Chloroplast nucleoids are highly dynamic in ploidy, number, and structure during angiosperm leaf development

SummaryChloroplast nucleoids are large, compact nucleoprotein structures containing multiple copies of the plastid genome. Studies on structural and quantitative changes of plastid DNA (ptDNA) during leaf development are scarce and have produced controversial data. We have systematically investigated nucleoid dynamics and ptDNA quantities in mesophyll ofArabidopsis, tobacco, sugar beet, and maize from the early post-meristematic stage until necrosis. DNA of individual nucleoids was quantified by DAPI-based supersensitive epifluorescence microscopy. Nucleoids occurred in scattered, stacked or ring-shaped arrangements and in recurring patterns during leaf development remarkably similar between the species studied. Nucleoids per organelle varied from few in meristematic plastids to >30 in mature chloroplasts (corresponding to about 20-750 nucleoids per cell). Nucleoid ploidies ranged from haploid to >20-fold even within individual organelles, with average values between 2.6- and 6.7-fold and little changes during leaf development. DNA quantities per organelle increased gradually from about a dozen plastome copies in tiny plastids of apex cells to 70-130 copies in chloroplasts of about 7 μm diameter in mature mesophyll tissue, and from about 80 plastome copies in meristematic cells to 2,600-3,300 copies in mature diploid mesophyll cells without conspicuous decline during leaf development. Pulsed-field electrophoresis, restriction of high-molecular weight DNA from chloroplasts and gerontoplasts, and CsCl equilibrium centrifugation of single- and double-stranded ptDNA revealed no noticeable fragmentation of the organelle DNA during leaf development, implying that plastid genomes in mesophyll tissues are remarkably stable until senescence.Significance StatementPlastid DNA is organized in nucleoids that are highly dynamic in organization, structure and amount during leaf development. The present investigation fully resolves now this dynamic and is a precise cytogenetic characterization of nucleoids DNA spanning the entire life cycle of the leaf.

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Two Plastid DNA Lineages—Rapa/Oleracea and Nigra—within the Tribe Brassiceae Can Be Best Explained by Reciprocal Crosses at Hexaploidy: Evidence from Divergence Times of the Plastid Genomes and R-Block Genes of the A and B Genomes of Brassica juncea

PLoS ONE ◽

10.1371/journal.pone.0093260 ◽

2014 ◽

Vol 9 (4) ◽

pp. e93260 ◽

Cited By ~ 12

Author(s):

Sarita Sharma ◽

K. Lakshmi Padmaja ◽

Vibha Gupta ◽

Kumar Paritosh ◽

Akshay K. Pradhan ◽

...

Keyword(s):

Brassica Juncea ◽

Plastid Dna ◽

Divergence Times ◽

Reciprocal Crosses ◽

Plastid Genomes

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Plastome Diversity and Phylogenomic Relationships in Asteraceae

Plants ◽

10.3390/plants10122699 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2699

Author(s):

Joan Pere Pascual-Díaz ◽

Sònia Garcia ◽

Daniel Vitales

Keyword(s):

Ribosomal Rna ◽

Evolutionary Rate ◽

Plastid Dna ◽

Single Copy ◽

Phylogenomic Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Plastid Genomes ◽

The Family ◽

Rna Genes

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae—as well as in the sister family Calyceraceae—lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family’s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

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Plastid Development in Leaf Epidermis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100099519 ◽

1981 ◽

Vol 39 ◽

pp. 618-619

Author(s):

Jacob P. Varkey ◽

Mathew J. Nadakavukaren

Keyword(s):

Leaf Development ◽

Osmium Tetroxide ◽

Leaf Epidermis ◽

Plastid Development ◽

Mesophyll Cells ◽

Plastid Ultrastructure ◽

Epidermal Tissue ◽

Standard Procedures ◽

Growth Chambers ◽

Light:Dark Cycle

Changes in the plastid ultrastructure during development of a leaf have been studied extensively. Most studies have been done on the development of chloroplasts in mesophyll cells. Chloroplasts are small and few in number or plastids never develop into chloroplasts in epidermal cells of leaves of many species. Not much is known about the development of plastids in the epidermal tissue. Sunflower was selected to study the plastid development in the epidermal tissue.Sunflower plants were grown from seeds in growth chambers maintained on a 14:10 light:dark cycle at a daytime temperature of 78 F and nighttime temperature of 70 F with 80% humidity. Samples for ultrastructural study were taken from primary leaves at different stages of development. Because the rate of leaf development can vary from plant to plant, samples were taken from the same primary leaves of selected seedlings. These samples fixed in glutaraldehyde followed by osmium tetroxide were processed for electron microscopy using standard procedures.

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A Comparison of Three Circular Mitochondrial Genomes of Fagus sylvatica from Germany and Poland Reveals Low Variation and Complete Identity of the Gene Space

Forests ◽

10.3390/f12050571 ◽

2021 ◽

Vol 12 (5) ◽

pp. 571

Author(s):

Bagdevi Mishra ◽

Bartosz Ulaszewski ◽

Joanna Meger ◽

Sebastian Ploch ◽

Jaroslaw Burczyk ◽

...

Keyword(s):

Mitochondrial Genome ◽

Central Europe ◽

Glacial Refugia ◽

The Other ◽

Mitochondrial Genomes ◽

Organelle Dna ◽

Phylogenetic Studies ◽

Low Degree ◽

Multiple Copies ◽

Mitochondrial Sequences

Similar to chloroplast loci, mitochondrial markers are frequently used for genotyping, phylogenetic studies, and population genetics, as they are easily amplified due to their multiple copies per cell. In a recent study, it was revealed that the chloroplast offers little variation for this purpose in central European populations of beech. Thus, it was the aim of this study to elucidate, if mitochondrial sequences might offer an alternative, or whether they are similarly conserved in central Europe. For this purpose, a circular mitochondrial genome sequence from the more than 300-year-old beech reference individual Bhaga from the German National Park Kellerwald-Edersee was assembled using long and short reads and compared to an individual from the Jamy Nature Reserve in Poland and a recently published mitochondrial genome from eastern Germany. The mitochondrial genome of Bhaga was 504,730 bp, while the mitochondrial genomes of the other two individuals were 15 bases shorter, due to seven indel locations, with four having more bases in Bhaga and three locations having one base less in Bhaga. In addition, 19 SNP locations were found, none of which were inside genes. In these SNP locations, 17 bases were different in Bhaga, as compared to the other two genomes, while 2 SNP locations had the same base in Bhaga and the Polish individual. While these figures are slightly higher than for the chloroplast genome, the comparison confirms the low degree of genetic divergence in organelle DNA of beech in central Europe, suggesting the colonisation from a common gene pool after the Weichsel Glaciation. The mitochondrial genome might have limited use for population studies in central Europe, but once mitochondrial genomes from glacial refugia become available, it might be suitable to pinpoint the origin of migration for the re-colonising beech population.

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Changes in the density of microtubular networks in mesophyll cells and mesophyll derived protoplasts of Nicotiana and Triticum during leaf development

Planta ◽

10.1007/bf00195669 ◽

1993 ◽

Vol 190 (1) ◽

Cited By ~ 10

Author(s):

G. Jung ◽

A. Hellmann ◽

W. Wernicke

Keyword(s):

Leaf Development ◽

Mesophyll Cells

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Developmental Effects on Relative Use of PEPCK and NADP-ME Pathways of C4 Photosynthesis in Maize

10.1101/2021.06.25.449949 ◽

2021 ◽

Author(s):

Jennifer J Arp ◽

Shrikaar Kambhampati ◽

Kevin Chu ◽

Somnath Koley ◽

Lauren M Jenkins ◽

...

Keyword(s):

Enzyme Activity ◽

Leaf Development ◽

Phosphoenolpyruvate Carboxykinase ◽

C4 Photosynthesis ◽

Leaf Age ◽

Bundle Sheath ◽

Decarboxylase Activity ◽

Mesophyll Cells ◽

Source To Sink ◽

Canopy Position

C4 photosynthesis is an adaptive photosynthetic pathway which concentrates CO2 around Rubisco in specialized bundle sheath cells to reduce photorespiration. Historically, the pathway has been characterized into three different subtypes based on the decarboxylase involved, although recent work has provided evidence that some plants can use multiple decarboxylases, with maize in particular using both the NADP-malic enzyme (NADP-ME) pathway and phosphoenolpyruvate carboxykinase (PEPCK) pathway. Parallel C4 pathways could be advantageous in balancing energy and reducing equivalents between bundle sheath and mesophyll cells, in decreasing the size of the metabolite gradients between cells and may better accommodate changing environmental conditions or source to sink demands on growth. The enzyme activity of C4 decarboxylases can fluctuate with different stages of leaf development, but it remains unclear if the pathway flexibility is an innate aspect of leaf development or an adaptation to the leaf microenvironment that is regulated by the plant. In this study, variation in the two C4 pathways in maize were characterized at nine plant ages throughout the life cycle. Two positions in the canopy were examined for variation in physiology, gene expression, metabolite concentration, and enzyme activity, with particular interest in asparagine as a potential regulator of C4 decarboxylase activity. Variation in C4 and C3 metabolism was observed for both leaf age and canopy position, reflecting the ability of C4 pathways to adapt to changing microenvironments.

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Plastome Diversity and Phylogenomic Relationships in Asteraceae

10.20944/preprints202111.0167.v1 ◽

2021 ◽

Author(s):

Joan Pere Pascual-Díaz ◽

Sònia Garcia ◽

Daniel Vitales

Keyword(s):

Ribosomal Rna ◽

Evolutionary Rate ◽

Plastid Dna ◽

Single Copy ◽

Phylogenomic Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Plastid Genomes ◽

The Family ◽

Rna Genes

Plastid genomes are in general highly conserved given their slow evolutionary rate, thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridisation, both processes usually complicating systematic inferences. In this study, we have generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity, and repeat composition of these sequences. By comparing the whole plastome sequences obtained, we confirmed the double inversion located in the long single copy region, for most of the species analysed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also show that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae -as well as in the sister family Calyceraceae - are lacking the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, are overall consistent with the general consensus for the family’s phylogeny, while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

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Count does not recover major events of gene flux in real biological data

10.1101/246272 ◽

2018 ◽

Author(s):

Nils Kapust ◽

Shijulal Nelson-Sathi ◽

Barbara Schönfeld ◽

Einat Hazkani-Covo ◽

David Bryant ◽

...

Keyword(s):

Gene Transfer ◽

Lateral Gene Transfer ◽

Evolutionary Process ◽

Plastid Dna ◽

Biological Data ◽

Distribution Data ◽

Plastid Genomes ◽

Host Lineage ◽

Genome Analyses ◽

Phylogenetic Models

AbstractIn prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional birth-and-death phylogenetic models to investigate prokaryote genome evolution to claim that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here we test the ability of Count, a birth-and-death based program, to recover known events of mass acquisition and differential loss using plastid genomes and eukaryotic protein families that were acquired from plastids. Count showed a strong bias towards reconstructed histories having gene acquisitions distributed uniformly across the tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, Count recovered gradual and continuous lateral gene transfer among lineages, even when massive gains followed by gradual differential loss is the true evolutionary process that generated the gene distribution data.

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