Eukaryotic cells tightly regulate their populations of endosymbiotically-derived organelles. Organelle populations can be described in terms of size, number, or coverage, the latter being the collective planar area taken up by the organellar population relative to that of the cell. As the photosynthetic organelle, chloroplasts are vital, and alterations to chloroplast population morphology can affect photosynthetic performance and biomass accumulation. However, how the cell perceives and regulates its chloroplast population remains a mystery. Division at the mid-plastid (binary fission) is the primary mechanism by which chloroplasts increase their population sizes. It has been well established that lower division rates result in a small population of enlarged chloroplasts, suggesting the existence of a compensatory mechanism ensuring that total chloroplast coverage within the cell is preserved through a tradeoff between chloroplast division and expansion. Most model plants keep a relatively large number of chloroplasts in their leaf cells (>50 per cell). In expanding leaf cells, multiple rounds of chloroplast division typically increase the number of chloroplasts per cell. However, a number of natural adaptive alterations to chloroplast morphology have been observed in several tropical plant species, primarily those native to low-light environments. The tropical plant genus Peperomia (Piperaceae) offers a unique opportunity for understanding the regulation of chloroplast population morphology, as some Peperomia spp. contain two to six giant chloroplasts in their palisade mesophyll cells at maturity, while most others have higher numbers of small chloroplasts in their mesophyll cells. I have characterized chloroplast population morphology in Peperomia, of which six species had not been studied previously, and shown that chloroplast division is inhibited in the palisade cells of Peperomia pellucida. Further, I have assembled and annotated the genome of Peperomia dahlstedtii, the first genome for this genus, and produced a novel transcriptome assembly for P. pellucida. Lastly, I have analyzed gene expression in these two species differing in palisade cell chloroplast population morphology and identified several candidate genes potentially underlying the differences in phenotype. For the first time, I also have described the expression of the chloroplast division genes in these two species. By characterizing variation in chloroplast population morphology in Peperomia, my work builds upon existing research on this trait over leaf development, provides the resources necessary for Peperomia to be used as a model, and identifies potential causes behind the large-chloroplast phenotype documented in several species.
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