The rates and patterns of somatic mutations in wild plants, as well as how they relate to longevity, are largely unknown. Here, we examined the somatic mutation landscapes of slow- and fast-growing tropical species in central Borneo, Indonesia. Using newly-constructed genomes, we identified an average of 480 mutations in the slow-growing species (265-year-old, 44.1 m in height), which was five times greater than that observed in the fast-growing species (66-year-old, 43.9 m). The number of somatic mutations increased linearly with branch length. The somatic mutation rate per meter was higher in the slow-growing species, yet the rate per year remained constant across both species. The mutational spectra exhibited a dominance of spontaneous mutations, specifically cytosine-to-thymine substitutions at CpG sites. An analysis of nucleotide substitutions at both the intra- and inter-individual level revealed that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. We developed a model to evaluate the relative contribution of cell division on mutational processes, and postulate that cell-division independent mutagenesis predominates. These findings deepen our understanding of mutational processes underlying the generation of genetic diversity in a tropical ecosystem.
In the family Fagaceae, fertilization is delayed by several weeks to 1 year after pollination, leading to 1‐ or 2‐year fruiting species depending on whether fruiting occurs in the same or the next year after flowering. To investigate physiological responses underlying the regulation of delayed fertilization, we monitored seasonal changes in genome‐wide gene expression in tissues including leaves and buds over 2 years under natural conditions in one‐ (Quercus glauca) and 2‐year fruiting species (Lithocarpus edulis). Genes associated with metabolic changes in response to winter cold, photosynthesis and cell proliferation, which are essential for survival and growth, showed highly conserved seasonal expression profiles between species. However, seasonal expression profiles diverged between species in genes associated with pollination, an important process contributing to the origin and maintenance of the reproductive barrier between plant species. By comparing seasonal progression of ovule development and gene expression in pistillate flowers, we revealed that ovules started developing after winter in the 2‐year fruiting species, which could be linked to the activation of genes involved in fertilization and female gametophyte development after winter. These findings suggest that the 2‐year fruiting species may have evolved a requirement of winter cold to prevent fertilization before winter and facilitate fertilization and embryo development in the following spring when temperature rises. This study offers new possibilities to explore the evolution of reproductive strategies in Fagaceae.
In the family Fagaceae, fertilization is delayed by several weeks to one year after pollination, leading to one- or two-year fruiting species depending on whether fruiting occurs in the same or the next year after flowering. To investigate physiological responses underlying the regulation of delayed fertilization, we monitored seasonal changes in genome-wide gene expression in tissues including leaves and buds over two years under natural conditions in one- (Quercus glauca) and two-year fruiting species (Lithocarpus edulis). Genes associated with the responses to cold stress, photosynthesis, and cell proliferation, which are essential for survival and growth, showed highly conserved seasonal expression profiles regardless of species. However, seasonal expression profiles diverged between the one- and two-year fruiting species in genes associated with pollination, an important process contributing to the origin and maintenance of the reproductive barrier between plant species. By comparing seasonal progression of ovule development and gene expression in pistillate flowers, we revealed that ovules started developing after winter in the two-year fruiting species, which could be linked to the activation of genes involved in fertilization and female gametophyte development after winter. These findings suggest that the two-year fruiting species may have evolved a requirement of winter cold to prevent fertilization before winter and facilitate fertilization and embryo development in the following spring when temperature rises. This study offers new possibilities to explore the evolution of reproductive strategies in Fagaceae.
The rates and patterns of somatic mutations in wild plants, as well as how they relate to longevity, are largely unknown 1–3 . Here, we examined the somatic mutation landscapes of slow- and fast-growing tropical species in central Borneo, Indonesia. Using newly-constructed genomes, we identified an average of 480 mutations in the slow-growing species (265-year-old, 44.1 m in height), which was five times greater than that observed in the fast-growing species (66-year-old, 43.9 m). The number of somatic mutations increased linearly with branch length. The somatic mutation rate per meter was higher in the slow-growing species, yet the rate per year remained constant across both species. The mutational spectra exhibited a dominance of spontaneous mutations, specifically cytosine-to-thymine substitutions at CpG sites. An analysis of nucleotide substitutions at both the intra- and inter-individual level revealed that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. We developed a model to evaluate the relative contribution of cell division on mutational processes, and postulate that cell-division independent mutagenesis predominates. These findings deepen our understanding of mutational processes underlying the generation of genetic diversity in a tropical ecosystem.
The rates and patterns of somatic mutations in wild plants, as well as how they relate to longevity, are largely unknown 1–3 . Here, we examined the somatic mutation landscapes of slow- and fast-growing tropical species in central Borneo, Indonesia. Using newly-constructed genomes, we identified an average of 480 mutations in the slow-growing species (265-year-old, 44.1 m in height), which was five times greater than that observed in the fast-growing species (66-year-old, 43.9 m). The number of somatic mutations increased linearly with branch length. The somatic mutation rate per meter was higher in the slow-growing species, yet the rate per year remained constant across both species. The mutational spectra exhibited a dominance of spontaneous mutations, specifically cytosine-to-thymine substitutions at CpG sites. An analysis of nucleotide substitutions at both the intra- and inter-individual level revealed that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. We developed a model to evaluate the relative contribution of cell division on mutational processes, and postulate that cell-division independent mutagenesis predominates. These findings deepen our understanding of mutational processes underlying the generation of genetic diversity in a tropical ecosystem.
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