A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens

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).

An aldo-keto reductase is responsible for Fusarium toxin-degrading activity in a soil Sphingomonas strain

“…A BAC vector was prepared with Hin d III (Fermentas, MA, USA) from the high-copy composite vector pHZAUBAC1 and was used for construction of a BAC library with Hin d III digested genomic DNA isolated from strain S3-4 as previously described 31 . One mL overnight culture for each BAC clone was suspended in 1 mL MM containing DON (20 μg/mL).…”

Status of Rice False Smut Disease in Natore District of Bangladesh

“…High relative humidity (>90%), temperature between 25 and 30°C and rainydays at the time of flowering are the favourable environmental factors for the disease infection, as mentioned by Atia (2004). However, wide use of high-yielding varieties with semidwarf characteristics (Wang et al, 2013) and especially hybrids (Han et al, 2015) with heavy application of nitrogenous (Li et al, 2013) and phosphorus fertilizer (Wang et al, 2013) in rice cultivation and late sowing have also favoured the disease. All those claims, hypotheses and speculations have not been tested under Bangladesh conditions.…”

Chloramphenicol Derivatives with Antibacterial Activity Identified by Functional Metagenomics

“…Thus, protection of the C-3 primary hydroxy group of 1 with TBSCl using imidazole as a base in dichloromethane gave compound 13. Acylation of 13 with acyl chloride using pyridine as a base in dichloromethane afforded compound 14, which was deprotected with ptoluenesulfonic acid in H 2 O−THF (1:4) to furnish the final products 1-acetylchloramphenicol (15), 1-propanoylchloramphenicol (16), 1-cinnamoylchloramphenicol (17), and 1-p-nitrobenzoylchloramphenicol (18) (Scheme 2; see detailed synthetic procedures in the Supporting Information). a Both have the same structure, with 9 an isolated natural product and 11 a synthetic compound.…”

“…19 Screening larger-insert metagenomic libraries for antimicrobial activity is advantageous due to the higher probability that a recombinant clone will encode an intact biosynthetic gene cluster or antimicrobial peptides. In this study, we screened a soil metagenomic library containing 110 Kb average size inserts constructed in a copy-inducible BAC vector 17,20 for recombinant clones that inhibited MRSA metabolic activity. We identified seven metagenomic clones that were capable of modifying chloramphenicol (Cm) to biologically active Cm derivatives.…”