Dynamic Replication and Transcription of Organellar Genomes in Developing Fiber Cells of Upland Cotton (Gossypium hirsutum L.)

The DNA of plant cells is located in three compartments, the nucleus, chloroplasts and mitochondria.
The genomes of the organelles, chloroplasts and mitochondria, are present in many copies in the
cells of most tissues, with multiple organelles per cell and often multiple genomes per organelle.
Even in non-green tissues, the chloroplasts and mitochondria are the sites of metabolism critical to
energy production. Here we report that the copy number of organellar genomes changes during cotton
fiber development. We also describe the transcriptional program of each organelle during fiber cell
development and identify differences between the wild-type program and those of cotton fiber
mutants. While the chloroplast genome replicates like a single circular chromosome, the
mitochondrial genome can divide into subgenomic circles by means of direct repeats. We observed
that the mitochondrial subgenomes vary in relative abundance during fiber cell development. We
examined the correlation between mitochondrial gene copy number and transcript abundance and propose
that subgenome replication dynamics may support the transcriptional program of mitochondria in
developing cotton fibers.