**4. The importance of collaboration and coordination between**  *Dunaliella* **genomes**

Nuclear monitoring of chloroplast transcription is essential for harmony. The expression of genes encoded by the chloroplast genome is highly dependent on a wide range of factors of nuclear origin. In turn, these factors regulate the expression of plastid genes in response to various environmental and developmental signals. Regulatory factors are widely present at various stages of plastid gene expression, including transcription, RNA editing, post-transcriptional RNA modification, RNA binding, and translation [15].

The transcription system of prokaryotes is different and simplest than that of eukaryotes. It is believed that the prokaryotic gene transcription features have been hired for genome transcription in chloroplasts. Although, at the plastome whole-genome level, the polycistronic operon transcription model cannot account for all the chloroplast transcription products, especially regarding various RNA isoforms. Analysis of algal and higher plants plastids and cyanobacteria transcriptomes revealed that the entire plastome is transcribed and that this attribute is inherited from prokaryotic cyanobacteria, the ancestor of the chloroplast genomes that separated about 1 billion years ago. A multiple arrangement transcription model was proposed by Shi and Wang that multiple transcription initiations and terminations combine randomly to execute the genome transcription followed by subsequent RNA processing events, which elucidates the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs [16].

Despite living in eukaryotic host cells for almost one billion years since their coexistence event, plastids still retain their prokaryotic properties. Previous studies have shown that plastids preserved some prokaryotic properties, such as prokaryotic gene promoters and terminators, and clustered transcripts of the gene. At first, it was thought that some chloroplast functional genes are transcribed as polystyrene transcripts and then processed into small, mature RNAs. There are almost 20 large transcription units and most of these areas are not transcribed, such as areas between two transcription units. Under such a polystyrene operon transcription model, plastome genes can be transcribed from intrinsic true promoters and later constituted constant-size transcripts. However, this model cannot consider all transcription products across the genome, including massive plastidencoded RNA output, gene-like transcription, multiple or multiple alternative promoters and terminators, overlapping isoforms, and gene transcription binding in the same polystyrene. This transcriptional and heterogeneous dynamics suggest that an additional overall transcriptional mechanism causes transcription of the entire plastom.

Transcription of chloroplast genome genes is controlled by various factors of nuclear origin. Primary factors affecting the transcription of genes in the chloroplast genome are NEP and additional and non-nuclear PEP subunits. In a group of additional PEP subunits, additional nuclear-encoded protein factors (PAPs) and transcription initiation factors (sigma factors) can be detected. It is well known that PAPs are essential in transcription regulation, however, some of their exact functions have not been proven.
