Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex

2001 ◽  
Vol 40 (4) ◽  
pp. 932-940 ◽  
Author(s):  
N. Handa ◽  
Y. Nakayama ◽  
M. Sadykov ◽  
I. Kobayashi
Keyword(s):  
Genome Evolution ◽  
Large Scale ◽  
Genome Rearrangements ◽  
Gene Complex ◽  
Restriction Modification

scholarly journals Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics)

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Xyrus X. Maurer-Alcalá ◽  
Rob Knight ◽  
Laura A. Katz
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Gc Content ◽  
Gene Families ◽  
Genome Rearrangements ◽  
Paramecium Tetraurelia ◽  
Protein Coding ◽  
Genome Data ◽  
Large Gene ◽  
Disproportionate Number

ABSTRACTSeparate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences. Most studies of germline genome architecture in ciliates have focused on the model ciliatesOxytricha trifallax,Paramecium tetraurelia, andTetrahymena thermophila, for which the complete germline genome sequences are known. Outside of these model taxa, only a few dozen germline loci have been characterized from a limited number of cultivable species, which is likely due to difficulties in obtaining sufficient quantities of “purified” germline DNA in these taxa. Combining single-cell transcriptomics and genomics, we have overcome these limitations and provide the first insights into the structure of the germline genome of the ciliateChilodonella uncinata, a member of the understudied classPhyllopharyngea. Our analyses reveal the following: (i) large gene families contain a disproportionate number of genes from scrambled germline loci; (ii) germline-soma boundaries in the germline genome are demarcated by substantial shifts in GC content; (iii) single-cell omics techniques provide large-scale quality germline genome data with limited effort, at least for ciliates with extensively fragmented somatic genomes. Our approach provides an efficient means to understand better the evolution of genome rearrangements between germline and soma in ciliates.IMPORTANCEOur understanding of the distinctions between germline and somatic genomes in ciliates has largely relied on studies of a few model genera (e.g.,Oxytricha,Paramecium,Tetrahymena). We have used single-cell omics to explore germline-soma distinctions in the ciliateChilodonella uncinata, which likely diverged from the better-studied ciliates ~700 million years ago. The analyses presented here indicate that developmentally regulated genome rearrangements between germline and soma are demarcated by rapid transitions in local GC composition and lead to diversification of protein families. The approaches used here provide the basis for future work aimed at discerning the evolutionary impacts of germline-soma distinctions among diverse ciliates.

scholarly journals Hyperthermophilic DNA Methyltransferase M.PabI from the Archaeon Pyrococcus abyssi

2006 ◽  
Vol 72 (8) ◽  
pp. 5367-5375 ◽  
Author(s):  
Miki Watanabe ◽  
Harumi Yuzawa ◽  
Naofumi Handa ◽  
Ichizo Kobayashi
Keyword(s):  
Dna Methyltransferase ◽  
Dna Methyltransferases ◽  
Type I ◽  
Type Ii ◽  
Gene Complex ◽  
Sequence Comparisons ◽  
Novel Structure ◽  
Dna Engineering ◽  
Pyrococcus Abyssi ◽  
Restriction Modification

ABSTRACT Genome sequence comparisons among multiple species of Pyrococcus, a hyperthermophilic archaeon, revealed a linkage between a putative restriction-modification gene complex and several large genome polymorphisms/rearrangements. From a region apparently inserted into the Pyrococcus abyssi genome, a hyperthermoresistant restriction enzyme [PabI; 5′-(GTA/C)] with a novel structure was discovered. In the present work, the neighboring methyltransferase homologue, M.PabI, was characterized. Its N-terminal half showed high similarities to the M subunit of type I systems and a modification enzyme of an atypical type II system, M.AhdI, while its C-terminal half showed high similarity to the S subunit of type I systems. M.PabI expressed within Escherichia coli protected PabI sites from RsaI, a PabI isoschizomer. M.PabI, purified following overexpression, was shown to generate 5′-GTm6AC, which provides protection against PabI digestion. M.PabI was found to be highly thermophilic; it showed methylation at 95°C and retained at least half the activity after 9 min at 95°C. This hyperthermophilicity allowed us to obtain activation energy and other thermodynamic parameters for the first time for any DNA methyltransferases. We also determined the kinetic parameters of k cat, Km , DNA, and Km , AdoMet. The activity of M.PabI was optimal at a slightly acidic pH and at an NaCl concentration of 200 to 500 mM and was inhibited by Zn2+ but not by Mg2+, Ca2+, or Mn2+. These and previous results suggest that this unique methyltransferase and PabI constitute a type II restriction-modification gene complex that inserted into the P. abyssi genome relatively recently. As the most thermophilic of all the characterized DNA methyltransferases, M.PabI may help in the analysis of DNA methylation and its application to DNA engineering.

scholarly journals Re-evaluating inheritance in genome evolution: widespread transfer of LINEs between species

2017 ◽  
Author(s):  
Atma M. Ivancevic ◽  
R. Daniel Kortschak ◽  
Terry Bertozzi ◽  
David L. Adelson
Keyword(s):  
Genome Evolution ◽  
Dna Sequences ◽  
Large Scale ◽  
Mobile Dna ◽  
Long Term Effects ◽  
New Host ◽  
Transfer Event ◽  
Blood Sucking ◽  
Foreign Dna

Transposable elements (TEs) are mobile DNA sequences, colloquially known as ‘jumping genes’ because of their ability to replicate to new genomic locations. Given a vector of transfer (e.g. tick or virus), TEs can jump further: between organisms or species in a process known as horizontal transfer (HT). Here we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient HT events. Using a 503-genome dataset, we identify multiple ancient L1 HT events in eukaryotes and provide evidence that L1s infiltrated the mammalian lineage after the monotreme-therian split. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new potential blood-sucking parasite vectors and occurrences in new lineages (e.g. bats, frog). Given that these TEs make up nearly half of the genome sequence in today’s mammals, our results provide the first evidence that HT can have drastic and long-term effects on the new host genomes. This revolutionizes our perception of genome evolution to consider external factors, such as the natural introduction of foreign DNA. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be the first of many large-scale phylogenomic analyses exploring the role of HT in genome evolution.Significance statementLINE-1 (L1) elements occupy about half of most mammalian genomes (1), and they are believed to be strictly vertically inherited (2). Mutagenic L1 insertions are thought to account for approximately 1 of every 1000 random, disease-causing insertions in humans (4-7). Our research indicates that the very presence of L1s in humans, and other therian mammals, is due to an ancient transfer event – which has drastic implications for our perception of genome evolution. Using a machina analyses over 503 genomes, we trace the origins of L1 and BovB retrotransposons across the tree of life, and provide evidence of their long-term impact on eukaryotic evolution.

scholarly journals An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2

2020 ◽  
Author(s):  
Yunchao Ling ◽  
Ruifang Cao ◽  
Jiaqiang Qian ◽  
Jiefu Li ◽  
Haokui Zhou ◽  
...  
Keyword(s):  
Network Analysis ◽  
Genome Evolution ◽  
Viral Genome ◽  
Large Scale ◽  
Phylogenetic Network ◽  
Detection Algorithm ◽  
Viral Genomes ◽  
Network Analyses ◽  
Community Detection Algorithm ◽  
Analysis System

AbstractComprehensive analyses of viral genomes can provide a global picture on SARS-CoV-2 transmission and help to predict the oncoming trends of pandemic. This molecular tracing is mainly conducted through extensive phylogenetic network analyses. However, the rapid accumulation of SARS-CoV-2 genomes presents an unprecedented data size and complexity that has exceeded the capacity of existing methods in constructing evolution network through virus genotyping. Here we report a Viral genome Evolution Network Analysis System (VENAS), which uses Hamming distances adjusted by the minor allele frequency to construct viral genome evolution network. The resulting network was topologically clustered and divided using community detection algorithm, and potential evolution paths were further inferred with a network disassortativity trimming algorithm. We also employed parallel computing technology to achieve rapid processing and interactive visualization of >10,000 viral genomes, enabling accurate detection and subtyping of the viral mutations through different stages of Covid-19 pandemic. In particular, several core viral mutations can be independently identified and linked to early transmission events in Covid-19 pandemic. As a general platform for comprehensive viral genome analysis, VENAS serves as a useful computational tool in the current and future pandemics.

scholarly journals Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
Shai Carmi ◽  
George M. Church ◽  
Erez Y. Levanon
Keyword(s):  
Genome Evolution ◽  
Large Scale ◽  
Mammalian Genome ◽  
Dna Editing

scholarly journals Cellular Responses to Postsegregational Killing by Restriction-Modification Genes

2000 ◽  
Vol 182 (8) ◽  
pp. 2218-2229 ◽  
Author(s):  
Naofumi Handa ◽  
Asao Ichige ◽  
Kohji Kusano ◽  
Ichizo Kobayashi
Keyword(s):  
Viable Cell ◽  
Underlying Mechanism ◽  
Temperature Sensitive ◽  
Dependent Manner ◽  
Bacterial Cells ◽  
Gene Complex ◽  
Cellular Processes ◽  
Cell Counts ◽  
Gene Complexes ◽  
Restriction Modification

ABSTRACT Plasmids that carry one of several type II restriction modification gene complexes are known to show increased stability. The underlying mechanism was proposed to be the lethal attack by restriction enzyme at chromosomal recognition sites in cells that had lost the restriction modification gene complex. In order to examine bacterial responses to this postsegregational cell killing, we analyzed the cellular processes following loss of the EcoRI restriction modification gene complex carried by a temperature-sensitive plasmid in anEscherichia coli strain that is wild type with respect to DNA repair. A shift to the nonpermissive temperature blocked plasmid replication, reduced the increase in viable cell counts and resulted in loss of cell viability. Many cells formed long filaments, some of which were multinucleated and others anucleated. In a mutant defective in RecBCD exonuclease/recombinase, these cell death symptoms were more severe and cleaved chromosomes accumulated. Growth inhibition was also more severe in recA, ruvAB, ruvC,recG, and recN mutants. The cells induced the SOS response in a RecBC-dependent manner. These observations strongly suggest that bacterial cells die as a result of chromosome cleavage after loss of a restriction modification gene complex and that the bacterial RecBCD/RecA machinery helps the cells to survive, at least to some extent, by repairing the cleaved chromosomes. These and previous results have led us to hypothesize that the RecBCD/Chi/RecA system serves to destroy restricted “nonself” DNA and repair restricted “self” DNA.

scholarly journals Unraveling Genome Evolution Throughout Visual Analysis: The XCout Portal

2021 ◽  
Vol 15 ◽  
pp. 117793222110214
Author(s):  
Sergio Diaz-del-Pino ◽  
Esteban Perez-Wohlfeil ◽  
Oswaldo Trelles
Keyword(s):  
Genome Evolution ◽  
Visual Analytics ◽  
Scientific Community ◽  
Large Scale ◽  
Visual Analysis ◽  
Genome Comparison ◽  
Data Generation ◽  
Evolutionary Mechanisms ◽  
Sequence Comparisons ◽  
Evolutionary Studies

Due to major breakthroughs in sequencing technologies throughout the last decades, the time and cost per sequencing experiment have reduced drastically, overcoming the data generation barrier during the early genomic era. Such a shift has encouraged the scientific community to develop new computational methods that are able to compare large genomic sequences, thus enabling large-scale studies of genome evolution. The field of comparative genomics has proven itself invaluable for studying the evolutionary mechanisms and the forces driving genome evolution. In this line, a full genome comparison study between 2 species requires a quadratic number of comparisons in terms of the number of sequences (around 400 chromosome comparisons in the case of mammalian genomes); however, when studying conserved syntenies or evolutionary rearrangements, many sequence comparisons can be skipped for not all will contain significant signals. Subsequently, the scientific community has developed fast heuristics to perform multiple pairwise comparisons between large sequences to determine whether significant sets of conserved similarities exist. The data generation problem is no longer an issue, yet the limitations have shifted toward the analysis of such massive data. Therefore, we present XCout, a Web-based visual analytics application for multiple genome comparisons designed to improve the analysis of large-scale evolutionary studies using novel techniques in Web visualization. XCout enables to work on hundreds of comparisons at once, thus reducing the time of the analysis by identifying significant signals between chromosomes across multiple species. Among others, XCout introduces several techniques to aid in the analysis of large-scale genome rearrangements, particularly (1) an interactive heatmap interface to display comparisons using automatic color scales based on similarity thresholds to ease detection at first sight, (2) an overlay system to detect individual signal contributions between chromosomes, (3) a tracking tool to trace conserved blocks across different species to perform evolutionary studies, and (4) a search engine to search annotations throughout different species.

scholarly journals The potential of family-free rearrangements towards gene orthology inference

2021 ◽  
Author(s):  
Diego P. Rubert ◽  
Daniel Doerr ◽  
Marília D. V. Braga
Keyword(s):  
Large Scale ◽  
Real Data ◽  
Gene Families ◽  
Genome Rearrangements ◽  
Second Step ◽  
Genomic Distance ◽  
Optimal Matching ◽  
Natural Family

Recently, we proposed an efficient ILP formulation [Rubert DP, Martinez FV, Braga MDV, Natural family-free genomic distance, Algorithms Mol Biol 16:4, 2021] for exactly computing the rearrangement distance of two genomes in a family-free setting. In such a setting, neither prior classification of genes into families, nor further restrictions on the genomes are imposed. Given two genomes, the mentioned ILP computes an optimal matching of the genes taking into account simultaneously local mutations, given by gene similarities, and large-scale genome rearrangements. Here, we explore the potential of using this ILP for inferring groups of orthologs across several species. More precisely, given a set of genomes, our method first computes all pairwise optimal gene matchings, which are then integrated into gene families in the second step. Our approach is implemented into a pipeline incorporating the pre-computation of gene similarities. It can be downloaded from gitlab.ub.uni-bielefeld.de/gi/FFGC. We obtained promising results with experiments on both simulated and real data.

scholarly journals An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2

2022 ◽  
Author(s):  
Yunchao Ling ◽  
Ruifang Cao ◽  
Jiaqiang Qian ◽  
Jiefu Li ◽  
Haokui Zhou ◽  
...  
Keyword(s):  
Network Analysis ◽  
Genome Evolution ◽  
Viral Genome ◽  
Large Scale ◽  
Analysis System
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