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Due to their bacterial endosymbiotic origin plastids are organelles with both nuclear-encoded and plastid-encoded proteins. Therefore, a highly integrated modulation of gene expression between the nucleus and the plastome is needed in plant cell development. Plastids have retained for the most part a prokaryotic gene expression machinery but, differently from prokaryotes and eukaryotes, they have largely abandoned transcriptional control and switched to predominantly translational control of their gene expression. Some transcriptional regulation is known to occur, but the coordinate expression between the nucleus and the plastome takes place mainly through translational regulation. However, the regulatory mechanisms of plastid gene expression (PGE) are mediated by intricate plastid-nuclear interactions and are still far from being fully understood. Although, for example, translational autoregulation mechanisms in algae have been described for subunits of heteromeric protein complexes and termed control by epistasy of synthesis (CES), only few autoregulatory proteins have been identified in plant plastids. It should be noted of course that PGE in C. reinhardtii is different from that in plants in many aspects. Another example of investigation in this research area is to understand the interactions that occur during RNA binding between nucleus-encoded RNA-binding proteins and the respective RNA sequences, and how this influences the translation initiation process. In addition to this, the plastid retains a whole series of mechanisms for the preservation of its protein balance (proteostasis), including specific proteases, as well as molecular chaperones and enzymes useful in protein folding. After synthesis, plastid proteins must rapidly fold into stable three dimensional structures and often undergo co- and posttranslational modifications to perform their biological mission, avoiding aberrant folding, aggregation and targeting with the help of molecular chaperones and proteases. We believe that this topic is highly interesting for many research areas because the regulation of PGE is not only of wide interest for plant biologists but has also biotechnological implications. Indeed, plastid transformation turns out to be a very promising tool for the production of recombinant proteins in plants, yet some limitations must still be overcome and we believe that this is mainly due to our limited knowledge of the mechanisms in plastids influencing the maintenance of proteostasis.

plastome --- regulation --- nuclear-plastid interactions --- gene expression --- protein balance

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Due to their bacterial endosymbiotic origin plastids are organelles with both nuclear-encoded and plastid-encoded proteins. Therefore, a highly integrated modulation of gene expression between the nucleus and the plastome is needed in plant cell development. Plastids have retained for the most part a prokaryotic gene expression machinery but, differently from prokaryotes and eukaryotes, they have largely abandoned transcriptional control and switched to predominantly translational control of their gene expression. Some transcriptional regulation is known to occur, but the coordinate expression between the nucleus and the plastome takes place mainly through translational regulation. However, the regulatory mechanisms of plastid gene expression (PGE) are mediated by intricate plastid-nuclear interactions and are still far from being fully understood. Although, for example, translational autoregulation mechanisms in algae have been described for subunits of heteromeric protein complexes and termed control by epistasy of synthesis (CES), only few autoregulatory proteins have been identified in plant plastids. It should be noted of course that PGE in C. reinhardtii is different from that in plants in many aspects. Another example of investigation in this research area is to understand the interactions that occur during RNA binding between nucleus-encoded RNA-binding proteins and the respective RNA sequences, and how this influences the translation initiation process. In addition to this, the plastid retains a whole series of mechanisms for the preservation of its protein balance (proteostasis), including specific proteases, as well as molecular chaperones and enzymes useful in protein folding. After synthesis, plastid proteins must rapidly fold into stable three dimensional structures and often undergo co- and posttranslational modifications to perform their biological mission, avoiding aberrant folding, aggregation and targeting with the help of molecular chaperones and proteases. We believe that this topic is highly interesting for many research areas because the regulation of PGE is not only of wide interest for plant biologists but has also biotechnological implications. Indeed, plastid transformation turns out to be a very promising tool for the production of recombinant proteins in plants, yet some limitations must still be overcome and we believe that this is mainly due to our limited knowledge of the mechanisms in plastids influencing the maintenance of proteostasis.

plastome --- regulation --- nuclear-plastid interactions --- gene expression --- protein balance --- plastome --- regulation --- nuclear-plastid interactions --- gene expression --- protein balance

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The papers included in this Special Issue address a variety of important aspects of Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles, including new advances in the sequencing of both mitochondria and chloroplasts’ genomes using Next-Generation Sequencing technology in plant species and algae including important crop and tree species, in vitro culture protocol, and identification of a core module of genes involved in plastid development. In particular, the published studies focus on the description of adaptive evolution, elucidate mitochondrial mRNA processing, highlight the effect of domestication process on plastome variability and report the development of molecular markers. A meta-analysis of recently published genome-wide expression studies allowed the identification of novel nuclear genes, involved in the complex and still unrevealed mechanisms at the basis of communication between chloroplast and nucleus (retrograde signalling) during plastid development (biogenic control). Finally, an optimized regeneration protocol useful in plastid transformation of recalcitrant species, such as sugarcane, has been reported.

Research & information: general --- mitochondrial genome --- buckwheat --- plastid genome --- genetic diversity --- long reads --- targeted assembly --- genome assembly --- Fagus --- Fagaceae --- Fagales --- molecular marker --- mitochondrial marker --- taxon assignment --- CAPS marker --- SNP --- next-generation sequencing --- Solanum --- Italian landraces --- plastome --- molecular markers --- phylogenetic analysis --- plastid transformation --- sugarcane --- unfurled leaves --- streptomycin --- heteroplasmy --- mesophyll and bundle sheath cells --- plastids --- photomorphogenesis --- retrograde control --- biogenic signals --- lincomycin --- norflurazon --- pap7-1 mutant --- mitochondria --- RNA processing --- algal evolution --- circular RNA --- polycytidylation --- PacBio Iso-Seq --- Capparaceae --- chloroplast genome --- Cadaba --- Maerua --- phylogenetic relationships --- mitochondrial genome --- buckwheat --- plastid genome --- genetic diversity --- long reads --- targeted assembly --- genome assembly --- Fagus --- Fagaceae --- Fagales --- molecular marker --- mitochondrial marker --- taxon assignment --- CAPS marker --- SNP --- next-generation sequencing --- Solanum --- Italian landraces --- plastome --- molecular markers --- phylogenetic analysis --- plastid transformation --- sugarcane --- unfurled leaves --- streptomycin --- heteroplasmy --- mesophyll and bundle sheath cells --- plastids --- photomorphogenesis --- retrograde control --- biogenic signals --- lincomycin --- norflurazon --- pap7-1 mutant --- mitochondria --- RNA processing --- algal evolution --- circular RNA --- polycytidylation --- PacBio Iso-Seq --- Capparaceae --- chloroplast genome --- Cadaba --- Maerua --- phylogenetic relationships

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The papers included in this Special Issue address a variety of important aspects of Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles, including new advances in the sequencing of both mitochondria and chloroplasts’ genomes using Next-Generation Sequencing technology in plant species and algae including important crop and tree species, in vitro culture protocol, and identification of a core module of genes involved in plastid development. In particular, the published studies focus on the description of adaptive evolution, elucidate mitochondrial mRNA processing, highlight the effect of domestication process on plastome variability and report the development of molecular markers. A meta-analysis of recently published genome-wide expression studies allowed the identification of novel nuclear genes, involved in the complex and still unrevealed mechanisms at the basis of communication between chloroplast and nucleus (retrograde signalling) during plastid development (biogenic control). Finally, an optimized regeneration protocol useful in plastid transformation of recalcitrant species, such as sugarcane, has been reported.

mitochondrial genome --- buckwheat --- plastid genome --- genetic diversity --- long reads --- targeted assembly --- genome assembly --- Fagus --- Fagaceae --- Fagales --- molecular marker --- mitochondrial marker --- taxon assignment --- CAPS marker --- SNP --- next-generation sequencing --- Solanum --- Italian landraces --- plastome --- molecular markers --- phylogenetic analysis --- plastid transformation --- sugarcane --- unfurled leaves --- streptomycin --- heteroplasmy --- mesophyll and bundle sheath cells --- plastids --- photomorphogenesis --- retrograde control --- biogenic signals --- lincomycin --- norflurazon --- pap7-1 mutant --- mitochondria --- RNA processing --- algal evolution --- circular RNA --- polycytidylation --- PacBio Iso-Seq --- Capparaceae --- chloroplast genome --- Cadaba --- Maerua --- phylogenetic relationships

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This book provides reviews and primary research articles that discuss the replication, repair, maintenance, and structures of plant organelle genomes. Rearrangements of these genomes are common and provide a way to distinguish closely related plant species. Some articles in the book discuss recent advances in identifying specific proteins and potential mechanisms involved in DNA replication, recombination, and repair in plant mitochondria and chloroplasts.

Research & information: general --- Biology, life sciences --- DNA replication --- recombination-dependent replication (RDR) --- plant mitochondrial DNA --- chloroplast DNA --- DNA repair --- divergent inverted repeats --- short-globose cacti --- novel gene rearrangements --- pseudogenization --- sunflower --- cytoplasmic male sterility (CMS) --- mitochondrial genome --- reorganizations --- next generation sequencing (NGS) --- evolution --- replisome --- recombination-dependent replication --- Lilium --- phylogenomics --- plastome --- molecular markers --- gene tree --- species tree --- chloroplast --- mitochondrion --- genome stability --- homologous recombination repair --- repeated sequence --- Physcomitrella patens --- mitochondria --- double-strand break repair --- uracil-N-glycosylase --- Piperales --- Hydnoraceae --- Hydnora --- Prosopanche --- parasitic plants --- holoparasite --- plastid genome --- organelles --- plastid phylogenetics --- DNA recombination --- plant organelle genome structure --- DNA replication --- recombination-dependent replication (RDR) --- plant mitochondrial DNA --- chloroplast DNA --- DNA repair --- divergent inverted repeats --- short-globose cacti --- novel gene rearrangements --- pseudogenization --- sunflower --- cytoplasmic male sterility (CMS) --- mitochondrial genome --- reorganizations --- next generation sequencing (NGS) --- evolution --- replisome --- recombination-dependent replication --- Lilium --- phylogenomics --- plastome --- molecular markers --- gene tree --- species tree --- chloroplast --- mitochondrion --- genome stability --- homologous recombination repair --- repeated sequence --- Physcomitrella patens --- mitochondria --- double-strand break repair --- uracil-N-glycosylase --- Piperales --- Hydnoraceae --- Hydnora --- Prosopanche --- parasitic plants --- holoparasite --- plastid genome --- organelles --- plastid phylogenetics --- DNA recombination --- plant organelle genome structure