scholarly journals Reconstructing plastome evolution across the phylogenetic backbone of the parasitic plant genus Cuscuta (Convolvulaceae)

2020 ◽  
Vol 194 (4) ◽  
pp. 423-438
Author(s):  
Arjan Banerjee ◽  
Saša Stefanović
Keyword(s):  
Parasitic Plants ◽  
Closely Related Species ◽  
Sequence Composition ◽  
Genomic Changes ◽  
Photosynthetic Genes ◽  
Plastome Evolution ◽  
Composition And Structure ◽  
Parasitic Lifestyle ◽  
Photosynthesis Genes ◽  
Substantial Degree

Abstract Parasitic plants have evolved to have reduced or completely lost ability to conduct photosynthesis and are usually characterized by sweeping morphological, physiological and genomic changes. The plastid genome (or plastome) is highly conserved in autotrophic plants and houses many key photosynthesis genes. This molecule is thus a useful system for documenting the genomic effects of a loss of autotrophy. Cuscuta (dodders) represents one of 12 independent transitions to a parasitic lifestyle in angiosperms. This near-cosmopolitan genus contains > 200 obligate parasitic species circumscribed in four subgenera: Grammica, Pachystigma, Cuscuta and Monogynella. With respect to photosynthesis, Cuscuta is a heterogeneous group, containing both hemi- and holoparasitic members that are, respectively, partially or entirely reliant on parasitism to meet their carbon budget. Plastomes in this genus have been reported to show a substantial degree of diversification in terms of length and gene composition. Considered together with well-understood phylogenetic relationships, this genus presents an opportunity for fine-scale comparisons among closely related species of heterotrophic plants. This research documents changes in sequence composition and structure that occurred as these plants evolved along the trophic spectrum by using multiple whole-plastome assemblies from each of the four subgenera. By ‘triangulating’ the positions of genomic changes, we construct a step-by-s’tep model of plastome evolution across the phylogenetic backbone of Cuscuta and highlight the remarkable retention of most photosynthetic genes in these parasitic plants.

scholarly journals Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat

2019 ◽  
Vol 11 (10) ◽  
pp. 2789-2796 ◽  
Author(s):  
Xiao-Jian Qu ◽  
Shou-Jin Fan ◽  
Susann Wicke ◽  
Ting-Shuang Yi
Keyword(s):  
Inverted Repeat ◽  
Chlorophyll Biosynthesis ◽  
Housekeeping Genes ◽  
Parasitic Plants ◽  
Structural Features ◽  
Regulation System ◽  
Biosynthesis Pathway ◽  
Plastid Genomes ◽  
Plastome Evolution ◽  
Selection For

Abstract Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report the plastome of the only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, of which 33 encode proteins, 31 tRNAs, and four rRNAs in a plastome of 85.3-kb length, Parasitaxus has both the smallest and the functionally least capable plastid genome of gymnosperms. Although the heterotroph retains chlorophyll, all genes for photosynthesis are physically or functionally lost, making photosynthetic energy gain impossible. The pseudogenization of the three plastome-encoded light-independent chlorophyll biosynthesis genes chlB, chlL, and chlN implies that Parasitaxus relies on either only the light-dependent chlorophyll biosynthesis pathway or another regulation system. Nesting within a group of gymnosperms known for the absence of the large inverted repeat regions (IRs), another unusual feature of the Parasitaxus plastome is the existence of a 9,256-bp long IR. Its short length and a gene composition that completely differs from those of IR-containing gymnosperms together suggest a regain of this critical, plastome structure-stabilizing feature. In sum, our findings highlight the particular path of lifestyle-associated reductive plastome evolution, where structural features might provide additional cues of a continued selection for plastome maintenance.

scholarly journals Genomics of Aerobic Photoheterotrophs in Wheat Phyllosphere Reveals Divergent Evolutionary Patterns of Photosynthetic Genes in Methylobacterium spp.

2019 ◽  
Vol 11 (10) ◽  
pp. 2895-2908 ◽  
Author(s):  
Athanasios Zervas ◽  
Yonghui Zeng ◽  
Anne Mette Madsen ◽  
Lars H Hansen
Keyword(s):  
Infrared Imaging ◽  
Triticum Aestivum L ◽  
Evolutionary Patterns ◽  
Bacterial Colony ◽  
Anoxygenic Phototrophs ◽  
Maldi Tof ◽  
Photosynthetic Genes ◽  
Oxford Nanopore ◽  
Photosynthesis Genes ◽  
Recent Addition

Abstract Phyllosphere is a habitat to a variety of viruses, bacteria, fungi, and other microorganisms, which play a fundamental role in maintaining the health of plants and mediating the interaction between plants and ambient environments. A recent addition to this catalogue of microbial diversity was the aerobic anoxygenic phototrophs (AAPs), a group of widespread bacteria that absorb light through bacteriochlorophyll α (BChl a) to produce energy without fixing carbon or producing molecular oxygen. However, culture representatives of AAPs from phyllosphere and their genome information are lacking, limiting our capability to assess their potential ecological roles in this unique niche. In this study, we investigated the presence of AAPs in the phyllosphere of a winter wheat (Triticum aestivum L.) in Denmark by employing bacterial colony based infrared imaging and MALDI-TOF mass spectrometry (MS) techniques. A total of ∼4,480 colonies were screened for the presence of cellular BChl a, resulting in 129 AAP isolates that were further clustered into 21 groups based on MALDI-TOF MS profiling, representatives of which were sequenced using the Illumina NextSeq and Oxford Nanopore MinION platforms. Seventeen draft and four complete genomes of AAPs were assembled belonging in Methylobacterium, Rhizobium, Roseomonas, and a novel Alsobacter. We observed a diverging pattern in the evolutionary rates of photosynthesis genes among the highly homogenous AAP strains of Methylobacterium (Alphaproteobacteria), highlighting an ongoing genomic innovation at the gene cluster level.

Multiple and different genomic rearrangements of the rbcL gene are present in the parasitic orchid Neottia nidus-avis

Genome ◽  
2012 ◽  
Vol 55 (09) ◽  
pp. 629-637 ◽  
Author(s):  
Donata Cafasso ◽  
Gianni Chinali
Keyword(s):  
Plastid Genome ◽  
Photosynthetic Capacity ◽  
Parasitic Plants ◽  
Flowering Plants ◽  
Genomic Rearrangements ◽  
Rbcl Gene ◽  
Individual Plant ◽  
Fixed Carbon ◽  
Photosynthetic Genes ◽  
Rbcl Sequences

In parasitic plants that have lost most, if not all, of their photosynthetic genes, the genome of their plastids has also undergone a dramatic reduction. For example, photosynthetic genes, such as rbcL, frequently become pseudogenes, in which large portions of the gene have been found to be deleted. Orchids are flowering plants with several parasitic lineages. This is consistent with the observation that parasitic orchids can invade pre-existing mutualistic associations between ectomycorrhizal trees and fungi to obtain fixed carbon and nutrients. In addition, some parasitic species are devoid of chlorophyll, and consequently, have lost their photosynthetic capacity. Here, the organization of the plastid genome of the parasitic orchid Neottia nidus-avis (L.) Rich. was investigated using sequencing and hybridization experiments. In particular, genomic rearrangements in the rbcL region of this parasitic orchid were analyzed. At least three distinct rbcL sequences were found to be present as pseudogenes and were likely located in the plastid genome. Based on these results, it is hypothesized that N. nidus-avis contains different plastomes, each with a different pseudogene, and these can exist within the same individual plant.

scholarly journals Gene Duplication and Gain in the Trematode Atriophallophorus Winterbourni Contributes to Adaptation to Parasitism

2021 ◽  
Author(s):  
Natalia Zajac ◽  
Stefan Zoller ◽  
Katri Seppälä ◽  
David Moi ◽  
Christophe Dessimoz ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Analysis ◽  
Enrichment Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Genomic Changes ◽  
Go Enrichment ◽  
Duplication Events ◽  
Parasitic Lifestyle ◽  
Host Parasite

Abstract Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 MYA (± 120.4 MY). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used Hierarchical Orthologous Groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, i.e. newly acquired. We found 13 gene families in A. winterbourni to have had more than 10 genes arising through these recent duplications; all of which have functions potentially relating to host behavioural manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host-parasite adaptation.

scholarly journals Relaxed selection underlies genome erosion in socially parasitic ant species

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lukas Schrader ◽  
Hailin Pan ◽  
Martin Bollazzi ◽  
Morten Schiøtt ◽  
Fredrick J. Larabee ◽  
...  
Keyword(s):  
Olfactory Receptors ◽  
Social Parasite ◽  
Effective Population ◽  
Social Parasites ◽  
Free Living ◽  
Closely Related Species ◽  
Genomic Changes ◽  
The Social ◽  
Population Sizes ◽  
Leaf Cutting

AbstractInquiline ants are highly specialized and obligate social parasites that infiltrate and exploit colonies of closely related species. They have evolved many times convergently, are often evolutionarily young lineages, and are almost invariably rare. Focusing on the leaf-cutting ant genus Acromyrmex, we compared genomes of three inquiline social parasites with their free-living, closely-related hosts. The social parasite genomes show distinct signatures of erosion compared to the host lineages, as a consequence of relaxed selective constraints on traits associated with cooperative ant colony life and of inquilines having very small effective population sizes. We find parallel gene losses, particularly in olfactory receptors, consistent with inquiline species having highly reduced social behavioral repertoires. Many of the genomic changes that we uncover resemble those observed in the genomes of obligate non-social parasites and intracellular endosymbionts that branched off into highly specialized, host-dependent niches.

scholarly journals The features of xylem tracheary elements in some herbaceous members of the family Convolvulaceae Horan.

Turczaninowia ◽  
2021 ◽  
Vol 24 (3) ◽  
pp. 129-137
Author(s):  
Yevgeniya V. Goremykina ◽  
Aleksandra D. Azaryan ◽  
Esong Linda Akime ◽  
Kseniya Y. Leshchina
Keyword(s):  
Parasitic Plants ◽  
Tracheary Elements ◽  
Convolvulus Arvensis ◽  
Climbing Plants ◽  
Conducting Tissue ◽  
The Family ◽  
Cuscuta Campestris ◽  
Order Of Magnitude ◽  
Parasitic Lifestyle ◽  
Calystegia Sepium

Numerous narrow xylem tracheary elements (tracheids and vessels) are present in liana stems, along with a few wide vessels that perform the main water-conducting function. This trait, known as “vessel dimorphism”, has been identified in studies on water-conducting tissue in autotrophic plants, including a large number of perennial climbing plants and a number of annual vines. Information is lacking on the presence of vessel dimorphism in parasitic plants of the lianescent habit. In this study, we performed a structural analysis of stems in the autotrophic herbaceous vines of Convolvulus arvensis L. and Calystegia sepium (L.) R. Br., as well as in the parasitic vines of Cuscuta monogyna Vahl, Cuscuta planiflora Ten., Cuscuta approximata Bab., and Cuscuta campestris Yunck., of the family of Convolvulaceae Horan. The xylem of C. arvensis and C. sepium contains a few wide conductive elements and many narrow ones. This feature is typical of autotrophic climbing plants. Only narrow tracheary elements are present in the xylem of the parasitic vines of the genus of Cuscuta L. (dodders). The total number of the tracheary elements is an order of magnitude less in the dodders than it is in the autotrophic vines. It is possible that the autotrophic ancestor of dodders lost the characteristic feature of the xylem of climbing plants, known as vessel dimorphism, during its transition to the parasitic lifestyle.

Crystal Structure Analysis of Cu-Zr Alloys by Convergent Beam Diffraction

1981 ◽  
Vol 39 ◽  
pp. 354-355
Author(s):  
A. F. Marshall ◽  
J. W. Steeds ◽  
D. Bouchet ◽  
S. L. Shinde ◽  
R. G. Walmsley
Keyword(s):  
Crystal Structure ◽  
Point Group ◽  
Intermetallic Phase ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Ion Milling ◽  
Composition And Structure ◽  
Unit Cells ◽  
Sputter Deposited ◽  
Convergent Beam

Convergent beam electron diffraction is a powerful technique for determining the crystal structure of a material in TEM. In this paper we have applied it to the study of the intermetallic phases in the Cu-rich end of the Cu-Zr system. These phases are highly ordered. Their composition and structure has been previously studied by microprobe and x-ray diffraction with sometimes conflicting results.The crystalline phases were obtained by annealing amorphous sputter-deposited Cu-Zr. Specimens were thinned for TEM by ion milling and observed in a Philips EM 400. Due to the large unit cells involved, a small convergence angle of diffraction was used; however, the three-dimensional lattice and symmetry information of convergent beam microdiffraction patterns is still present. The results are as follows:1) 21 at% Zr in Cu: annealed at 500°C for 5 hours. An intermetallic phase, Cu3.6Zr (21.7% Zr), space group P6/m has been proposed near this composition (2). The major phase of our annealed material was hexagonal with a point group determined as 6/m.

Off-axis electron holography applied to the study of interfaces

1992 ◽  
Vol 50 (1) ◽  
pp. 244-245
Author(s):  
J.K. Weiss ◽  
M. Gajdardziska-Josifovska ◽  
M. R. McCartney ◽  
David J. Smith
Keyword(s):  
Electric Fields ◽  
Resolution Enhancement ◽  
Interfacial Structure ◽  
Atomic Scale ◽  
Bulk Property ◽  
Electron Holography ◽  
Specimen Thickness ◽  
Composition And Structure ◽  
Chemical Segregation ◽  
Diffraction Effects

Interfacial structure is a controlling parameter in the behavior of many materials. Electron microscopy methods are widely used for characterizing such features as interface abruptness and chemical segregation at interfaces. The problem for high resolution microscopy is to establish optimum imaging conditions for extracting this information. We have found that off-axis electron holography can provide useful information for the study of interfaces that is not easily obtained by other techniques.Electron holography permits the recovery of both the amplitude and the phase of the image wave. Recent studies have applied the information obtained from electron holograms to characterizing magnetic and electric fields in materials and also to atomic-scale resolution enhancement. The phase of an electron wave passing through a specimen is shifted by an amount which is proportional to the product of the specimen thickness and the projected electrostatic potential (ignoring magnetic fields and diffraction effects). If atomic-scale variations are ignored, the potential in the specimen is described by the mean inner potential, a bulk property sensitive to both composition and structure. For the study of interfaces, the specimen thickness is assumed to be approximately constant across the interface, so that the phase of the image wave will give a picture of mean inner potential across the interface.

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