Abstract
BackgroundRice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. However, the genomic information for this fungal pathogen is limited and the pathogenic mechanism of this disease is still not clear. To facilitate genetic, molecular and genomic studies of this fungal pathogen, we constructed the first BAC-based physical map and performed the first genome survey for this species.ResultsHigh molecular weight genomic DNA was isolated from young mycelia of the Villosiclava virens strain UV-8b and a high-quality, large-insert and deep-coverage Bacterial Artificial Chromosome (BAC) library was constructed with the restriction enzyme HindIII. The BAC library consisted of 5,760 clones, which covers 22.7-fold of the UV-8b genome, with an average insert size of 140 kb and an empty clone rate of lower than 1%. BAC fingerprinting generated successful fingerprints for 2,290 BAC clones. Using the fingerprints, a whole genome-wide BAC physical map was constructed that contained 194 contigs (2,035 clones) spanning 51.2 Mb in physical length. Bidirectional-end sequencing of 4,512 BAC clones generated 6,560 high quality BAC end sequences (BESs), with a total length of 3,030,658 bp, representing 8.54% of the genome sequence. Analysis of the BESs revealed general genome information, including 51.52% GC content, 22.51% repetitive sequences, 376.12/Mb simple sequence repeat (SSR) density and approximately 36.01% coding regions. Sequence comparisons to other available fungal genome sequences through BESs showed high similarities to Metarhizium anisopliae, Trichoderma reesei, Nectria haematococca and Cordyceps militaris, which were generally in agreement with the 18S rRNA gene analysis results.ConclusionThis study provides the first BAC-based physical map and genome information for the important rice fungal pathogen Villosiclava virens. The BAC clones, physical map and genome information will serve as fundamental resources to accelerate the genetic, molecular and genomic studies of this pathogen, including positional cloning, comparative genomic analysis and whole genome sequencing. The BAC library and physical map have been opened to researchers as public genomic resources (http://gresource.hzau.edu.cn/resource/resource.html).
Highlights
Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world
Phylogenetic analysis of strain UV-8b The V. virens strain UV-8b was a single spore isolated from Japonica rice Zhonghua 11
Analysis of 180 random Bacterial Artificial Chromosome (BAC) clones showed that the library had an average insert size of 140 kb with a size range from 25 to 190 kb and an empty-vector rate of lower than 1% (Table 1; Additional file 2: Figure S2)
Summary
Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. Rice false smut caused by Villosiclava virens (Cooke Tak) (anamorph Ustilaginoidea virens) [1,2] has emerged as a devastating disease in rice, due to the intense application of nitrogen and phosphorus fertilizers and the cultivation of high-yielding semi-dwarf rice cultivars worldwide [3]. Rice false smut was considered as a minor rice disease because of its rare occurrence in limited regions, but this disease has spread widely in the last 20 years and. Atia et al first investigated rice false smut in Egypt and reported that the production loss caused by this pathogen ranged from 1.0% to 10.9% [8]. Fu et al described the morphologic characteristics more precisely [3]
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