41 Results
for author "Yun-Xin Fu"
Figure 1Procedures used to explore new REs for GBS application. A flow chart for exploring restriction enzyme (RE) pairs for a genome-by-sequencing (GBS) application to increase genome coverage of a species through in silico analysis and empirical validation. The genome coverage is measured by the proportion of the genome covered by a selected set of DNA fragments digested with a RE or RE pair. IgC and EgC are the genome coverages of a species estimated from in silico analysis and empirical validation, respectively. Two shell scripts (IgCoverage1RE.sh and IgCoverage2RE.sh) are part of software IgCoverage developed for this study.- Table 1The in silico genome coverages (IgC; %) of four plant species by DNA fragments of different lengths (100–600 bp) obtained from in silico digestions with 60 individual restriction enzymes
- Table 2The in silico genome coverages (IgC; %) of 22 species with sequenced genomes (eight plant, 13 animal, and one fungus) by DNA fragments of different ends and lengths (100–600 bp) obtained from in silico digestions with the top 21 restriction enzyme pairs and the GBS reference pair PstI + MspI
Figure 2Fragment distributions detected in silico on selected chromosomes of Arabidopsis and rice. Distributions of DNA fragments generated by in silico digestions with three restriction enzyme combinations on two chromosomes of Arabidopsis thaliana (A, B) and Oryza sativa (C, D). The number of DNA fragments and the average enzyme-cutting position based on a 100 kb sliding-window of a given chromosome are calculated and shown with a colored line for each enzyme combination. The corresponding horizontal linear line represents the average fragment count for an enzyme combination on the chromosome. More digestions were found for HinfI + HpyCh4IV than the other two enzyme combinations.- Table 3The empirical genomic coverages (EgC) for three restriction enzyme combinations (PM = PstI + MspI, AB = AvaII + BfaI, and HH = HinfI + HpyCH4IV) and the ratio of the EgC relative to PM (Ratio to PM) in six dicot and six monocot species
- Table 4Statistics of contig and mean contig length per sample obtained for two restriction enzyme combinations (PM = PstI + MspI; HH = HinfI + HpyCH4IV) in combined runs of 12 Arabidopsis and 12 rice samples
- Table 5Statistics of contigs and single nucleotide polymorphisms obtained for two restriction enzyme combinations (PM = PstI + MspI; HH = HinfI + HpyCH4IV) in combined runs of 12 Arabidopsis and 12 rice samples
Figure 3SNP distributions for two RE pairs in Arabidopsis and rice. Distribution of total single nucleotide polymorphisms detected with respect to the number of samples present, and average number of reads per sample, for two restriction enzyme combinations (PM = PstI + MspI; HH = HinfI + HpyCH4IV) in combined runs of 12 Arabidopsis and 12 rice samples.