scholarly journals Global Genome and Transcriptome Analyses of Magnaporthe oryzae Epidemic Isolate 98-06 Uncover Novel Effectors and Pathogenicity-Related Genes, Revealing Gene Gain and Lose Dynamics in Genome Evolution

2015 ◽  
Vol 11 (4) ◽  
pp. e1004801 ◽  
Author(s):  
Yanhan Dong ◽  
Ying Li ◽  
Miaomiao Zhao ◽  
Maofeng Jing ◽  
Xinyu Liu ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Magnaporthe Oryzae ◽  
Gene Gain ◽  
Transcriptome Analyses

scholarly journals Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jaime Iranzo ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Itamar Sela
Keyword(s):  
Homologous Recombination ◽  
Genome Evolution ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Gene Gain ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Branch Lengths ◽  
Gain And Loss ◽  
Recombination Gene

AbstractBacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation.

scholarly journals Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations

2019 ◽  
Author(s):  
Jaime Iranzo ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Itamar Sela
Keyword(s):  
Homologous Recombination ◽  
Genome Evolution ◽  
Phylogenetic Trees ◽  
Prokaryotic Genome ◽  
Sequence Divergence ◽  
Mechanistic Explanation ◽  
Gene Gain ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Gain And Loss

AbstractEvolution of bacterial and archaeal genomes is a highly dynamic process that involves extensive gain and loss of genes. Therefore, phylogenetic trees of prokaryotes can be constructed both by the traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we found that the terminal branches of gene trees were systematically compressed compared to those of genome trees. Thus, sequence evolution seems to be significantly delayed with respect to genome evolution by gene gain and loss. The extent of this delay widely differs among bacterial and archaeal lineages. We develop and explore mathematical models demonstrating that the delay of sequence divergence can be explained by sequence homogenization that is caused by homologous recombination. Once evolving genomes become isolated by barriers that impede homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. This model of prokaryotic genome evolution gives a mechanistic explanation of our previous finding that archaeal genomes contain a class of genes that turn over rapidly, before significant sequence divergence occurs, and provides a framework for correcting phylogenetic trees, to make them consistent with the dynamics of gene turnover.

Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae

2007 ◽  
Vol 43 (3) ◽  
pp. 1066-1075 ◽  
Author(s):  
Nan Wang ◽  
Pierre F. Baldi ◽  
Brandon S. Gaut
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Evolution ◽  
Gene Gain

Poxvirus genome evolution by gene gain and loss

2005 ◽  
Vol 35 (1) ◽  
pp. 186-195 ◽  
Author(s):  
Austin L. Hughes ◽  
Robert Friedman
Keyword(s):  
Genome Evolution ◽  
Gene Gain ◽  
Poxvirus Genome ◽  
Gain And Loss

scholarly journals Genome Rearrangement ShapesProchlorococcusEcological Adaptation

2018 ◽  
Vol 84 (17) ◽  
Author(s):  
Wei Yan ◽  
Shuzhen Wei ◽  
Qiong Wang ◽  
Xilin Xiao ◽  
Qinglu Zeng ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genome Rearrangement ◽  
Marine Ecosystems ◽  
Biogeochemical Cycles ◽  
Ecological Niches ◽  
Gene Gain ◽  
Low Light ◽  
Free Living ◽  
Content Type ◽  
Photosynthetic Microorganism

ABSTRACTProchlorococcusis the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles.Prochlorococcuscan be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted clade I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructedProchlorococcusevolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role inProchlorococcusevolution. We also found that theProchlorococcusclades with streamlined genomes maintained relatively high synteny throughout most of their genomes, and several regions served as rearrangement hotspots. Backbone analysis showed that different clades shared a conserved backbone but also had clade-specific regions, and the genes in these regions were associated with ecological adaptations.IMPORTANCEProchlorococcus, the most abundant and smallest known free-living photosynthetic microorganism, plays a key role in marine ecosystems and biogeochemical cycles.Prochlorococcusgenome evolution is a fundamental issue related to howProchlorococcusclades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted theProchlorococcusgenome evolution from the perspective of genome structure and associated the genome rearrangement with theProchlorococcusclade differentiation and subsequent ecological adaptation.

scholarly journals Transposon-mediated telomere destabilization: a driver of genome evolution in the blast fungus

2020 ◽  
Author(s):  
Mostafa Rahnama ◽  
Olga Novikova ◽  
John H Starnes ◽  
Shouan Zhang ◽  
Li Chen ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Magnaporthe Oryzae ◽  
Tandem Repeats ◽  
Collateral Damage ◽  
High Frequencies ◽  
Chromosome Architecture ◽  
Molecular Alterations ◽  
Rdna Sequences ◽  
And Function ◽  
Independent Expansion

Abstract The fungus Magnaporthe oryzae causes devastating diseases of crops, including rice and wheat, and in various grasses. Strains from ryegrasses have highly unstable chromosome ends that undergo frequent rearrangements, and this has been associated with the presence of retrotransposons (Magnaporthe oryzae Telomeric Retrotransposons—MoTeRs) inserted in the telomeres. The objective of the present study was to determine the mechanisms by which MoTeRs promote telomere instability. Targeted cloning, mapping, and sequencing of parental and novel telomeric restriction fragments (TRFs), along with MinION sequencing of genomic DNA allowed us to document the precise molecular alterations underlying 109 newly-formed TRFs. These included truncations of subterminal rDNA sequences; acquisition of MoTeR insertions by ‘plain’ telomeres; insertion of the MAGGY retrotransposons into MoTeR arrays; MoTeR-independent expansion and contraction of subtelomeric tandem repeats; and a variety of rearrangements initiated through breaks in interstitial telomere tracts that are generated during MoTeR integration. Overall, we estimate that alterations occurred in approximately sixty percent of chromosomes (one in three telomeres) analyzed. Most importantly, we describe an entirely new mechanism by which transposons can promote genomic alterations at exceptionally high frequencies, and in a manner that can promote genome evolution while minimizing collateral damage to overall chromosome architecture and function.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

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