A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens
1 State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
2 College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
3 College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
BMC Genomics 2013, 14:883 doi:10.1186/1471-2164-14-883Published: 16 December 2013
Additional file 1: Figure S1:
Neighbor-joining phylogenetic tree of 18S rRNA gene sequences. Phylogenetic tree showing the phylogenetic position of the strain UV-8b and the strains of the genera Villosiclava, Trichoderma, Metarhizium, Cordyceps and Torrubiella. Percentages at nodes are bootstrap values based on 1,000 replications. The scale bar represents 0.01 substitutions per nucleotide position. The 18S rRNA gene sequences of the strains UV-8b and UV-2 were generated in our laboratory. The 18S rRNA gene sequence of T. reesei QM6a was obtained by the draft genome sequence in BLAST. The 18S rRNA gene sequences of other strains were obtained from GenBank.
Format: PNG Size: 423KB Download file
Additional file 2: Figure S2:
Insert size analysis of randomly selected UV-8b BAC clones. The plasmid DNA of 180 randomly selected BAC clones from the UV-8b BAC library were digested with I-SceI, and the DNA fragments were separated on 1% CHEF agarose gel. Lane 21 was the MidRange PFG marker I (NEB). V is vector.
Format: PNG Size: 311KB Download file
Additional file 3:
Contig quality evaluation. The primers have been designed from repeat sequence masked BAC end sequences and were used to verify the overlap between clones in PhaseIA contig.
Format: DOC Size: 5.9MB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 4: Table S1:
Information about the SSRs and the primers. With the SSRs and their flanking sequences as input, a total of 836 pairs primers were designed for SSR loci by Primer3 program.
Format: XLS Size: 224KB Download file
This file can be viewed with: Microsoft Excel Viewer