scholarly journals Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote

2019 ◽  
Author(s):  
Mitsuhiro Matsuo ◽  
Atsushi Katahata ◽  
Makoto Tachikawa ◽  
Yohei Minakuchi ◽  
Hideki Noguchi ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Evolutionary Process ◽  
Whole Genome Sequence ◽  
Dna Virus ◽  
Photosynthetic Eukaryotes ◽  
Genome Reorganization ◽  
Terrestrial Life ◽  
Photosynthetic Organism ◽  
Rapid Amplification ◽  
Endosymbiotic Evolution

AbstractChloroplasts in photosynthetic eukaryotes originated from a cyanobacterial endosymbiosis far more than 1 billion years ago1-3. Due to this ancientness, it remains unclear how this evolutionary process proceeded. To unveil this mystery, we analysed the whole genome sequence of a photosynthetic rhizarian amoeba4, Paulinella micropora5,6, which has a chloroplast-like organelle that originated from another cyanobacterial endosymbiosis7-10 about 0.1 billion years ago11. Here we show that the predacious amoeba that engulfed cyanobacteria evolved into a photosynthetic organism very quickly in the evolutionary time scale, probably aided by the drastic genome reorganization activated by large DNA virus. In the endosymbiotic evolution of eukaryotic cells, gene transfer from the endosymbiont genome to the host nucleus is essential for the evolving host cell to control the endosymbiont-derived organelle12. In P. micropora, we found that the gene transfer from the free-living and endosymbiotic bacteria to the amoeba nucleus was rapidly activated but both simultaneously ceased within the initiation period of the endosymbiotic evolution, suggesting that the genome reorganization drastically proceeded and completed. During this period, large DNA virus appeared to have infected the amoeba, followed by the rapid amplification and diversification of virus-related genes. These findings led us to re-examine the conventional endosymbiotic evolutionary scenario that exclusively deals with the host and the symbiont, and to extend it by incorporating a third critical player, large DNA virus, which activates the drastic gene transfer and genome reorganization between them. This Paulinella version of the evolutionary hypothesis deserves further testing of its generality in evolutionary systems and could shed light on the unknown roles of large DNA viruses13 in the evolution of terrestrial life.

scholarly journals Association of a Novel DNA Virus with the Grapevine Vein-Clearing and Vine Decline Syndrome

2011 ◽  
Vol 101 (9) ◽  
pp. 1081-1090 ◽  
Author(s):  
Yu Zhang ◽  
Kashmir Singh ◽  
Ravneet Kaur ◽  
Wenping Qiu
Keyword(s):  
United States ◽  
Small Rnas ◽  
The United States ◽  
Wide Distribution ◽  
Whole Genome Sequence ◽  
Cdna Libraries ◽  
Dna Virus ◽  
Vein Clearing ◽  
Vine Decline ◽  
Midwest Region

A severe vein-clearing and vine decline syndrome has emerged on grapevines (Vitis vinifera) and hybrid grape cultivars in the Midwest region of the United States. The typical symptoms are translucent vein-clearing on young leaves, short internodes and decline of vine vigor. Known viral pathogens of grapevines were not closely associated with the syndrome. To obtain a comprehensive profile of viruses in a diseased grapevine, small RNAs were enriched and two cDNA libraries were constructed from a symptomatic grapevine and a symptomless grapevine, respectively. Deep sequencing of the two cDNA libraries showed that the most abundant viral small RNAs align with the genomes of viruses in the genus Badnavirus, the family Caulimoviridae. Amplification of the viral DNA by polymerase chain reaction allowed the assembly of the whole genome sequence of a grapevine DNA virus, which shared the highest homology with the Badnavirus sequences. This is the first report of a DNA virus in grapevines. The new DNA virus is closely associated with the vein-clearing symptom, and thus has been given a provisional name Grapevine vein clearing virus (GVCV). GVCV was detected in six grapevine cultivars showing vein-clearing and vine decline syndrome in Missouri, Illinois, and Indiana, suggesting its wide distribution in the Midwest region of the United States. Discovery of DNA viruses in grapevines merits further studies on their epidemics and economic impact on grape production worldwide.

scholarly journals Gene exchange networks define species-like units in marine prokaryotes

2020 ◽  
Author(s):  
R. Stepanauskas ◽  
J.M. Brown ◽  
U. Mai ◽  
O. Bezuidt ◽  
M. Pachiadaki ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dynamic Environment ◽  
Evolutionary Process ◽  
Gene Exchange ◽  
Marine Microorganisms ◽  
Nucleotide Difference ◽  
Tropical Ocean ◽  
Exchange Networks ◽  
Taxonomic Marker

SUMMARYAlthough horizontal gene transfer is recognized as a major evolutionary process in Bacteria and Archaea, its general patterns remain elusive, due to difficulties tracking genes at relevant resolution and scale within complex microbiomes. To circumvent these challenges, we analyzed a randomized sample of >12,000 genomes of individual cells of Bacteria and Archaea in the tropical and subtropical ocean - a well-mixed, global environment. We found that marine microorganisms form gene exchange networks (GENs) within which transfers of both flexible and core genes are frequent, including the rRNA operon that is commonly used as a conservative taxonomic marker. The data revealed efficient gene exchange among genomes with <28% nucleotide difference, indicating that GENs are much broader lineages than the nominal microbial species, which are currently delineated at 4-6% nucleotide difference. The 42 largest GENs accounted for 90% of cells in the tropical ocean microbiome. Frequent gene exchange within GENs helps explain how marine microorganisms maintain millions of rare genes and adapt to a dynamic environment despite extreme genome streamlining of their individual cells. Our study suggests that sharing of pangenomes through horizontal gene transfer is a defining feature of fundamental evolutionary units in marine planktonic microorganisms and, potentially, other microbiomes.

scholarly journals Genome Sequence of Canine Adenovirus Type 1 Isolated from a Wolf (Canis lupus) in Southern Italy

2017 ◽  
Vol 5 (16) ◽  
Author(s):  
Federica Pizzurro ◽  
Maurilia Marcacci ◽  
Guendalina Zaccaria ◽  
Massimiliano Orsini ◽  
Francesca Cito ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Canis Lupus ◽  
Hepatitis A ◽  
Southern Italy ◽  
Adenovirus Type ◽  
Whole Genome Sequence ◽  
Dna Virus ◽  
The Family ◽  
Free Ranging

ABSTRACT Canine adenovirus type 1 (CAdV-1), a DNA virus of the family Adenoviridae, causes infectious canine hepatitis, a highly contagious disease primarily affecting canids. In this report, we describe the isolation and whole-genome sequence of a CAdV-1 isolate from the liver of a free-ranging wolf (Canis lupus).

Horizontal gene transfer in the evolution of photosynthetic eukaryotes

2012 ◽  
Vol 51 (1) ◽  
pp. 13-29 ◽  
Author(s):  
Jinling HUANG ◽  
Jipei YUE
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Photosynthetic Eukaryotes

scholarly journals Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria

2017 ◽  
Vol 372 (1735) ◽  
pp. 20160424 ◽  
Author(s):  
James P. J. Hall ◽  
Michael A. Brockhurst ◽  
Ellie Harrison
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Vertical Transmission ◽  
Gene Pool ◽  
Biological Systems ◽  
Evolutionary Process ◽  
Mobile Genetic Elements ◽  
Social Consequences ◽  
Ecological Traits ◽  
Mobile Gene

In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also ‘horizontally’ between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’.

scholarly journals Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Mick Van Vlierberghe ◽  
Hervé Philippe ◽  
Denis Baurain
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Study ◽  
Data Set ◽  
Cellular Compartment ◽  
Photosynthetic Eukaryotes ◽  
Eukaryotic Proteins ◽  
Photosynthetic Organism ◽  
Diversity Of Life ◽  
Similarity Searches ◽  
Phylogenomic Study

Abstract Objectives Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accurate as possible, proteomes of good quality are needed. Here, our objective is to assemble a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary. Data description We submitted 73 top-quality and taxonomically diverse proteomes to OrthoFinder. We obtained 47,266 orthogroups and identified 11,775 orthogroups with at least two algae. Whenever possible, sequences were functionally annotated with eggNOG and tagged after their genomic and target compartment(s). Then we aligned and computed phylogenetic trees for the orthogroups with IQ-TREE. Finally, these trees were further processed by identifying and pruning the subtrees exclusively composed of plastid-bearing organisms to yield a set of 31,784 clans suitable for studying photosynthetic organism genome evolution.

scholarly journals Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron in Variovorax

2019 ◽  
Author(s):  
Başak Öztürk ◽  
Johannes Werner ◽  
Jan P. Meier-Kolthoff ◽  
Boyke Bunk ◽  
Cathrin Spröer ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Whole Genome Sequence ◽  
Broad Host Range ◽  
Genetic Adaptation ◽  
Full Genome ◽  
Catabolic Gene ◽  
Genome Sequences ◽  
Phenylurea Herbicide ◽  
Gene Functions

AbstractBiodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full genome sequences of six linuron degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight in the mechanisms of genetic adaptation towards linuron metabolism in Variovorax. Whole genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed (i) high conservation and synteny and (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071 elements forming composite transposon structures appointing IS1071 as key for catabolic gene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation.ImportanceThe genus Variovorax and especially a clade of strains that phylogenetically separates from the majority of Variovorax species, appears to be a specialist in the biodegradation of the phenyl urea herbicide linuron. Horizontal gene transfer (HGT) likely played an essential role in the genetic adaptation of those strain to acquire the linuron catabolic genotype. However, we do not know the genetic repertoire involved in this adaptation both regarding catabolic gene functions as well as gene functions that promote HGT neither do we know how this varies between the different strains. These questions are addressed in this paper by analyzing the full genome sequences of six linuron degrading Variovorax strains. This knowledge is important for understanding the mechanisms that steer world-wide genetic adaptation in a particular species and this for a particular phenotypic trait as linuron biodegradation.

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

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.

scholarly journals Pan-genome analysis reveals the molecular basis of niche adaptation ofStaphylococcus epidermidisstrains

2019 ◽  
Author(s):  
Fei Su ◽  
Rui Tian ◽  
Yi Yang ◽  
Lihui Zou ◽  
Xiaomao Xu ◽  
...  
Keyword(s):  
Large Scale ◽  
Evolutionary Process ◽  
Bloodstream Infections ◽  
Vital Role ◽  
Whole Genome Sequence ◽  
Host Bacterium ◽  
Pan Genome ◽  
Source Of Infection ◽  
Niche Adaptation ◽  
Core Proteins

AbstractStaphylococcus epidermidisis the most commonly isolated species from human skin and the second leading cause of bloodstream infections. Here, we performed a large-scale comparative study without any pre-assigned reference to identify genomic determinants associated with their diversity and adaptation as a “double-side spy”, a skin dominant colonization, and a successful pathogen. The pan-genome ofS. epidermidisis open with 435 core proteins and a pan-genome size of 8034 proteins. Genome-wide phylogenetic tree shows that whole genome sequence is a powerful tool to analyze the complex evolutionary process ofS. epidermidisand investigate the source of infection. Comparative genome analyses demonstrate the high diversity of antimicrobial resistances, especially mobile genetic elements. The complicated relationships of host-bacterium and bacterium-bacterium helpS. epidermidisto play a vital role in balancing the epithelial microflora. The highly variable and dynamic nature of theS. epidermidisgenome may be the result of its success in adapting to broad habitats, which is necessary to deal with complex environments. This study gives the general landscape ofS. epidermidispan-genome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible species.

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