Genome Structure and Gene Content in Plant and Protist Mitochondrial DNAs

2004 ◽  
pp. 520-523
Author(s):  
Michael W. Gray
Keyword(s):  
Genome Structure ◽  
Gene Content ◽  
Mitochondrial Dnas

scholarly journals Unique Mitochondrial Genome Structure in Diplonemids, the Sister Group of Kinetoplastids

2005 ◽  
Vol 4 (6) ◽  
pp. 1137-1146 ◽  
Author(s):  
William Marande ◽  
Julius Lukeš ◽  
Gertraud Burger
Keyword(s):  
Electron Microscopy ◽  
Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Genome Structure ◽  
Sister Group ◽  
Dense Networks ◽  
Guide Rnas ◽  
Fluorescence And Electron Microscopy ◽  
Mitochondrial Dnas

ABSTRACT Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules: maxicircles bearing protein and mitoribosomal genes and minicircles specifying guide RNAs, which mediate uridine insertion/deletion RNA editing. These circles are interlocked with one another to form dense networks. Whether these peculiar mtDNA features are restricted to kinetoplastids or prevail throughout Euglenozoa (euglenids, diplonemids, and kinetoplastids) is unknown. Here, we describe the mitochondrial genome and the mitochondrial ultrastructure of Diplonema papillatum, a member of the diplonemid flagellates, the sister group of kinetoplastids. Fluorescence and electron microscopy show a single mitochondrion per cell with an ultrastructure atypical for Euglenozoa. In addition, DNA is evenly distributed throughout the organelle rather than compacted. Molecular and electron microscopy studies distinguish numerous 6- and 7-kbp-sized mitochondrial chromosomes of monomeric circular topology and relaxed conformation in vivo. Remarkably, the cox1 gene (and probably other mitochondrial genes) is fragmented, with separate gene pieces encoded on different chromosomes. Generation of the contiguous cox1 mRNA requires trans-splicing, the precise mechanism of which remains to be determined. Taken together, the mitochondrial gene/genome structure of Diplonema is not only different from that of kinetoplastids but unique among eukaryotes as a whole.

scholarly journals The Complete Chloroplast Genome Sequence of Podocarpus lambertii: Genome Structure, Evolutionary Aspects, Gene Content and SSR Detection

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e90618 ◽  
Author(s):  
Leila do Nascimento Vieira ◽  
Helisson Faoro ◽  
Marcelo Rogalski ◽  
Hugo Pacheco de Freitas Fraga ◽  
Rodrigo Luis Alves Cardoso ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Genome Structure ◽  
Gene Content ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Evolutionary Aspects

scholarly journals The First Plastid Genome of the Holoparasitic Genus Prosopanche (Hydnoraceae)

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 306 ◽  
Author(s):  
Matthias Jost ◽  
Julia Naumann ◽  
Nicolás Rocamundi ◽  
Andrea A. Cocucci ◽  
Stefan Wanke
Keyword(s):  
Plastid Genome ◽  
Essential Gene ◽  
Genome Structure ◽  
Gene Content ◽  
Recent Common Ancestor ◽  
Ribosomal Protein Genes ◽  
Most Recent Common Ancestor ◽  
Gene Sets ◽  
Evolutionary Trajectories ◽  
Mycoheterotrophic Plants

Plastomes of parasitic and mycoheterotrophic plants show different degrees of reduction depending on the plants’ level of heterotrophy and host dependence in comparison to photoautotrophic sister species, and the amount of time since heterotrophic dependence was established. In all but the most recent heterotrophic lineages, this reduction involves substantial decrease in genome size and gene content and sometimes alterations of genome structure. Here, we present the first plastid genome of the holoparasitic genus Prosopanche, which shows clear signs of functionality. The plastome of Prosopanche americana has a length of 28,191 bp and contains only 24 unique genes, i.e., 14 ribosomal protein genes, four ribosomal RNA genes, five genes coding for tRNAs and three genes with other or unknown function (accD, ycf1, ycf2). The inverted repeat has been lost. Despite the split of Prosopanche and Hydnora about 54 MYA ago, the level of genome reduction is strikingly congruent between the two holoparasites although highly dissimilar nucleotide sequences are observed. Our results lead to two possible evolutionary scenarios that will be tested in the future with a larger sampling: 1) a Hydnoraceae plastome, similar to those of Hydnora and Prosopanche today, existed already in the most recent common ancestor and has not changed much with respect to gene content and structure, or 2) the genome similarities we observe today are the result of two independent evolutionary trajectories leading to almost the same endpoint. The first hypothesis would be most parsimonious whereas the second would point to taxon dependent essential gene sets for plants released from photosynthetic constraints.

scholarly journals The Chloroplast Genome Evolution of Venus Slipper (Paphiopedilum): IR Expansion, SSC Contraction, and Highly Rearranged SSC Regions

2021 ◽  
Author(s):  
Yan-Yan Guo ◽  
Jia-Xing Yang ◽  
Guo-Qiang Zhang ◽  
Zhong-Jian Liu
Keyword(s):  
Gene Order ◽  
Inverted Repeat ◽  
Genome Structure ◽  
Single Copy ◽  
Gene Content ◽  
Comparative Genomic ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Ideal System ◽  
Small Single Copy

Abstract Background: Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species. The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum.Results: The plastomes of Paphiopedilum have conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of inverted repeat/small single copy (IR/SSC) boundaries varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates.Conclusions: We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

scholarly journals Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy.

Genetics ◽  
1989 ◽  
Vol 123 (4) ◽  
pp. 825-836 ◽  
Author(s):  
T M Boyce ◽  
M E Zwick ◽  
C F Aquadro
Keyword(s):  
Mitochondrial Dna ◽  
Rare Variants ◽  
Size Structure ◽  
Genome Structure ◽  
Size Variation ◽  
Gene Content ◽  
Coding Region ◽  
Rich Region ◽  
Large Size ◽  
And Function

Abstract Mitochondrial DNA of higher animals has been described as an example of extreme efficiency in genome structure and function. Where exceptionally large size molecules have been found (greater than 20 kb), most have occurred as rare variants within a species, suggesting that these variants arise infrequently and do not persist for long periods in evolutionary time. In contrast, all individuals of at least three species of bark weevil (Curculionidae: Pissodes) possess a mitochondrial genome of unusually large size (30-36 kb). The molecule owes its large size to a dramatically enlarged A + T-rich region (9-13 kb). Gene content and order outside of this region appear to be identical to that found in Drosophila. A series of 0.8-2.0-kb repeated sequences occur adjacent to the large A + T rich region and have perhaps played a role in the generation of the large size as well as an unprecedented frequency of size variant heteroplasmy. Every weevil sampled in all three species (n = 219) exhibits anywhere from two to five distinct size classes of mtDNA. The persistence of this large amount of size polymorphism through two speciation events combined with the abundant size variation within individuals suggests that these molecules may not be subject to strong selection for small overall size and efficiency of replication. This pattern of variation contrasts strongly with the conservation of gene content and arrangement in the coding region of the molecule.

scholarly journals Genome Rearrangements, Deletions, and Amplifications in the Natural Population of Bartonella henselae

2006 ◽  
Vol 188 (21) ◽  
pp. 7426-7439 ◽  
Author(s):  
Hillevi Lindroos ◽  
Olga Vinnere ◽  
Alex Mira ◽  
Dirk Repsilber ◽  
Kristina Näslund ◽  
...  
Keyword(s):  
Antigenic Variation ◽  
Bartonella Henselae ◽  
Genome Structure ◽  
Dna Amplification ◽  
Human Infection ◽  
Replication Initiation ◽  
Natural Host ◽  
Genomic Islands ◽  
Gene Content ◽  
Multiple Sources

ABSTRACT Cats are the natural host for Bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. Here, we have analyzed the natural variation in gene content and genome structure of 38 Bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (PFGE) blots. The variation in gene content was modest and confined to the prophage and the genomic islands, whereas the PFGE analyses indicated extensive rearrangements across the terminus of replication with breakpoints in areas of the genomic islands. We observed no difference in gene content or structure between feline and human strains. Rather, the results suggest multiple sources of human infection from feline B. henselae strains of diverse genotypes. Additionally, the microarray hybridizations revealed DNA amplification in some strains in the so-called chromosome II-like region. The amplified segments were centered at a position corresponding to a putative phage replication initiation site and increased in size with the duration of cultivation. We hypothesize that the variable gene pool in the B. henselae population plays an important role in the establishment of long-term persistent infection in the natural host by promoting antigenic variation and escape from the host immune response.

Existence of DNA in yeast microbodies

1978 ◽  
Vol 36 (2) ◽  
pp. 232-233
Author(s):  
Masako Osumi ◽  
Misuzu Nagano ◽  
Hiroko Kazama
Keyword(s):  
Catalase Activity ◽  
Buoyant Density ◽  
Model System ◽  
Contour Length ◽  
Native State ◽  
Normal Alkane ◽  
Remarkable Increase ◽  
Dna Molecule ◽  
Mitochondrial Dnas

We have found that microbodies appeared profusely together with a remarkable increase in catalase activity in normal alkane-grown cells of hydrocarbon-utilizing Candida yeasts, and that the microbodies multiplied by division in these cells. These features of Candida yeasts seem to provide a useful model system for studies on the biogenesis of the microbody. Subsequently, we have succeeded in isolation of Candida microbodies in an apparently native state, as judged biochemically and morphologically. The presence of DNA in the purified microbody fraction thus obtained was proved by the diphenylamine method. DNA molecule of about 15 urn in contour length was released from an isolated microbody. The physicochemical analyses of the microbody DNA revealed that its buoyant density differed from nuclear and mitochondrial DNAs. All these results lead us to the possibility that there is a novel type of DNA in microbodies.

Sign in / Sign up

Export Citation Format

Share Document