Chromosome segments representing the organization of genes in islands (color coded arrows and note colors beneath the bars).

<p>Expression at 200 DAI (heatmap red scale) and <i>in vitro</i>(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</p

Syntenic view of two chromosomes of <i>S. reilianum</i> that merged as one in <i>S. scitamineum</i>.

<p>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 <i>S. reilianum</i>. The most inner circle represents the RNAseq coverage of each chromosome region. Red lines are RNAseq data of <i>S. scitamineum</i> growing in planta and blue lines growing <i>in vitro</i>. Circle images of all chromosomes are available in the Supporting Information <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129318#pone.0129318.s003" target="_blank">S3 File</a>.</p

Representation of all chromosomes and contigs assembled of the strain SSC39 genome compared to the strain 2014001 scaffolds.

<p>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 <i>loci</i></p

Blocks of synteny between chromosome 2 of <i>S. scitamineum</i> and chromosomes 1 and 20 of <i>S. reilianum</i> and schematic representation of the linked mating-type <i>loci</i> in <i>S. scitamineum</i>.

<p>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 <i>S. scitamineum</i> 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) <i>c1d1</i> putative nuclear regulator; B and C) homeodomain transcription factor <i>bE1</i> and <i>bW1</i>, respectively; D) <i>nat1</i> putative N-terminal acetyltransferase; E, F, M, N, P, Q and R) Uncharacterized protein; G, J, M and S) Related to transposase; H) <i>sla</i>—cytoskeleton assembly control protein; I) RPN5-26S proteasome regulatory protein; K) <i>hhp1</i> casein kinase-1; L) related to reverse transcriptase; O) <i>arp2/3</i>—actin related protein 2/3 complex; T) <i>lba1</i> left border <i>a</i><i>locus</i>; U) and V) pheromone gene <i>mfa1.2</i> and <i>mfa1.3</i>, respectively; W) <i>pra1</i> pheromone receptor gene; X) <i>Rba2</i>—right border <i>a locus</i>; Y) <i>pan1</i>—pantoate-beta-alanine ligase.</p

Complete Genome Sequence of <i>Sporisorium scitamineum - Fig 1 </i> and Biotrophic Interaction Transcriptome with Sugarcane

<p>(A) Developmental stages in the <i>S. scitamineum</i> 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 <i>S. scitamineum</i> growth on parenchyma cells of bud tissue observed at 120 hr stained with lactophenol-cotton blue. (F) Photomicrograph of <i>S. scitamineum</i> 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 <i>μ</i>m</p

Comparative analysis of orthology among four smut fungi obtained by OrthoMCL.

<p>Comparative analysis of orthology among four smut fungi obtained by OrthoMCL.</p

Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane

Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage.Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions