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Genes Jul 2023Mutations and subsequent repair processes are known to be strongly context-dependent in the flowering-plant chloroplast genome. At least six flanking bases, three on...
Mutations and subsequent repair processes are known to be strongly context-dependent in the flowering-plant chloroplast genome. At least six flanking bases, three on each side, can have an influence on the relative rates of different types of mutation at any given site. In this analysis, examine context and substitution at noncoding and fourfold degenerate coding sites in gymnosperm DNA. The sequences are analyzed in sets of three, allowing the inference of the substitution direction and the generation of context-dependent rate matrices. The size of the dataset limits the analysis to the tetranucleotide context of the sites, but the evidence shows that there are significant contextual effects, with patterns that are similar to those observed in angiosperms. These effects most likely represent an influence on the underlying mutation/repair dynamics. The data extend the plastome lineages that feature very complex patterns of mutation, which can have significant effects on the evolutionary dynamics of the chloroplast genome.
Topics: DNA, Chloroplast; Cycadopsida; Mutation; Genome, Chloroplast; Magnoliopsida
PubMed: 37510396
DOI: 10.3390/genes14071492 -
Genome Feb 2023Lingxiaohua (Campsis Flos, (Thunb.) K. Schum) is a medicinal herb used for promoting diuresis and treating blood-related disorders by the promotion of blood...
Lingxiaohua (Campsis Flos, (Thunb.) K. Schum) is a medicinal herb used for promoting diuresis and treating blood-related disorders by the promotion of blood circulation. It also possesses anti-inflammatory and antioxidative properties. This non-poisonous plant is frequently confused with poisonous Yangjinhua (Daturae Metelis Flos, Linnaeus) in the market, resulting in serious anticholinergic poisoning. The confusion of these two herbs is due to the similarity in their appearances. In our study, we compared the complete chloroplast genomes of the two plants and found that they are very different in terms of their gene content and gene arrangement. There were also significant differences in the number and repeating motifs of microsatellites and complex repeats. We used universal primers for the amplification of , and regions and successfully differentiated the two plants. Furthermore, we designed two pairs of primers based on the nucleotide differences in chloroplast genomes at the and regions to provide additional authentication markers. The universal primers and specific primers when used together can accurately discriminate Lingxiaohua and Yangjinhua.
Topics: DNA Barcoding, Taxonomic; DNA, Plant; Genome, Chloroplast; Plants, Medicinal; Chloroplasts; Genetic Markers; DNA, Chloroplast
PubMed: 36516431
DOI: 10.1139/gen-2022-0063 -
Molecular Ecology Resources Sep 2017Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and... (Review)
Review
Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation-sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short-range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.
Topics: Computational Biology; DNA, Chloroplast; Genome, Plastid; Genomics; Plants; Sequence Analysis, DNA
PubMed: 27790830
DOI: 10.1111/1755-0998.12626 -
Nature Plants Dec 2022Chloroplast DNA (cpDNA) encodes up to 315 (typically, 120-130) genes, including those for essential components in photosystems I and II and the large subunit of RuBisCo,...
Chloroplast DNA (cpDNA) encodes up to 315 (typically, 120-130) genes, including those for essential components in photosystems I and II and the large subunit of RuBisCo, which catalyses CO fixation in plants. Targeted mutagenesis in cpDNA will be broadly useful for studying the functions of these genes in molecular detail and for developing crops and other plants with desired traits. Unfortunately, CRISPR-Cas9 and CRISPR-derived base editors, which enable targeted genetic modifications in nuclear DNA, are not suitable for organellar DNA editing, owing to the difficulty of delivering guide RNA into organelles. CRISPR-free, protein-only base editors (including DddA-derived cytosine base editors and zinc finger deaminases), originally developed for mitochondrial DNA editing in mammalian cells, can be used for C-to-T, rather than A-to-G, editing in cpDNA. Here we show that heritable homoplasmic A-to-G edits can be induced in cpDNA, leading to phenotypic changes, using transcription activator-like effector-linked deaminases.
Topics: Animals; Gene Editing; CRISPR-Cas Systems; DNA, Chloroplast; DNA, Mitochondrial; Crops, Agricultural; Mammals
PubMed: 36456803
DOI: 10.1038/s41477-022-01279-8 -
BMC Biotechnology Apr 2024Obtaining high-quality chloroplast genome sequences requires chloroplast DNA (cpDNA) samples that meet the sequencing requirements. The quality of extracted cpDNA...
BACKGROUND
Obtaining high-quality chloroplast genome sequences requires chloroplast DNA (cpDNA) samples that meet the sequencing requirements. The quality of extracted cpDNA directly impacts the efficiency and accuracy of sequencing analysis. Currently, there are no reported methods for extracting cpDNA from Erigeron breviscapus. Therefore, we developed a suitable method for extracting cpDNA from E. breviscapus and further verified its applicability to other medicinal plants.
RESULTS
We conducted a comparative analysis of chloroplast isolation and cpDNA extraction using modified high-salt low-pH method, the high-salt method, and the NaOH low-salt method, respectively. Subsequently, the number of cpDNA copies relative to the nuclear DNA (nDNA ) was quantified via qPCR. As anticipated, chloroplasts isolated from E. breviscapus using the modified high-salt low-pH method exhibited intact structures with minimal cell debris. Moreover, the concentration, purity, and quality of E. breviscapus cpDNA extracted through this method surpassed those obtained from the other two methods. Furthermore, qPCR analysis confirmed that the modified high-salt low-pH method effectively minimized nDNA contamination in the extracted cpDNA. We then applied the developed modified high-salt low-pH method to other medicinal plant species, including Mentha haplocalyx, Taraxacum mongolicum, and Portulaca oleracea. The resultant effect on chloroplast isolation and cpDNA extraction further validated the generalizability and efficacy of this method across different plant species.
CONCLUSIONS
The modified high-salt low-pH method represents a reliable approach for obtaining high-quality cpDNA from E. breviscapus. Its universal applicability establishes a solid foundation for chloroplast genome sequencing and analysis of this species. Moreover, it serves as a benchmark for developing similar methods to extract chloroplast genomes from other medicinal plants.
Topics: DNA, Chloroplast; Plants, Medicinal; Chloroplasts; Chromosome Mapping; Genome, Chloroplast; Phylogeny
PubMed: 38637734
DOI: 10.1186/s12896-024-00843-8 -
Trends in Genetics : TIG Apr 2018While the vast majority of cellular DNA in eukaryotes is contained in long linear strands in chromosomes, we have long recognized some exceptions like mitochondrial DNA,... (Review)
Review
While the vast majority of cellular DNA in eukaryotes is contained in long linear strands in chromosomes, we have long recognized some exceptions like mitochondrial DNA, plasmids in yeasts, and double minutes (DMs) in cancer cells where the DNA is present in extrachromosomal circles. In addition, specialized extrachromosomal circles of DNA (eccDNA) have been noted to arise from repetitive genomic sequences like telomeric DNA or rDNA. Recently eccDNA arising from unique (nonrepetitive) DNA have been discovered in normal and malignant cells, raising interesting questions about their biogenesis, function and clinical utility. Here, we review recent results and future directions of inquiry on these new forms of eccDNA.
Topics: Animals; Chromosomes, Human; DNA, Chloroplast; DNA, Circular; DNA, Kinetoplast; DNA, Mitochondrial; DNA, Neoplasm; Eukaryotic Cells; Humans; Kinetoplastida; Neoplasms; Neoplastic Cells, Circulating; Plants; Plasmids; Saccharomyces cerevisiae; Telomere
PubMed: 29329720
DOI: 10.1016/j.tig.2017.12.010 -
Bioscience, Biotechnology, and... Jan 1996The complete nucleotide sequence of chloroplast DNA (121,025 basepairs, bp) from a liverwort, Marchantia polymorpha, has made clear the entire gene organization of the... (Review)
Review
The complete nucleotide sequence of chloroplast DNA (121,025 basepairs, bp) from a liverwort, Marchantia polymorpha, has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. We also identified the complete nucleotide sequence of the liverwort mitochondrial DNA and deduced 96 possible genes in the sequence of 186,608 bp. The complete nucleotide sequence from chloroplast DNA comprises twenty introns (19 group II and 1 group I) in 18 different genes. One of the chloroplast group II introns separated the ribosomal protein gene in the trans-position. The mitochondrial genome also has thirty-two introns (25 group II and 7 group I) in the coding regions of 17 genes. From the evolutionary point of view, we describe the origin of organellar introns which gave the evidence for their vertical and horizontal transfers and their intragenic propagation, and RNA editing which was apparently lacking in the liverwort chloroplast and mitochondrial genomes.
Topics: Amino Acid Sequence; Base Sequence; DNA, Chloroplast; DNA, Mitochondrial; Electron Transport; Genes, Plant; Molecular Sequence Data; Plant Proteins; RNA Splicing; RNA, Chloroplast; RNA, Transfer
PubMed: 8824820
DOI: 10.1271/bbb.60.16 -
Scientific Reports Jul 2021To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS)...
To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: H = 0.499; ITS: H = 0.876) and a low level of genetic differentiation (cpDNA: F = 0.1628; ITS: F = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (N) was significantly higher than the number of substitution types (G), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.
Topics: DNA, Chloroplast; DNA, Ribosomal Spacer; Genetic Variation; Haplotypes; Phylogeny; Phylogeography; Prunus armeniaca
PubMed: 34211010
DOI: 10.1038/s41598-021-93050-w -
Biology Direct Jun 2010Several proposals have been made to explain the rise of multicellular life forms. An internal environment can be created and controlled, germ cells can be protected in...
BACKGROUND
Several proposals have been made to explain the rise of multicellular life forms. An internal environment can be created and controlled, germ cells can be protected in novel structures, and increased organismal size allows a "division of labor" among cell types. These proposals describe advantages of multicellular versus unicellular organisms at levels of organization at or above the individual cell. I focus on a subsequent phase of evolution, when multicellular organisms initiated the process of development that later became the more complex embryonic development found in animals and plants. The advantage here is realized at the level of the mitochondrion and chloroplast.
HYPOTHESIS
The extreme instability of DNA in mitochondria and chloroplasts has not been widely appreciated even though it was first reported four decades ago. Here, I show that the evolutionary success of multicellular animals and plants can be traced to the protection of organellar DNA. Three stages are envisioned. Sequestration allowed mitochondria and chloroplasts to be placed in "quiet" germ line cells so that their DNA is not exposed to the oxidative stress produced by these organelles in "active" somatic cells. This advantage then provided Opportunity, a period of time during which novel processes arose for signaling within and between cells and (in animals) for cell-cell recognition molecules to evolve. Development then led to the enormous diversity of animals and plants.
IMPLICATIONS
The potency of a somatic stem cell is its potential to generate cell types other than itself, and this is a systems property. One of the biochemical properties required for stemness to emerge from a population of cells might be the metabolic quiescence that protects organellar DNA from oxidative stress.
Topics: Animals; Biological Evolution; DNA, Chloroplast; DNA, Mitochondrial; Eukaryota; Models, Theoretical; Plants
PubMed: 20587059
DOI: 10.1186/1745-6150-5-42 -
Annals of Botany Feb 2009The presence of chloroplast-related DNA sequences in the nuclear genome is generally regarded as a relic of the process by which genes have been transferred from the... (Review)
Review
BACKGROUND
The presence of chloroplast-related DNA sequences in the nuclear genome is generally regarded as a relic of the process by which genes have been transferred from the chloroplast to the nucleus. The remaining chloroplast encoded genes are not identical across the plant kingdom indicating an ongoing transfer of genes from the organelle to the nucleus.
SCOPE
This review focuses on the active processes by which the nuclear genome might be acquiring or removing DNA sequences from the chloroplast genome. Present knowledge of the contribution to the nuclear genome of DNA originating from the chloroplast will be reviewed. In particular, the possible effects of stressful environments on the transfer of genetic material between the chloroplast and nucleus will be considered. The significance of this research and suggestions for the future research directions to identify drivers, such as stress, of the nuclear incorporation of plastid sequences are discussed.
CONCLUSIONS
The transfer to the nuclear genome of most of the protein-encoding functions for chloroplast-located proteins facilitates the control of gene expression. The continual transfer of fragments, including complete functional genes, from the chloroplast to the nucleus has been observed. However, the mechanisms by which the loss of functions and physical DNA elimination from the chloroplast genome following the transfer of those functions to the nucleus remains obscure. The frequency of polymorphism across chloroplast-related DNA fragments within a species will indicate the rate at which these DNA fragments are incorporated and removed from the chromosomes.
Topics: Cell Nucleus; Chloroplasts; DNA, Chloroplast; DNA, Plant; Plants; Stress, Physiological
PubMed: 18801916
DOI: 10.1093/aob/mcn173