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Current Biology : CB Jun 2021Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,...
Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton, which is responsible for around 50% of global net primary production. However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences. The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions, has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.
Topics: Haptophyta; Phylogeny; Phytoplankton; Plastids; RNA, Ribosomal, 16S
PubMed: 33773100
DOI: 10.1016/j.cub.2021.03.012 -
Trends in Genetics : TIG Feb 2021Though widespread, RNA editing is rare, except in endosymbiotic organelles. A combination of higher mutation rates, relaxation of energetic constraints, and high genetic... (Review)
Review
Though widespread, RNA editing is rare, except in endosymbiotic organelles. A combination of higher mutation rates, relaxation of energetic constraints, and high genetic drift is found within plastids and mitochondria and is conducive for evolution and expansion of editing processes, possibly starting as repair mechanisms. To illustrate this, we present an exhaustive phylogenetic overview of editing types.
Topics: Mitochondria; Mutation; Mutation Rate; Phylogeny; Plastids; RNA Editing; Symbiosis
PubMed: 33203574
DOI: 10.1016/j.tig.2020.10.004 -
Journal of Experimental Botany May 2022Fibrillins (FBNs) are a family of genes in cyanobacteria, algae, and plants. The proteins they encode possess a lipid-binding motif, exist in various types of plastids,... (Review)
Review
Fibrillins (FBNs) are a family of genes in cyanobacteria, algae, and plants. The proteins they encode possess a lipid-binding motif, exist in various types of plastids, and are associated with lipid bodies called plastoglobules, implicating them in lipid metabolism. FBNs present in the thylakoid and stroma are involved in the storage, transport, and synthesis of lipid molecules for photoprotective functions against high-light stress. In this review, the diversity of subplastid locations in the evolution of FBNs, regulation of FBNs expression by various stresses, and the role of FBNs in plastid lipid metabolism are comprehensively summarized and directions for future research are discussed.
Topics: Fibrillins; Lipids; Plants; Plastids; Thylakoids
PubMed: 35560204
DOI: 10.1093/jxb/erac087 -
Plant Biotechnology Journal Feb 2022In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating...
In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating relatively small constructs into the plastome, plastid engineering via homologous recombination of transgenes is over 30 years old. Here we show the design-build-test of a novel synthetic genome structure that does not disturb the native plastome: the 'mini-synplastome'. The mini-synplastome was inspired by dinoflagellate plastome organization, which is comprised of numerous minicircles residing in the plastid instead of a single organellar genome molecule. The first mini-synplastome in plants was developed in vitro to meet the following criteria: (i) episomal replication in plastids; (ii) facile cloning; (iii) predictable transgene expression in plastids; (iv) non-integration of vector sequences into the endogenous plastome; and (v) autonomous persistence in the plant over generations in the absence of exogenous selection pressure. Mini-synplastomes are anticipated to revolutionize chloroplast biotechnology, enable facile marker-free plastid engineering, and provide an unparalleled platform for one-step metabolic engineering in plants.
Topics: Genetic Engineering; Metabolic Engineering; Plants; Plastids; Synthetic Biology; Transgenes
PubMed: 34585834
DOI: 10.1111/pbi.13717 -
Annals of Botany Jul 2023Hybridization has long been recognized as an important process for plant evolution and is often accompanied by polyploidization, another prominent force in generating...
BACKGROUND AND AIMS
Hybridization has long been recognized as an important process for plant evolution and is often accompanied by polyploidization, another prominent force in generating biodiversity. Despite its pivotal importance in evolution, the actual prevalence and distribution of hybridization across the tree of life remain unclear.
METHODS
We used whole-genome shotgun (WGS) sequencing and cytological data to investigate the evolutionary history of Henckelia, a large genus in the family Gesneriaceae with a high frequency of suspected hybridization and polyploidization events. We generated WGS sequencing data at about 10× coverage for 26 Chinese Henckelia species plus one Sri Lankan species. To untangle the hybridization history, we separately extracted whole plastomes and thousands of single-copy nuclear genes from the sequencing data, and reconstructed phylogenies based on both nuclear and plastid data. We also explored sources of both genealogical and cytonuclear conflicts and identified signals of hybridization and introgression within our phylogenomic dataset using several statistical methods. Additionally, to test the polyploidization history, we evaluated chromosome counts for 45 populations of the 27 Henckelia species studied.
KEY RESULTS
We obtained well-supported phylogenetic relationships using both concatenation- and coalescent-based methods. However, the nuclear phylogenies were highly inconsistent with the plastid phylogeny, and we observed intensive discordance among nuclear gene trees. Further analyses suggested that both incomplete lineage sorting and gene flow contributed to the observed cytonuclear and genealogical discordance. Our analyses of introgression and phylogenetic networks revealed a complex history of hybridization within the genus Henckelia. In addition, based on chromosome counts for 27 Henckelia species, we found independent polyploidization events occurred within Henckelia after different hybridization events.
CONCLUSIONS
Our findings demonstrated that hybridization and polyploidization are common in Henckelia. Furthermore, our results revealed that H. oblongifolia is not a member of the redefined Henckelia and they suggested several other taxonomic treatments in this genus.
Topics: Phylogeny; Hybridization, Genetic; Cell Nucleus; Plastids; Gene Flow
PubMed: 37177810
DOI: 10.1093/aob/mcad047 -
Journal of Agricultural and Food... Nov 2022Greening is an undesirable trait that develops in potatoes upon light exposure. This condition lowers market value, increases tuber waste in retail stores, and... (Review)
Review
Greening is an undesirable trait that develops in potatoes upon light exposure. This condition lowers market value, increases tuber waste in retail stores, and consequently influences the price of product in the long run. When potatoes are subjected to artificial light, the amyloplast converts into chloroplast. Although the development of total glycoalkaloids (TGA) is independent of light, the greening induced by exposure of potato to artificial light is an indication of probable TGA acceleration, which could be present in a low amount initially. Several research studies on optimum postharvest factors (temperature, lighting condition, relative humidity, pretreatment, storage air composition, and packaging) have been carried out to avoid greening and TGA development. This current review highlights major postharvest factors and summarizes past research regarding cause of greening and TGA development in potatoes in retail stores. Additionally, it also portrays the potential solutions that could help mitigate this problem, ultimately reducing wastage and achieving food security.
Topics: Solanum tuberosum; Plant Tubers; Plastids; Chloroplasts; Phenotype
PubMed: 36260761
DOI: 10.1021/acs.jafc.2c01169 -
The New Phytologist Oct 2019Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered... (Review)
Review
Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered into a number of secondary endosymbioses with diverse eukaryotic hosts. These events had major consequences on the evolution and diversification of life on Earth. Although almost all plastid diversity derives from a single endosymbiotic event, the analysis of nuclear genomes of plastid-bearing lineages has revealed a mosaic origin of plastid-related genes. In addition to cyanobacterial genes, plastids recruited for their functioning eukaryotic proteins encoded by the host nucleus and also bacterial proteins of noncyanobacterial origin. Therefore, plastid proteins and plastid-localised metabolic pathways evolved by tinkering and using gene toolkits from different sources. This mixed heritage seems especially complex in secondary algae containing green plastids, the acquisition of which appears to have been facilitated by many previous acquisitions of red algal genes (the 'red carpet hypothesis').
Topics: Biological Evolution; Gene Expression Regulation; Gene Transfer, Horizontal; Photosynthesis; Plastids; Symbiosis
PubMed: 31135958
DOI: 10.1111/nph.15965 -
Protist Dec 2023Cryptophytes are single celled protists found in all aquatic environments. They are composed of a heterotrophic genus, Goniomonas, and a largely autotrophic group...
Cryptophytes are single celled protists found in all aquatic environments. They are composed of a heterotrophic genus, Goniomonas, and a largely autotrophic group comprising many genera. Cryptophytes evolved through secondary endosymbiosis between a host eukaryotic heterotroph and a symbiont red alga. This merger resulted in a four-genome system that includes the nuclear and mitochondrial genomes from the host and a second nuclear genome (nucleomorph) and plastid genome inherited from the symbiont. Here, we make use of different genomes (with potentially distinct evolutionary histories) to perform a phylogenomic study of the early history of cryptophytes. Using ultraconserved elements from the host nuclear genome and symbiont nucleomorph and plastid genomes, we produce a three-genome phylogeny of 91 strains of cryptophytes. Our phylogenetic analyses find that that there are three major cryptophyte clades: Clade 1 comprises Chroomonas and Hemiselmis species, Clade 2, a taxonomically rich clade, comprises at least twelve genera, and Clade 3, comprises the heterotrophic Goniomonas species. Each of these major clades include both freshwater and marine species, but subclades within these clades differ in degrees of niche conservatism. Finally, we discuss priorities for taxonomic revision to Cryptophyceae based on previous studies and in light of these phylogenomic analyses.
Topics: Phylogeny; Cryptophyta; Biological Evolution; Eukaryota; Genome, Mitochondrial; Plastids
PubMed: 37935085
DOI: 10.1016/j.protis.2023.125994 -
Yi Chuan = Hereditas Jun 2023With the advancement of plant synthetic biology, plastids have emerged as an optimal platform for the heterologous production of numerous commercially valuable secondary... (Review)
Review
With the advancement of plant synthetic biology, plastids have emerged as an optimal platform for the heterologous production of numerous commercially valuable secondary metabolites and therapeutic proteins. In comparison on nuclear genetic engineering, plastid genetic engineering offers unique advantages in terms of efficient expression of foreign genes and biological safety. However, the constitutive expression of foreign genes in the plastid system may impede plant growth. Therefore, it is imperative to further elucidate and design regulatory elements that can achieve precise regulation of foreign genes. In this review, we summarize the progress made in developing regulatory elements for plastid genetic engineering, including operon design and optimization, multi-gene coexpression regulation strategies, and identification of new expression regulatory elements. These findings provide valuable insights for future research.
Topics: Genetic Engineering; Plants; Plastids; Regulatory Sequences, Nucleic Acid; Transformation, Genetic; Plants, Genetically Modified
PubMed: 37340964
DOI: 10.16288/j.yczz.23-021 -
Postepy Biochemii Sep 2020Plastoglobules (PGs), as important components of plastids, are involved in many stages of their development: from the chloroplast biogenesis through the... (Review)
Review
Plastoglobules (PGs), as important components of plastids, are involved in many stages of their development: from the chloroplast biogenesis through the chloroplast-chromoplast transformations, and finally in the process of gerontoplast formation. The unique protein and lipid composition of these structures, depending on their location, suggests that PGs are both a reservoir of spare materials and a center for many metabolic reactions. Plastoglobules play an active role in the metabolism of prenylquinones, carotenoids, and jasmonic acid, and are responsible for recycling of the thylakoid disintegration products. Their direct connection with the thylakoids allows for tight relationships between these two structures and redistribution of materials, which contributes to PGs’ role in response to stressful conditions. Moreover, strongly hydrophobic nature of plastoglobules, their specific proteome and a sufficiently simple isolation procedure create extraordinary possibilities of their application in plant biotechnology.
Topics: Chloroplasts; Plant Cells; Plastids; Proteome; Thylakoids
PubMed: 33315313
DOI: 10.18388/pb.2020_347