In this study we sequenced, assembled and annotated the genome sequences of three F. fujikuroi isolates (FGSC 8932, KSU X-10626 and KSU 3368) and performed a comparative genomic analysis including two recently published F. fujikuroi genome sequences (IMI 58289 and B14). Sequencing was performed on the Illumina HiSeq 2000 platform or on the Illumina MiSeq. Assembly was performed by Velvet (http://www.ebi.ac.uk/~zerbino/velvet) while scaffolding was performed by SSPACE (http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE). Genome size were of 43.096, 43.110 and 43.199 Mb, with number of predicted coding genes of 14.832, 14.801 and 15.188 for FGSC 8932, X-10626 and KSU 3368 respectively. Species specific genes (SS = 1017) and Lineage specific genes (LS = 1210) are enriched in transcription factors, transporters and genes associated with secondary metabolites (SM) production. 496 SS and 547 LS genes appear to derive from F. fujikuroi recent gene duplication. Subtelomeric regions, which constitute about 14% of the genomes and contain 32% of the intra-specific SNPs, exhibit a marginal but significant increase (53% vs 51%) in AT content with respect to the rest of the genome as well as reduced gene density (0.25 genes per kb vs 0.38 genes per kb). These regions are significantly enriched in LS and SS genes in all F. fujikuroi isolates. Composition and rearrangement of genes and gene clusters involved in SM production are mostly conserved across all the F. fujikuroi strains. FGSC 8932 lacks the PKS19 gene and much of its putative gene cluster; it also lacks seven genes of the fumonisin biosynthetic cluster, consistent with the lack of fumonisin production by this isolate. Orthologs of the IMI58289 NRPS10 and NRPS31 genes are absent in KSU X-10626 and B14. In these two strains the distal subtelomeric region of chr IV, which is interested by a deletion in the proximal subtelomeric region in IMI58289, contains an additional PKS gene with an associated cluster of 6 genes, closely related to a homologous cluster in F. oxysporum. This cluster is partially conserved in FGSC 8932. Twenty-three SM clusters fall in sub-telomeric regions. All clusters predicted to be complete are potentially active as they contain no deletions or premature stop codons. Variations in SM cluster profiles are mostly explained by gene loss events. Our comparative analysis confirm that Fusarium genus has the genetic potential to produce many more SM than previously thought. Subtelomeric regions represent "hot-houses" for the generation of molecular diversity relevant for pathogenic lifestyles. Horizontal gene transfer and gene duplication are key elements in genome evolution in F. fujikuroi, although rapid divergence of recently duplicated sequences might be driven by a Repeat Induced Point Mutation-like mechanism.
Genome sequencing of multiple isolates highlights sub-telomeric genomic diversity within Fusarium fujikuroi
Fanelli F;Pesole G;Logrieco AF;
2015
Abstract
In this study we sequenced, assembled and annotated the genome sequences of three F. fujikuroi isolates (FGSC 8932, KSU X-10626 and KSU 3368) and performed a comparative genomic analysis including two recently published F. fujikuroi genome sequences (IMI 58289 and B14). Sequencing was performed on the Illumina HiSeq 2000 platform or on the Illumina MiSeq. Assembly was performed by Velvet (http://www.ebi.ac.uk/~zerbino/velvet) while scaffolding was performed by SSPACE (http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE). Genome size were of 43.096, 43.110 and 43.199 Mb, with number of predicted coding genes of 14.832, 14.801 and 15.188 for FGSC 8932, X-10626 and KSU 3368 respectively. Species specific genes (SS = 1017) and Lineage specific genes (LS = 1210) are enriched in transcription factors, transporters and genes associated with secondary metabolites (SM) production. 496 SS and 547 LS genes appear to derive from F. fujikuroi recent gene duplication. Subtelomeric regions, which constitute about 14% of the genomes and contain 32% of the intra-specific SNPs, exhibit a marginal but significant increase (53% vs 51%) in AT content with respect to the rest of the genome as well as reduced gene density (0.25 genes per kb vs 0.38 genes per kb). These regions are significantly enriched in LS and SS genes in all F. fujikuroi isolates. Composition and rearrangement of genes and gene clusters involved in SM production are mostly conserved across all the F. fujikuroi strains. FGSC 8932 lacks the PKS19 gene and much of its putative gene cluster; it also lacks seven genes of the fumonisin biosynthetic cluster, consistent with the lack of fumonisin production by this isolate. Orthologs of the IMI58289 NRPS10 and NRPS31 genes are absent in KSU X-10626 and B14. In these two strains the distal subtelomeric region of chr IV, which is interested by a deletion in the proximal subtelomeric region in IMI58289, contains an additional PKS gene with an associated cluster of 6 genes, closely related to a homologous cluster in F. oxysporum. This cluster is partially conserved in FGSC 8932. Twenty-three SM clusters fall in sub-telomeric regions. All clusters predicted to be complete are potentially active as they contain no deletions or premature stop codons. Variations in SM cluster profiles are mostly explained by gene loss events. Our comparative analysis confirm that Fusarium genus has the genetic potential to produce many more SM than previously thought. Subtelomeric regions represent "hot-houses" for the generation of molecular diversity relevant for pathogenic lifestyles. Horizontal gene transfer and gene duplication are key elements in genome evolution in F. fujikuroi, although rapid divergence of recently duplicated sequences might be driven by a Repeat Induced Point Mutation-like mechanism.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
