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Title: Genome Sequence of Fusarium oxysporum f. sp. melonis, a fungus causing wilt disease on melon

Author
item MA, LI-JUN - University Of Massachusetts
item SHEA, TERRANCE - Broad Institute Of Mit/harvard
item YOUNG, SARAH - Broad Institute Of Mit/harvard
item ZENG, QIANDONG - Broad Institute Of Mit/harvard
item Kistler, Harold

Submitted to: Genome Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/16/2014
Publication Date: 7/31/2014
Citation: Ma, L., Shea, T., Young, S., Zeng, Q., Kistler, H.C. 2014. Genome Sequence of Fusarium oxysporum f. sp. melonis, a fungus causing wilt disease on melon. Genome Announcements. 2(4):e00730-14.

Interpretive Summary: Fusarium oxysporum is a fungus responsible for billions of dollars in losses to agricultural plants. We have conducted research aimed at understanding how this harmful pathogen is able to cause disease on a broad range of plant species. To do this we have obtained the whole genome sequence of several strains of the fungus capable of causing disease on different hosts. This paper describes the characteristics of the genome of a strain that causes wilt disease on melons. By comparing this genome to previously described genomes from strains that infect other hosts we may be able to define those factors that are necessary for this host-specific virulence. Factors that control expression of important traits potentially could be exploited for disease control measures. These disease management strategies may involve disruption of vital fungal developmental pathways. The primary users of the research in this publication will be other scientists engaged in research to improve disease management on small grain crops.

Technical Abstract: This manuscript reports the genome sequence of F. oxysporum f. sp. melonis, a fungal pathogen that causes Fusarium wilt disease on melon (Cucumis melo). The project is part of a large comparative study designed to explore the genetic composition and evolutionary origin of this group of horizontally transferred chromosomes among a set of selected strains that capture the pathogenic and phenotypic diversity. The total genomic DNA was extracted from strain NRRL 26406, a field isolate originally collected from Mexico. The strain was deposited and available at the USDA ARS Culture Collection (also known as the NRRL Collection). Over 150-fold sequence coverage and over 100 physical coverage sequences were generated from two libraries, an 180-base fragment and 3-kb jumps. and sequenced using Illumina sequencing technology. Assemblies were generated using ALLPATHS-LG (versions R37753) run with default parameters (kmer size of 96) (Gnerre S, 2011 #1114). Mitochondrial sequences were removed by searching against an NCBI mitochondrial database. The genome size was estimated to be 68 Mb based on kmer frequency of initial reads using KmerSpectrum, a module run within ALLPATHS-LG (Gnerre S, 2011 #1114). The assembled genome size is 54.03 Mb with a GC content of 47.5%. The discrepancy in the estimated genome size and the assembled genome is caused by the highly repetitive nature of this genome. Over 28% of the original reads are repetitive. The assembly is organized in 1,832 contigs, in 1,152 scaffolds. The average base is found in a scaffold with an N50 of 2.2 Mb and a contig with an N50 of 430 kb.