatory protein; K) hhp1 casein kinase-1; L) related to reverse transcriptase; O) arp2/3—actin related protein 2/3 complex; T) lba1 left border a locus; U) and V) pheromone gene mfa1.2 and mfa1.3, respectively; W) pra1 pheromone receptor gene; X) Rba2—right border a locus; Y) pan1—pantoate-beta-alanine ligase.
Table 1.
Comparative analysis of orthology among four smut fungi obtained by OrthoMCL.
Fig 5.
Genes encoding secreted proteins and their expression level under all three conditions: in vitro, 5 DAI, 200 DAI as calculated by CLC Genomics Workbench.
Heatmaps were obtained using the function heatmap.2 of the package gplots in R language
Table 2.
List of selected differentially expressed genes up-regulated in planta. For complete list view Tables C and D in S8 File.
Fig 6.
Chromosome segments representing the organization of genes in islands (color coded arrows and note colors beneath the bars).
Expression at 200 DAI (heatmap red scale) and in vitro(heat map blue scale) are compared using the normalized number of mapped Illumina paired end reads, represented by the scales under each chromosome island. Gene names are presented at the borders of each segment of the chromosome, numbers represent the coordinates of these islands in kbp and red dots represent singlets as defined by OrthoMCL