Researchers from France and the US have developed a manually curated database of well-supported genotype-phenotype associations among eukaryotes. As they describe in Nucleic Acids Research this week, the researchers built up the database, dubbed Gephebase, over the past 10 years and it currently contains more than 1,700 entries. These entries represent pairs of alleles that are associated with trait variation, whether it be naturally occurring variation, breeder-directed variation, or variation that occurred in the lab. The researchers say their database is "highly complementary to other available databases, which are more species-specific and which usually include more detailed information about genotype-phenotype relationships.
A team from Spain's Universidad Miguel Hernández reports on their use of simulated data to shape their approach to designing a mutation cloning project involving whole-genome sequencing, an endeavor that can be costly. They first gauged which short-read sequencing approach would best for analyzing the gene-rich genomic regions of Arabidopsis and what sequencing depth they'd need to confidently call SNVs. They additionally evaluated different experimental designs and tested their analysis workflows. "Our approach allowed us to obtain highly meaningful results for some experiments while quickly discarding dead-end approaches, saving laboratory resources," the authors write.
Columbia University's Eric Greene and his colleagues used DNA curtains to visualize how Bloom helicase, which helps preserve genomic integrity, acts on DNA molecules. As they report in Nucleic Acids Research, the researchers found that Bloom helicase can act quickly to unwind long expanses of double-stranded DNA, but that it doesn't appear to interact with single-stranded DNA. This could, the researchers say, have implications for the role of Bloom helicase in DNA replication and repair.