Since it appears that most PPR genes in plants function by binding to one or a small number of specific target organelle transcripts, it is possible that changes in organelle genomes drive PPR gene evolution and thus the evolution of this gene family in plants likely reflects the co-evolution of nuclear and organelle genomes.
In case of polyA selection, organelle transcripts are automatically removed due to the lack of the polyA tail in organelle transcripts, whereas most of them were captured by our method of ribosomal RNA removal.
The nucleus controls organelle gene expression through a number of nuclear-encoded factors that act post-transcriptionally on specific organelle target transcripts (anterograde signaling pathway [ 27]) and that regulate the maturation, stability and/or translation of organelle transcripts.
However, it remains unclear how and why many organelle transcripts accumulated at the M-G1 phase, even in dark conditions.
Because the TSS library was constructed for nuclear transcripts, poly(A -containing mRNA -containinghed; however, organelle transcripts containing mRNAsications also appeared because of the high expression level.
Organelle transcripts have been encountered in other transcriptome studies before [ 37] but are usually dismissed without further explanation, or regarded as artifacts [ 27].
Unlike most organelles, mitochondria do not exchange phospholipids via vesicular transport.
For the PM and most organelles, notably the endoplasmic reticulum (ER) and organelles derived from it, the gradients are directed toward the cytosol.
While most organelle-targeted trGTPases are encoded in the nucleus and post-translationally targeted to their respective organelle, EF-Tu is an exception.
Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown.
