Biology subjects

Tomimoto, S.

Publications and source records attributed to Tomimoto, S..

3 recordsLinked to original sources

bioRxiv2023

The molecular clock in long-lived tropical trees is independent of growth rate

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly-constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation. Significance StatementThe significance of our study lies in the discovery of an absolute time-dependent accumulation of somatic mutations in long-lived tropical trees, independent of growth rate. Through a comparative analysis of somatic mutation landscapes in slow- and fast-growing species, we observed a clock-like accumulation of somatic mutations in both species, regardless of their growth rates. Although the majority of somatic mutations were restricted to a single branch, we also identified mutations present in multiple branches, likely transmitted during growth. Our findings suggest that older trees make a greater contribution towards generating genetic variation.

evolutionary biology↗

bioRxiv2022

The genetic structure within a single tree is determined by the behavior of the stem cells in the meristem

Genomic sequencing revealed that somatic mutations cause a genetic differentiation of the cells in a single tree. In this study, we consider a mathematical model for stem cell proliferation in the shoot apical meristem (abbrev. SAM), which results in genetic diversification between the cells differing in the distance along the shoot and the angle around a shoot axis. The assumptions are as follows. Stem cells in the SAM normally undergo asymmetric cell division and produce successor stem cells and differentiated cells. The differentiated cells proliferate and contribute to shoot elongation. Occasionally, a stem cell is replaced by a copy of an adjacent stem cell. We discuss the "coalescent length" between cells indicating their genetic difference with respect to neutral mutations. A mathematical analysis revealed the following. The genetic diversity of cells sampled at the same position along the shoot increases with the distance from the bottom of the shoot. Stem cells hold a larger variation if they are replaced only by the nearest neighbors than if they are replaced by any cells. The coalescent length between two cells increases not only with the difference in the position along the shoot but also in the angle around the shoot axis. The dynamics of stem cells at the SAM determine the genetic pattern of the entire shoot.

evolutionary biology↗

bioRxiv2022

Modelling somatic mutation accumulation and expansion in a long-lived tree with hierarchical modular architecture

In a long-lived organism with a modular architecture, such as trees, somatic mutations accumulate throughout the long lifespan and result in genetic mosaicism in each module within the same individual. In recent years, next-generation sequencing technology has provided a snapshot of such intra-organismal genetic variability. However, the dynamic processes underlying the accumulation and expansion of somatic mutations during the growth remain poorly understood. In this study, we constructed a model to describe these processes in a form that can be applied to a real tree. Given that the proliferation dynamics of meristematic cells vary across plant species, multiple possible processes for elongation and branching were comprehensively expressed in our model. Using published data from a poplar tree, we compared the prediction of the models with the observation and explained the cell lineage dynamics underlying somatic mutations accumulation that were not evident from the snapshot of the sequenced data. We showed that the somatic genetic drift during growth increases inter-meristem mosaicism, resulting in genetically distinct branches and less integrity within an individual tree. We also showed that the somatic genetic drift during branching leads to the mutation accumulation pattern that does not reflect the tree topology. Our modelling framework can help interpret and provide further insights into the empirical findings of genetic mosaicism in long-lived trees.

plant biology↗