Fig 1.
Alternative transcript splicing in R. solani AG1-IB 7/3/14.
Transcript isoforms for selected genes are shown. Each line with bars represents a transcript isoform. The pileup track below the isoforms shows the amount of reads that were mapped to the corresponding genomic region. (A) A gene for which only one transcript isoform was identified. Sharp intron-exon borders are visible. (B) Intron retention is the most common alternative splicing event observed in R. solani AG1-IB. (C) A gene whose transcript exists in three isoforms featuring exon-skipping as well as intron-retention.
Table 1.
Comparison of gene prediction results applying the specific vs. the C. cinerea gene model on the R. solani AG1-IB 7/3/14 draft genome.
Fig 2.
Comparison of gene prediction results applying the R. solani AG1-IB specific and the C. cinerea gene model.
The diagrams exemplarily illustrates the gene prediction results obtained by application of the new gene model based on R. solani AG1-IB gene structure data and the previous gene model based on C. cinerea parameters. (A) Contig84 and (B) Contig25832 were chosen as examples for gene prediction. Corresponding EST sequence were mapped to the contigs for reference purposes. Based on isotig mapping, wrongly detected intron-exon junctions could be detected in case of the gene prediction by the C. cinerea model. The black line above the alignment results represents the scale in base pairs [bp].
Table 2.
Genome features of completely sequenced R. solani isolates.
Fig 3.
Venn diagram of the gene-based genome comparison for the completely sequenced R. solani isolates representing AG1-IA, AG1-IB, AG3 and AG8.
The core genome of all isolates consists of 2922 genes. These genes are present in the genomes of all sequenced R. solani isolates: R. solani AG1-IB 7/3/14 [EMBL:CDGK01000001 –CDGK01018395 (Contigs); LN679100 –LN679996 (Scaffolds)], R. solani AG3 [GenBank: JATN0100000], R. solani AG1-IA [Genbank: AFRT00000000] and R. solani AG8 [GenBank: AVOZ0000000]. For computation of the Venn diagram, default settings of EDGAR [13] were applied.
Table 3.
Examples of predicted unique gene products for R. solani isolates representing AG1-IA, AG1-IB, AG3 and AG8.
Fig 4.
Taxonomic classification of the different R. solani isolates representing AG1-IA, AG1-IB, AG3 and AG8.
The phylogenetic tree is based on all core genes (725) of the selected strains as determined by means of the comparative genomics tool EDGAR [13]. The corresponding tree was calculated within EDGAR. It includes R. solani AG1-IB (isolate 7/3/14) [3,4], R. solani AG1-IA (isolate B275) [5], R. solani AG3 (isolate Rhs1AP) [6], R. solani AG8 (isolate WAC10335) [7], C. cinerea okayama 7#130 [24], P. indica DSM 11827 [25] and Cryptococcus neoformans var neoformans JEC21 [26].
Table 4.
Pairwise Average Nucleotide Identity (ANI) analyses for completely sequenced R. solani isolates.
Table 5.
Pairwise Average Amino-acid Identity (AAI) analyses for completely sequenced R. solani isolates.
Table 6.
Pairwise Average Amino-acid Identity (AAI) and Average Nucleotide Identity (ANI) analyses for completely sequenced fungal isolates.