Toxin-Antidote Elements Across the Tree of Life

2020 ◽  
Vol 54 (1) ◽  
pp. 387-415
Author(s):  
Alejandro Burga ◽  
Eyal Ben-David ◽  
Leonid Kruglyak
Keyword(s):  
Natural Populations ◽  
Tree Of Life ◽  
Evolutionary Origin ◽  
Next Generation ◽  
Bacterial Plasmids ◽  
Evolutionary Genetic ◽  
Unified View ◽  
Similarities And Differences ◽  
Eukaryotic Organisms

In life's constant battle for survival, it takes one to kill but two to conquer. Toxin-antitoxin or toxin-antidote (TA) elements are genetic dyads that cheat the laws of inheritance to guarantee their transmission to the next generation. This seemingly simple genetic arrangement—a toxin linked to its antidote—is capable of quickly spreading and persisting in natural populations. TA elements were first discovered in bacterial plasmids in the 1980s and have recently been characterized in fungi, plants, and animals, where they underlie genetic incompatibilities and sterility in crosses between wild isolates. In this review, we provide a unified view of TA elements in both prokaryotic and eukaryotic organisms and highlight their similarities and differences at the evolutionary, genetic, and molecular levels. Finally, we propose several scenarios that could explain the paradox of the evolutionary origin of TA elements and argue that these elements may be key evolutionary players and that the full scope of their roles is only beginning to be uncovered.

scholarly journals Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

PLoS ONE ◽  
2013 ◽  
Vol 8 (11) ◽  
pp. e80422 ◽  
Author(s):  
Christian Rellstab ◽  
Stefan Zoller ◽  
Andrew Tedder ◽  
Felix Gugerli ◽  
Martin C. Fischer
Keyword(s):  
Next Generation Sequencing ◽  
Plant Species ◽  
Natural Populations ◽  
Allele Frequencies ◽  
Next Generation ◽  
Model Plant ◽  
Generation Sequencing

scholarly journals A Novel Metagenomic Workflow for Biomonitoring across the Tree of Life using PCR-free Ultra-deep Sequencing of Extracellular eDNA

2021 ◽  
Author(s):  
Shivakumara Manu ◽  
Govindhaswamy Umapathy
Keyword(s):  
Large Scale ◽  
Rapid Assessment ◽  
Tree Of Life ◽  
Extracellular Dna ◽  
Anthropogenic Factors ◽  
Full Potential ◽  
Next Generation ◽  
Taxonomic Assignment ◽  
Biodiversity Crisis ◽  
Lowest Common Ancestor

Biodiversity is declining on a planetary scale at an alarming rate due to anthropogenic factors. Classical biodiversity monitoring approaches are time-consuming, resource-intensive, and not scalable to address the current biodiversity crisis. The environmental DNA-based next-generation biomonitoring framework provides an efficient, scalable, and holistic solution for evaluating changes in various ecological entities. However, its scope is currently limited to monitoring targeted groups of organisms using metabarcoding, which suffers from various PCR-induced biases. To utilise the full potential of next-generation biomonitoring, we intended to develop PCR-free genomic technologies that can deliver unbiased biodiversity data across the tree of life in a single assay. Here, we describe a novel metagenomic workflow comprising of a customised extracellular DNA enrichment protocol from large-volume filtered water samples, a completely PCR-free library preparation step, an ultra-deep next-generation sequencing, and a pseudo-taxonomic assignment strategy using the dual lowest common ancestor algorithm. We demonstrate the utility of our approach in a pilot-scale spatially-replicated experimental setup in Chilika, a large hyper-diverse brackish lagoon ecosystem in India. Using incidence-based statistics, we show that biodiversity across the tree of life, from microorganisms to the relatively low-abundant macroorganisms such as Arthropods and Fishes, can be effectively detected with about one billion paired-end reads using our reproducible workflow. With decreasing costs of sequencing and the increasing availability of genomic resources from the earth biogenome project, our approach can be tested in different ecosystems and adapted for large-scale rapid assessment of biodiversity across the tree of life

scholarly journals Next-generation phenomics for the Tree of Life

PLoS Currents ◽  
2013 ◽  
Author(s):  
Gordon Burleigh ◽  
Kenzley Alphonse ◽  
Andrew J Alverson ◽  
Holly M Bik ◽  
Carrine Blank ◽  
...  
Keyword(s):  
Tree Of Life ◽  
Next Generation

Phylogenomics of hyperthermophilic Archaea and Bacteria

2004 ◽  
Vol 32 (2) ◽  
pp. 175-178 ◽  
Author(s):  
H.-P. Klenk ◽  
M. Spitzer ◽  
T. Ochsenreiter ◽  
G. Fuellen
Keyword(s):  
New Species ◽  
Genome Sequencing ◽  
Genetic Information ◽  
Tree Of Life ◽  
Evolutionary Origin ◽  
Microbial Genome ◽  
Hyperthermophilic Archaea ◽  
Phylogenomic Analyses ◽  
Hot Environments ◽  
Hyperthermophilic Organisms

The location of hyperthermophilic organisms in the tree of life has been the source of many exciting discussions during the last two decades. It inspired not only novel hypotheses for the early evolution of the organisms, but also the isolation of many new species of Archaea and Bacteria from hot environments, as well as microbial genome sequencing and phylogenomic analyses. In view of the new wealth of genetic information generated from several analysed genomes of the hyperthermophiles, we can only conclude that the question of their exact phylogenetic location and evolutionary origin is presently as open as ever before.

scholarly journals Evolution of B Chromosomes: From Dispensable Parasitic Chromosomes to Essential Genomic Players

2021 ◽  
Vol 12 ◽  
Author(s):  
Martina Johnson Pokorná ◽  
Radka Reifová
Keyword(s):  
Sex Determination ◽  
Significant Role ◽  
Sex Chromosomes ◽  
Meiotic Drive ◽  
B Chromosomes ◽  
Next Generation ◽  
Multiple Copies ◽  
Genomic Studies ◽  
A Cell ◽  
Eukaryotic Organisms

B chromosomes represent additional chromosomes found in many eukaryotic organisms. Their origin is not completely understood but recent genomic studies suggest that they mostly arise through rearrangements and duplications from standard chromosomes. They can occur in single or multiple copies in a cell and are usually present only in a subset of individuals in the population. Because B chromosomes frequently show unstable inheritance, their maintenance in a population is often associated with meiotic drive or other mechanisms that increase the probability of their transmission to the next generation. For all these reasons, B chromosomes have been commonly considered to be nonessential, selfish, parasitic elements. Although it was originally believed that B chromosomes had little or no effect on an organism’s biology and fitness, a growing number of studies have shown that B chromosomes can play a significant role in processes such as sex determination, pathogenicity and resistance to pathogens. In some cases, B chromosomes became an essential part of the genome, turning into new sex chromosomes or germline-restricted chromosomes with important roles in the organism’s fertility. Here, we review such cases of “cellular domestication” of B chromosomes and show that B chromosomes can be important genomic players with significant evolutionary impact.

scholarly journals A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions

2017 ◽  
Author(s):  
Moises Exposito-Alonso ◽  
Rocío Gámez Rodríguez ◽  
Cristina Barragán ◽  
Giovanna Capovilla ◽  
Eunyoung Chae ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Natural Populations ◽  
Common Garden ◽  
Species Traits ◽  
Large Field ◽  
Model Species ◽  
Evolutionary Genetic ◽  
In The Wild ◽  
Genetic Level ◽  
Manipulation Experiment

The gold standard for studying natural selection and adaptation in the wild is to quantify lifetime fitness of individuals from natural populations that have been grown together in a common garden, or that have been reciprocally transplanted. By combining fitness values with species traits and genome sequences, one can infer selection coefficients at the genetic level. Here we present a rainfall-manipulation experiment with 517 whole-genome sequenced natural accessions of the plant Arabidopsis thaliana spanning the global distribution of the species. The experiments were conducted in two field stations in contrasting climates, in the Mediterranean and in Central Europe, where we built rainout shelters and simulated high and low rainfall. Using custom image analysis we quantified fitness- and phenology-related traits for 23,154 pots, which contained about 14,500 plants growing independently, and over 310,000 plants growing in small populations (max. 30 plants). This large field experiment dataset, which associates fitness and ecologically-relevant traits with genomes, will provide an important resource to test eco-evolutionary genetic theories and to understand the potential evolutionary impacts of future climates on an important plant model species.

scholarly journals Majaz Al-Qur'an dalam Perspektif Sejarah (Studi Perbandingan antara Abi Ubaidah, al-Jahizh dan Qadhi ‘Abdul Jabbar)

2020 ◽  
Vol 15 (2) ◽  
pp. 158
Author(s):  
Ekawati Ekawati
Keyword(s):  
Comprehensive Analysis ◽  
Point Of View ◽  
Analysis Method ◽  
Next Generation ◽  
Historical Approach ◽  
Library Research ◽  
Similarities And Differences ◽  
Language Styles

The aims of this paper are: (1) to analyze the paradigm of Abi Ubaidah, al-jahizh and Qadhi ‘Abdul Jabbar about the metaphors of The Koran from the historical point of view. (2) to interpret and describe metaphors analytically as one of the aesthetics of language styles in The Koran. This paper applies qualitative approach to discuss the problems as well as library research with comparative and comprehensive analysis method. It means that to know the paradigm of “mufassir” and metaphors in The Koran, the writer should know the similarities and differences among “mufassir' opinions, especially in the interpretation of controversial verses. To obtain the data of those three “mufassir” the writer uses historical approach. Abi Ubaidah and al-Farra’ have a great distribution in revealing the secret of the verses in The Koran, especially the meaning of metaphors. Both “mufassir” are the pioneers and inspirators of the next followers such as Al- Jahizh, Ubnu Qutaibah and Al-Qodhi, ‘Abdul Jabbar. The result of their thoughts will be inherited to the next generation as the medium of streng their belifs . Keywords: Majāz, Sejarah, al-Qur’an Tulisan ini bertujuan untuk (1) mengkaji cara pandang Abi Ubaidah, al-Jahizh dan al-Qadhi ‘Abdul Jabbar tentang majāz al-Qur’an ditinjau dari perspektif sejarah. (2) menginterpretasi atau mendeskripsikan secara analitis tentang Majāz sebagai salah satu bentuk keindahan gaya bahasa al-Qur’an. Tulisan ini menggunakan pendekatan kualitatif. Dan untuk membahas persoalan yang ada dalam penelitian ini, penulis menggunakan penelitian kepustakaan (library research), dengan pendekatan metode analisis komprehensif dan komparatif. Artinya, untuk mengetahui cara bergulirnya pandangan para mufassir tentang majāz dalam al-Qur’an, terlebih dahulu harus dilihat segi persamaan dan perbedaan antara dua atau lebih pendapat mereka pada lafazh atau ayat yang diperselisihkan penafsirannya. Untuk mendapatkan data mengenai ketiga tokoh tersebut, digunakan pendekatan sejarah. Abi Ubaidah dan al-Farra’ memiliki andil yang cukup besar dalam menguak rahasia kandungan susunan kalimat baik al-Qur’an maupun bahasa Arab dalam pengertian majāzī-nya. Keduanya merupakan pioner dan pembawa obor bagi generasi selanjutnya seperti al-Jahizh, Ibnu Qutaibah, dan Qadhi ‘Abdul jabbar. Hasil dari kedua pemikir tersebut, generasi selanjutnya dapat menjadikan ta’wīl al-Qur’an sebagai media memperteguh iman mereka. Kata Kunci: Majāz, Sejarah, al-Qur’an

scholarly journals Population genetics of transposable element load: a mechanistic account of observed overdispersion

2020 ◽  
Author(s):  
Ronald D. Smith ◽  
Joshua R. Puzey ◽  
Gregory D. Conradi Smith
Keyword(s):  
Population Genetics ◽  
Transposable Element ◽  
Natural Populations ◽  
Purifying Selection ◽  
Death Process ◽  
Stationary Population ◽  
Population Distributions ◽  
Evolutionary Genetic ◽  
Genetic Mechanisms ◽  
Copy And Paste

AbstractIn an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 100). To obtain insight regarding those evolutionary genetic mechanisms that are may underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and it extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analysis of stationary population distributions of TE load reveal that overdispersion is most likely to arise via copy-and-paste (as opposed to cut-and-paste) dynamics. Parameter studies suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.

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