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Scientific Reports Jun 2024In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising...
In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa's plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.
Topics: Nigella sativa; Phylogeny; Genome, Plastid
PubMed: 38914674
DOI: 10.1038/s41598-024-65073-6 -
Functional & Integrative Genomics Jun 2024Chloroplasts are not only critical photosynthesis sites in plants, but they also participate in plastidial retrograde signaling in response to developmental and...
Chloroplasts are not only critical photosynthesis sites in plants, but they also participate in plastidial retrograde signaling in response to developmental and environmental signals. MEcPP (2-C-Methyl-D-erythritol-2,4-cyclopyrophosphate) is an intermediary in the methylerythritol phosphate (MEP) pathway in chloroplasts. It is a critical precursor for the synthesis of isoprenoids and terpenoid derivatives, which play crucial roles in plant growth and development, photosynthesis, reproduction, and defense against environmental constraints. Accumulation of MEcPP under stressful conditions triggers the expression of IMPα-9 and TPR2, contributing to the activation of abiotic stress-responsive genes. In this correspondence, we discuss plastidial retrograde signaling in support of a recently published paper in Molecular Plant (Zeng et al. 2024). We hope that it can shed more insight on the retrograde signaling cascade.
Topics: Chloroplasts; Stress, Physiological; Gene Expression Regulation, Plant; Signal Transduction; Arabidopsis; Erythritol; Arabidopsis Proteins; Sugar Phosphates; MAP Kinase Kinase Kinase 5
PubMed: 38910225
DOI: 10.1007/s10142-024-01395-y -
Communications Biology Jun 2024Although the chloroplast genome (cpDNA) of higher plants is known to exist as a large protein-DNA complex called 'plastid nucleoid', researches on its DNA state and...
Although the chloroplast genome (cpDNA) of higher plants is known to exist as a large protein-DNA complex called 'plastid nucleoid', researches on its DNA state and regulatory elements are limited. In this study, we performed the assay for transposase-accessible chromatin sequencing (ATAC-seq) on five common tissues across five grasses, and found that the accessibility of different regions in cpDNA varied widely, with the transcribed regions being highly accessible and accessibility patterns around gene start and end sites varying depending on the level of gene expression. Further analysis identified a total of 3970 putative protein binding footprints on cpDNAs of five grasses. These footprints were enriched in intergenic regions and co-localized with known functional elements. Footprints and their flanking accessibility varied dynamically among tissues. Cross-species analysis showed that footprints in coding regions tended to overlap non-degenerate sites and contain a high proportion of highly conserved sites, indicating that they are subject to evolutionary constraints. Taken together, our results suggest that the accessibility of cpDNA has biological implications and provide new insights into the transcriptional regulation of chloroplasts.
Topics: Genome, Chloroplast; Poaceae; DNA, Chloroplast; Gene Expression Regulation, Plant; Chloroplasts
PubMed: 38909165
DOI: 10.1038/s42003-024-06374-4 -
Annals of Botany Jun 2024Progress in the systematic studies of the olive family (Oleaceae) during the last two decades provides the opportunity to update its backbone phylogeny and to...
BACKGROUND AND AIMS
Progress in the systematic studies of the olive family (Oleaceae) during the last two decades provides the opportunity to update its backbone phylogeny and to investigate its historical biogeography. We additionally aimed to understand the factors underlying the disjunct distribution pattern between East Asia and both West Asia and Europe that is found more commonly in this family than in any other woody plant families.
METHODS
Using a sampling of 298 species out of ca. 750, the largest in a phylogenetic study of Oleaceae thus far, and a set of 36 plastid and nuclear markers, we reconstructed and dated a new phylogenetic tree based on maximum likelihood and Bayesian methods and checked for any reticulation events. We also assessed the relative support of four competing hypotheses [Qinghai-Tibet Plateau uplift (QTP-only hypothesis), climatic fluctuations (Climate-only hypothesis), combined effects of QTP uplift and climate (QTP-Climate hypothesis), and no effects (Null hypothesis)] in explaining these disjunct distributions.
KEY RESULTS
We recovered all tribes and subtribes within Oleaceae as monophyletic, but uncertainty in the position of tribe Forsythieae remains. Based on this dataset, no reticulation event was detected. Our biogeographic analyses support the QTP-Climate hypothesis as the likely main explanation for the East-West Eurasian disjunctions in Oleaceae. Our results also show an earlier origin of Oleaceae at ca. 86 Mya and the role of Tropical Asia as a main source of species dispersals.
CONCLUSION
Our new family-wide and extensive phylogenetic tree highlights both the stable relationships within Oleaceae, including the polyphyly of the genus Chionanthus, and the need for further systematic studies within the family's largest and most under-sampled genera (Chionanthus and Jasminum). Increased sampling will also help to fine-tune biogeographic analyses across spatial scales and geological times.
PubMed: 38908009
DOI: 10.1093/aob/mcae100 -
Nature Communications Jun 2024The methylerythritol phosphate (MEP) pathway is responsible for biosynthesis of the precursors of isoprenoid compounds in eubacteria and plastids. It is a metabolic... (Review)
Review
The methylerythritol phosphate (MEP) pathway is responsible for biosynthesis of the precursors of isoprenoid compounds in eubacteria and plastids. It is a metabolic alternative to the well-known mevalonate pathway for isoprenoid production found in archaea and eukaryotes. Recently, a role for the MEP pathway in oxidative stress detection, signalling, and response has been identified. This role is executed in part through the unusual cyclic intermediate, methylerythritol cyclodiphosphate (MEcDP). We postulate that this response is triggered through the oxygen sensitivity of the MEP pathway's terminal iron-sulfur (Fe-S) cluster enzymes. MEcDP is the substrate of IspG, the first Fe-S cluster enzyme in the pathway; it accumulates under oxidative stress conditions and acts as a signalling molecule. It may also act as an antioxidant. Furthermore, evidence is emerging for a broader and highly nuanced role of the MEP pathway in oxidative stress responses, implemented through a complex system of differential regulation and sensitivity at numerous nodes in the pathway. Here, we explore the evidence for such a role (including the contribution of the Fe-S cluster enzymes and different pathway metabolites, especially MEcDP), the evolutionary implications, and the many questions remaining about the behaviour of the MEP pathway in the presence of oxidative stress.
Topics: Oxidative Stress; Erythritol; Sugar Phosphates; Iron-Sulfur Proteins; Signal Transduction; Terpenes
PubMed: 38906898
DOI: 10.1038/s41467-024-49483-8 -
Proceedings of the National Academy of... Jun 2024Hydrogen isotope ratios (δH) represent an important natural tracer of metabolic processes, but quantitative models of processes controlling H-fractionation in aquatic...
Hydrogen isotope ratios (δH) represent an important natural tracer of metabolic processes, but quantitative models of processes controlling H-fractionation in aquatic photosynthetic organisms are lacking. Here, we elucidate the underlying physiological controls of H/H fractionation in algal lipids by systematically manipulating temperature, light, and CO(aq) in continuous cultures of the haptophyte . We analyze the hydrogen isotope fractionation in alkenones (α), a class of acyl lipids specific to this species and other haptophyte algae. We find a strong decrease in the α with increasing CO(aq) and confirm α correlates with temperature and light. Based on the known biosynthesis pathways, we develop a cellular model of the δH of algal acyl lipids to evaluate processes contributing to these controls on fractionation. Simulations show that longer residence times of NADPH in the chloroplast favor a greater exchange of NADPH with H-richer intracellular water, increasing α. Higher chloroplast CO(aq) and temperature shorten NADPH residence time by enhancing the carbon fixation and lipid synthesis rates. The inverse correlation of α to CO(aq) in our cultures suggests that carbon concentrating mechanisms (CCM) do not achieve a constant saturation of CO at the Rubisco site, but rather that chloroplast CO varies with external CO(aq). The pervasive inverse correlation of α with CO(aq) in the modern and preindustrial ocean also suggests that natural populations may not attain a constant saturation of Rubisco with the CCM. Rather than reconstructing growth water, α may be a powerful tool to elucidate the carbon limitation of photosynthesis.
Topics: Carbon Dioxide; Haptophyta; Lipids; Photosynthesis; Hydrogen; Chloroplasts; Deuterium; NADP; Temperature; Chemical Fractionation; Lipid Metabolism
PubMed: 38905238
DOI: 10.1073/pnas.2318570121 -
Wellcome Open Research 2024We present a genome assembly from an individual (fireweed; Tracheophyta; Magnoliopsida; Myrtales; Onagraceae). The genome sequence is 655.9 megabases in span. Most of...
We present a genome assembly from an individual (fireweed; Tracheophyta; Magnoliopsida; Myrtales; Onagraceae). The genome sequence is 655.9 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 495.18 kilobases and 160.41 kilobases in length, respectively.
PubMed: 38903872
DOI: 10.12688/wellcomeopenres.21163.1 -
PhytoKeys 2024Here, we describe a new species of L. discovered in Mengla County, Xishuangbanna Dai Autonomous Prefecture, Yunnan, China. The new species, S.A.Rather, was confirmed...
Here, we describe a new species of L. discovered in Mengla County, Xishuangbanna Dai Autonomous Prefecture, Yunnan, China. The new species, S.A.Rather, was confirmed by identifying diagnostic morphological characteristics, performing principal component analyses of phenotypic traits, and phylogenetic analyses based on nuclear ITS and plastid K sequences. Phylogenetic analyses recovered the two accessions of the new species to be sister to Roxb. ex DC. In turn, these two species formed the sister clade to the two accessions of L. The morphometric analyses revealed that all three species were distinct, while the analyses of distinctive characters enabled unambiguous distinction of the new species by its growth habit, leaflets, flower structure and pod morphology. In contrast to the two related species, the new species is currently known only from 100 mature individuals. Thus, this species is considered to be critically endangered.
PubMed: 38903849
DOI: 10.3897/phytokeys.242.122407 -
Science Advances Jun 2024Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photooxidative damage. We have identified a...
Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photooxidative damage. We have identified a posttranslational mechanism linking the eukaryotic target of rapamycin (TOR) kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway of prokaryotic origins that regulates chloroplast activity and photosynthesis in particular. We find that RelA SpoT homolog 3 (RSH3), a nuclear-encoded enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific amino-terminal region which is phosphorylated in a TOR-dependent manner. Down-regulating TOR activity causes a rapid increase in ppGpp synthesis in RSH3 overexpressors and reduces photosynthetic capacity in an RSH-dependent manner in wild-type plants. The TOR-RSH3 signaling axis therefore regulates the equilibrium between chloroplast activity and plant growth, setting a precedent for the regulation of organellar function by TOR.
Topics: Photosynthesis; Chloroplasts; Arabidopsis Proteins; Signal Transduction; Arabidopsis; Phosphorylation; Protein Processing, Post-Translational; Gene Expression Regulation, Plant; Guanosine Tetraphosphate; TOR Serine-Threonine Kinases; Phosphatidylinositol 3-Kinases
PubMed: 38896607
DOI: 10.1126/sciadv.adj3268 -
BioRxiv : the Preprint Server For... Jun 2024Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the...
Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in . We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of mutant lines lacking , , or . In contrast, and mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.
PubMed: 38895361
DOI: 10.1101/2024.06.03.597120