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PLoS One
2014 Jan 14;91:e81832. doi: 10.1371/journal.pone.0081832.
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The genome sequence of the fungal pathogen Fusarium virguliforme that causes sudden death syndrome in soybean.
Srivastava SK
,
Huang X
,
Brar HK
,
Fakhoury AM
,
Bluhm BH
,
Bhattacharyya MK
.
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UNLABELLED: Fusarium virguliforme causes sudden death syndrome (SDS) of soybean, a disease of serious concern throughout most of the soybean producing regions of the world. Despite the global importance, little is known about the pathogenesis mechanisms of F. virguliforme. Thus, we applied Next-Generation DNA Sequencing to reveal the draft F. virguliforme genome sequence and identified putative pathogenicity genes to facilitate discovering the mechanisms used by the pathogen to cause this disease.
METHODOLOGY/PRINCIPAL FINDINGS: We have generated the draft genome sequence of F. virguliforme by conducting whole-genome shotgun sequencing on a 454 GS-FLX Titanium sequencer. Initially, single-end reads of a 400-bp shotgun library were assembled using the PCAP program. Paired end sequences from 3 and 20 Kb DNA fragments and approximately 100 Kb inserts of 1,400 BAC clones were used to generate the assembled genome. The assembled genome sequence was 51 Mb. The N50 scaffold number was 11 with an N50 Scaffold length of 1,263 Kb. The AUGUSTUS gene prediction program predicted 14,845 putative genes, which were annotated with Pfam and GO databases. Gene distributions were uniform in all but one of the major scaffolds. Phylogenic analyses revealed that F. virguliforme was closely related to the pea pathogen, Nectria haematococca. Of the 14,845 F. virguliforme genes, 11,043 were conserved among five Fusarium species: F. virguliforme, F. graminearum, F. verticillioides, F. oxysporum and N. haematococca; and 1,332 F. virguliforme-specific genes, which may include pathogenicity genes. Additionally, searches for candidate F. virguliforme pathogenicity genes using gene sequences of the pathogen-host interaction database identified 358 genes.
CONCLUSIONS: The F. virguliforme genome sequence and putative pathogenicity genes presented here will facilitate identification of pathogenicity mechanisms involved in SDS development. Together, these resources will expedite our efforts towards discovering pathogenicity mechanisms in F. virguliforme. This will ultimately lead to improvement of SDS resistance in soybean.
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24454689
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Figure 1. Synteny of Fusarium virguliforme Mont1 sequences to the Nectria haematococca chromosomal sequences.The colored blocks show the alignment of F. virguliforme sequences to the sequences of the N. haematococca chromosomes. Blocks below the central line indicate the regions that align in the reverse complement orientation.
Figure 2. Non-uniform gene density in the F. virguliforme genome.Gene density of over 23 major scaffolds of the F. virguliforme genome is presented. Size of individual scaffold is presented in blue histograms covering 36.2 Mb (scale on the left) of the total 51 Mb genome. Gene density (number of genes/10 Kb) is presented with the green line (scale of the right).
Figure 3. Heat-map depicting the Pfam domains in all Fusarium species.
F. virguliforme genome is rich in Pkinase_Tyr (Protein tyrosine kinase), Ank (Ankyrin repeat), and HET (Heterokaryon incompatibility proteins) as compared to the other Fusarium genomes.
Figure 4. Phylogenetic tree showing the relationship of F. virguliforme with other Fusarium species.The tree was constructed using 10 randomly selected single copy orthologous genes using PHYML program (WAG model of evolution) with 1,000 bootstraps.
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