Fusarium species section Liseola namely F. fujikuroi, F. proliferatum, F. andiyazi, F. verticillioides, and F. sacchari are well-known plant pathogens on rice, sugarcane and maize. In the present study, restriction analysis of the intergenic spacer regions (IGS) was used to characterize the five Fusarium species isolated from rice, sugarcane and maize collected from various locations in Peninsular Malaysia. From the analysis, and based on restriction patterns generated by the six restriction enzymes, Bsu151, BsuRI, EcoRI, Hin6I, HinfI, and MspI, 53 haplotypes were recorded among 74 isolates. HinfI showed the most variable restriction patterns (with 11 patterns), while EcoRI showed only three patterns. Although a high level of variation was observed, it was possible to characterize closely related species and isolates from different species. UPGMA cluster analysis showed that the isolates of Fusarium from the same species were grouped together regardless of the hosts. We conclude that restriction analysis of the IGS regions can be used to characterize Fusarium species section Liseola and to discriminate closely related species as well as to clarify their taxonomic position.
Restriction endonuclease analyses (REAs) constitute the only inexpensive molecular approach capable of typing and characterizing human adenovirus (HAdV) strains based on the entire genome. However, the application of this method is limited by the need for time-consuming and labor-intensive procedures. We herein developed a simple and cost-effective REA for assessing HAdV. The method consists of (1) simple and cost-effective DNA extraction, (2) fast restriction endonuclease (RE) digestion, and (3) speedy mini agarose gel electrophoresis. In this study, DNA was isolated according to the kit-based method and 21.0 to 28.0 μg of viral DNA was extracted from prototypes (HAdV-1, HAdV-3, HAdV-4, and HAdV-37) in each flask. The amount of DNA ranged from 11.4 to 57.0 μg among the HAdV-3 (n=73) isolates. The obtained viral DNA was found to be applicable to more than 10 types of REAs. Fast-cut restriction endonucleases (REs) were able to digest the DNA within 15 minutes, and restriction fragments were easily separated via horizontal mini agarose gel electrophoresis. The whole procedure for 10 samples can be completed within approximately six hours (the conventional method requires at least two days). These results show that our REA is potentially applicable in many laboratories in which HAdVs are isolated.
The blue swimming crab (Portunus pelagicus) is a valuable marine fishery resource in Indo-West Pacific Ocean. So far, rare genetic resource of this species is available. In this report, the restriction-site associated DNA (RAD) approach was employed to mine the genomic information and identify molecular markers in P. pelagicus. A total of 0.82 Gbp clean data were generated from the genome of individual "X2A". De novo assembly produced 85,796 contigs with an average length of 339 bp. A total of 45,464 putative SNPs and 17,983 microsatellite loci were identified from the genomes of ten individuals. Furthermore, 31 pairs of primers were successfully designed, with 16 of them exhibiting polymorphism in a wild population. For these polymorphic loci, the expected and observed alleles per locus ranged from 1.064 to 7.314 and from 2 to 11, respectively. The expected and observed heterozygosity per locus ranged from 0.0615 to 0.819 and from 0.0626 to 1.000, respectively. Nine loci showed high informative with polymorphism information content (PIC) > 0.5. Five loci significantly deviated from Hardy-Weinberg equilibrium in the samples analyzed. No linkage disequilibrium was found among the 16 polymorphic microsatellite loci. This study provided massive genetic resource and polymorphic molecular markers that should be helpful for studies on conservation genetics, population dynamics and genetic diversity of P. pelagicus and related crab species.