Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica
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PROVIDER: S-EPMC10923649 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Plastids are one of the main distinguishing characteristics of the plant cell. The plastid genome (plastome) of most autotrophic seed plants possesses a highly conserved quadripartite structure containing a large single-copy (LSC) and a small single-copy (SSC) region separated by two copies of the inverted repeat (termed as IRA and IRB). The IRs have been inferred to stabilize the plastid genome via homologous recombination-induced repair mechanisms. IR loss has been documented in seven autotrophic flowering plant lineages and two autotrophic gymnosperm lineages, and the plastomes of these species (with a few exceptions) are rearranged to a great extent. However, some plastomes containing normal IRs also show high structural variation. Therefore, the role of IRs in maintaining plastome stability is still controversial. In this study, we first integrated and compared genome structure and sequence evolution of representative plastomes of all nine reported IR-lacking lineages and those of their closest relative(s) with canonical inverted repeats (CRCIRs for short) to explore the role of the IR in maintaining plastome structural stability and sequence evolution. We found the plastomes of most IR-lacking lineages have experienced significant structural rearrangement, gene loss and duplication, accumulation of novel small repeats, and acceleration of synonymous substitution compared with those of their CRCIRs. However, the IR-lacking plastomes show similar structural variation and sequence evolution rate, and even less rearrangement distance, dispersed repeat number, tandem repeat number, indels frequency and GC3 content than those of IR-present plastomes with variation in Geraniaceae. We argue that IR loss is not a driver of these changes but is instead itself a consequence of other processes that more broadly shape both structural and sequence-level plastome evolution.
| S-EPMC9560873 | biostudies-literature
Project description:In field conditions, the zebra2 (z2) mutant in rice (Oryza sativa) produces leaves with transverse pale-green/yellow stripes. It was recently reported that ZEBRA2 encodes carotenoid isomerase (CRTISO) and that low levels of lutein, an essential carotenoid for non-photochemical quenching, cause leaf variegation in z2 mutants. However, we found that the z2 mutant phenotype was completely suppressed by growth under continuous light (CL; permissive) conditions, with concentrations of chlorophyll, carotenoids and chloroplast proteins at normal levels in z2 mutants under CL. In addition, three types of reactive oxygen species (ROS; superoxide [O₂⁻], hydrogen peroxide [H₂O₂], and singlet oxygen [¹O₂]) accumulated to high levels in z2 mutants grown under short-day conditions (SD; alternate 10-h light/14-h dark; restrictive), but do not accumulate under CL conditions. However, the levels of lutein and zeaxanthin in z2 leaves were much lower than normal in both permissive CL and restrictive SD growth conditions, indicating that deficiency of these two carotenoids is not responsible for the leaf variegation phenotype. We found that the CRTISO substrate tetra-Cis-lycopene accumulated during the dark periods under SD, but not under CL conditions. Its accumulation was also positively correlated with ¹O₂ levels generated during the light period, which consequently altered the expression of ¹O₂-responsive and cell death-related genes in the variegated z2 leaves. Taking these results together, we propose that the z2 leaf variegation can be largely attributed to photoperiodic accumulation of tetra-cis-lycopene and generation of excessive ¹O₂ under natural day-night conditions.
| S-EPMC3887748 | biostudies-literature
Project description:Main conclusionCsERF2, an ethylene response factor, plays a role in leaf variegation. Leaf variegation is a main ornamental characteristic in Cymbidium sinense (C. sinense). However, the mechanisms of leaf color variegation remain largely unclear. In the present study, we analyzed the cytological and physiological features, as well as molecular analyses of leaves from wild-type (WT) and leaf variegation mutants of Cymbidium sinense 'Dharma'. Chloroplasts with typical and functional structures were discovered in WT and green sectors of the mutants leaves (MG), but not in yellow sectors of the mutant leaves (MY). The activities of key enzymes involved in chlorophyll (Chl) degradation and their substrate contents were significantly increased in MY. Genes related to Chl degradation also showed a significant up-regulation in MY. Transcriptomic analysis showed that the expression of all identified ethylene response factors (ERFs) was significantly up-regulated, and the 1-aminocyclopropane-1-carboxylic acid (ACC) content in MY was significantly higher compared with MG. QRT-PCR analysis validated that the expression levels of genes related to Chl degradation could be positively affected by ethylene (ETH) treatment. Stable overexpression of CsERF2 in Nicotiana tabacum (N. tabacum) led to a decrease in Chl content and abnormal chloroplast. Transcriptomic analysis and qRT-PCR results showed that the KEGG pathway related to chloroplast development and function showed significant change in transgenic N. tabacum. Therefore, the leaf color formation of C. sinense was greatly affected by chloroplast development and Chl metabolism. CsERF2 played an important role in leaf variegation of C. sinense.
| S-EPMC7387381 | biostudies-literature
Project description:Changes in chromatin state may drive changes in gene expression, and it is of growing interest to understand the population genetic forces that drive differences in chromatin state. Here, we use the phenomenon of position effect variegation (PEV), a well-studied proxy for chromatin state, to survey variation in PEV among a naturally derived population. Further, we explore the genetic architecture of natural variation in factors that modify PEV. While previous mutation screens have identified over 150 suppressors and enhancers of PEV, it remains unknown to what extent allelic variation in these modifiers mediate interindividual variation in PEV. Is natural variation in PEV mediated by segregating genetic variation in known Su(var) and E(var) genes, or is the trait polygenic, with many variants mapping elsewhere in the genome? We designed a dominant mapping study that directly answers this question and suggests that the bulk of the variance in PEV does not map to genes with prior annotated impact to PEV. Instead, we find enrichment of top P-value ranked associations that suggest impact to active promoter and transcription start site proximal regions. This work highlights extensive variation in PEV within a population, and provides a quantitative view of the role naturally segregating autosomal variants play in modifying PEV-a phenomenon that continues to shape our understanding of chromatin state and epigenetics.
| S-EPMC5676239 | biostudies-literature
Project description:Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35-40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90-93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.
| S-EPMC8372910 | biostudies-literature
Project description:Chloroplasts are semiautonomous organelles, retaining their own genomes and gene expression apparatuses but controlled by nucleus genome encoded protein factors during evolution. To analyze the genetic regulatory network of FtsH-mediated chloroplast development in Arabidopsis, a set of suppressor mutants of yellow variegated (var2) have been identified. In this research, we reported the identification of another new var2 suppressor locus, SUPPRESSOR OF VARIEGATION11 (SVR11), which encodes a putative chloroplast-localized prokaryotic type translation elongation factor EF-Tu. SVR11 is likely essential to chloroplast development and plant survival. GUS activity reveals that SVR11 is abundant in the juvenile leaf tissue, lateral roots, and root tips. Interestingly, we found that SVR11 and SVR9 together regulate leaf development, including leaf margin development and cotyledon venation patterns. These findings reinforce the notion that chloroplast translation state triggers retrograde signals regulate not only chloroplast development but also leaf development.
| S-EPMC6423176 | biostudies-literature
Project description:Variegation is a frequently observed genetic phenomenon in landscaping. In this study, an ethyl methanesulfonate induced variegated leaf (Csvl) mutant in cucumber (Cucumis sativus L.) was identified. The Csvl mutant displayed green-yellow-white variegation phenotype throughout the whole growth cycle, while the leaf of wild type plants was normal green. The photosynthetic pigment contents and photosynthetic parameters of Csvl was significantly lower than wild type. The cytology observation results showed that the mesophyll cells of Csvl mutant contained defective chloroplasts. Genetic analysis indicated that variegated leaf phenotype was monogenic recessive inheritance. MutMap and genotyping results revealed that Csa6G405290 (Cscs), encoding chorismate synthase, was the candidate gene for variegated leaf mutant in cucumber. The expression level of Cscs was similar between wild type and variegated leaf mutant leaves. Transcriptome profile analysis of leaves of Csvl mutant identified 183 candidate genes involved in variegated leaf development in cucumber, including genes that encode heat shock protein, zinc finger protein. Cscs may regulate variegated leaf in cucumber by interacting with these genes. In a word, these results revealed that Cscs might regulate the variegated leaf phenotype in cucumber.
| S-EPMC6345225 | biostudies-literature
Project description:Chloroplasts (and other plastids) harbor their own genetic material, with a bacterial-like gene-expression systems. Chloroplast RNA metabolism is complex and is predominantly mediated by nuclear-encoded RNA-binding proteins. In addition to these nuclear factors, the chloroplast-encoded intron maturase MatK has been suggested to perform as a splicing factor for a subset of chloroplast introns. MatK is essential for plant cell survival in tobacco, and thus null mutants have not yet been isolated. We therefore attempted to over-express MatK from a neutral site in the chloroplast, placing it under the control of a theophylline-inducible riboswitch. This ectopic insertion of MatK lead to a variegated cotyledons phenotype. The addition of the inducer theophylline exacerbated the phenotype in a concentration-dependent manner. The extent of variegation was further modulated by light, sucrose and spectinomycin, suggesting that the function of MatK is intertwined with photosynthesis and plastid translation. Inhibiting translation in the transplastomic lines has a profound effect on the accumulation of several chloroplast mRNAs, including the accumulation of an RNA antisense to rpl33, a gene coding for an essential chloroplast ribosomal protein. Our study further supports the idea that MatK expression needs to be tightly regulated to prevent detrimental effects and establishes another link between leaf variegation and chloroplast translation.
| S-EPMC6180158 | biostudies-literature
Project description:Leaf variegation is an ornamental trait that is not only biologically but also economically important. In our previous study, a Mg-protoporphyrin IX monomethyl ester cyclase homologue, EaZIP (Epipremnum aureum leucine zipper) was found to be associated with leaf variegation in Epipremnum aureum (Linden & Andre) G.S. Bunting. The protein product of this nuclear-encoded gene is targeted back to chloroplast involving in chlorophyll biosynthesis. Based on a web-based homology analysis, the EaZIP was found to lack a chloroplast transit peptide (cTP) sequence. In the present study, we tested if overexpression of the EaZIP cDNA with or without the cTP sequence could affect leaf variegation. Transgenic tobacco plants overexpressing EaZIP genes with (EaZIPwcTP) and without (EaZIPwocTP) cTP sequence were generated. Many plant lines harboring EaZIPwocTP showed variegated leaves, while none of the plant lines with EaZIPwcTP produced such a phenotype. Molecular analysis of T0 plants and selfed T1 progeny, as well as observations of tagged marker GFP (green fluorescent protein) did not show any other difference in patterns of gene integrity and expression. Results from this study indicate that transgenic approach for expressing EaZIPwocTP could be a novel method of generating variegated plants even through the underlying mechanisms remain to be elucidated.
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