A universal sequencing read interpreter.

Massively parallel DNA sequencing has led to the rapid growth of highly multiplexed experiments in biology. These experiments produce unique sequencing results that require specific analysis pipelines to decode highly structured reads. However, no versatile framework that interprets sequencing reads to extract their encoded information for downstream biological analysis has been developed. Here, we report INTERSTELLAR (interpretation, scalable transformation, and emulation of large-scale sequencing reads) that decodes data values encoded in theoretically any type of sequencing read and translates them into sequencing reads of another structure of choice. We demonstrated that INTERSTELLAR successfully extracted information from a range of short- and long-read sequencing reads and translated those of single-cell (sc)RNA-seq, scATAC-seq, and spatial transcriptomics to be analyzed by different software tools that have been developed for conceptually the same types of experiments. INTERSTELLAR will greatly facilitate the development of sequencing-based experiments and sharing of data analysis pipelines.

Genome-wide analysis of intraspecific DNA polymorphism in 'Micro-Tom', a model cultivar of tomato (Solanum lycopersicum).

Tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. The genome sequencing of the tomato cultivar 'Heinz 1706' was recently completed. To accelerate the progress of tomato genomics studies, systematic bioresources, such as mutagenized lines and full-length cDNA libraries, have been established for the cultivar 'Micro-Tom'. However, these resources cannot be utilized to their full potential without the completion of the genome sequencing of 'Micro-Tom'. We undertook the genome sequencing of 'Micro-Tom' and here report the identification of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) between 'Micro-Tom' and 'Heinz 1706'. The analysis demonstrated the presence of 1.23 million SNPs and 0.19 million indels between the two cultivars. The density of SNPs and indels was high in chromosomes 2, 5 and 11, but was low in chromosomes 6, 8 and 10. Three known mutations of 'Micro-Tom' were localized on chromosomal regions where the density of SNPs and indels was low, which was consistent with the fact that these mutations were relatively new and introgressed into 'Micro-Tom' during the breeding of this cultivar. We also report SNP analysis for two 'Micro-Tom' varieties that have been maintained independently in Japan and France, both of which have served as standard lines for 'Micro-Tom' mutant collections. Approximately 28,000 SNPs were identified between these two 'Micro-Tom' lines. These results provide high-resolution DNA polymorphic information on 'Micro-Tom' and represent a valuable contribution to the 'Micro-Tom'-based genomics resources.

Examination of the relationship between the working conditions of young workers and the content of the meals they buy at convenience stores.

The aim of this study was to investigate the relationship between the working conditions of young workers and the meals they buy at convenience stores, and to consider the prevention of obesity. The subjects of this study were 284 workers under 29 yr of age employed at a transportation company in Ishikawa prefecture. Questionnaires were sent to participants, and 193 valid responses were obtained. Working types, night duty and working time were correlated with convenience store patronage, although working situations were not obviously associated with the content of meal selection at convenience stores. The study results revealed a tendency for the proportion of the fat in meals to be greater than 25% for the majority of working situations. It was also shown that foods selected with high frequency contained a high proportion of fat. There results suggest that this situation increases the risk of obesity. In addition, the more days per week convenience stores were patronized, the greater the number of participants felt "The need to improve meals." Therefore, we believe it is essential that young workers consider the prevention of obesity by observing nutritional information when selecting foods. An environment in which such information is easy to obtain at convenience stores should be arranged.