scholarly journals Viruses and mobile elements as drivers of evolutionary transitions

2016 ◽  
Vol 371 (1701) ◽  
pp. 20150442 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Genomic Analysis ◽  
Life Forms ◽  
Comparative Genomic ◽  
Biological Organization ◽  
Evolutionary Transitions ◽  
Selfish Genetic Elements ◽  
Cellular Life ◽  
History Of ◽  
Eusocial Animals ◽  
Multicellular Organisms

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’.

scholarly journals The order of trait emergence in the evolution of cyanobacterial multicellularity

2019 ◽  
Author(s):  
Katrin Hammerschmidt ◽  
Giddy Landan ◽  
Fernando Domingues Kümmel Tria ◽  
Jaime Alcorta ◽  
Tal Dagan
Keyword(s):  
Division Of Labor ◽  
Phenotypic Trait ◽  
Evolutionary Transition ◽  
Evolutionary Transitions ◽  
Differentiated Cells ◽  
Labor Theory ◽  
Significant Events ◽  
Reproductive Life ◽  
History Of ◽  
Multicellular Organisms

AbstractThe transition from unicellular to multicellular organisms is one of the most significant events in the history of life. Key to this process is the emergence of Darwinian individuality at the higher level: groups must become single entities capable of reproduction for selection to shape their evolution. Evolutionary transitions in individuality are characterized by cooperation between the lower level entities and by division of labor. Theory suggests that division of labor may drive the transition to multicellularity by eliminating the trade-off between two incompatible processes that cannot be performed simultaneously in one cell. Here we examine the evolution of the most ancient multicellular transition known today, that of cyanobacteria, where we reconstruct the sequence of ecological and phenotypic trait evolution. Our results show that the prime driver of multicellularity in cyanobacteria was the expansion in metabolic capacity offered by nitrogen fixation, which was accompanied by the emergence of the filamentous morphology and succeeded by a reproductive life cycle. This was followed by the progression of multicellularity into higher complexity in the form of differentiated cells and patterned multicellularity.Significance StatementThe emergence of multicellularity is a major evolutionary transition. The oldest transition, that of cyanobacteria, happened more than 3 to 3.5 billion years ago. We find N2 fixation to be the prime driver of multicellularity in cyanobacteria. This innovation faced the challenge of incompatible metabolic processes since the N2 fixing enzyme (nitrogenase) is sensitive to oxygen, which is abundantly found in cyanobacteria cells performing photosynthesis. At the same time, N2-fixation conferred an adaptive benefit to the filamentous morphology as cells could divide their labour into performing either N2-fixation or photosynthesis. This was followed by the culmination of complex multicellularity in the form of differentiated cells and patterned multicellularity.

scholarly journals Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Min Zhang ◽  
Delong Meng ◽  
Xueduan Liu ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Evolutionary History ◽  
Mine Drainage ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Ecological Functions ◽  
History Of

ABSTRACT Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

scholarly journals The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Xian-Gui Yi ◽  
Xia-Qing Yu ◽  
Jie Chen ◽  
Min Zhang ◽  
Shao-Wei Liu ◽  
...  
Keyword(s):  
Plant Disease Resistance ◽  
De Novo ◽  
Genomic Analysis ◽  
Gene Families ◽  
Single Copy ◽  
Comparative Genomic ◽  
Sequencing Technologies ◽  
History Of ◽  
Flowering Cherry ◽  
Plant Disease Resistance Genes

Abstract Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

On the Origin of Cells and Viruses: A Comparative-Genomic Perspective

2006 ◽  
Vol 52 (3-4) ◽  
pp. 299-318 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Biological Evolution ◽  
Empirical Support ◽  
Molecular Complexes ◽  
Life Forms ◽  
Comparative Genomic ◽  
Cellular Origin ◽  
Cellular Life ◽  
Universal Common Ancestor ◽  
Replication Systems ◽  
Lines Of Descent

It is proposed that the pre-cellular stage of biological evolution, including the Last Universal Common Ancestor (LUCA) of modern cellular life forms, occurred within networks of inorganic compartments that hosted a diverse mix of virus-like genetic elements. This viral model of cellular origin recapitulates the early ideas of J.B.S. Haldane, sketched in his 1928 essay on the origin of life. However, unlike in Haldane's day, there is substantial empirical support for this scenario from three major lines of evidence provided by comparative genomics: (i) the lack of homology among the core components of the DNA replication systems between the two primary lines of descent of cellular life forms, archaea and bacteria, (ii) the similar lack of homology between the enzymes of lipid biosynthesis in conjunction with distinct membrane chemistries in archaea and bacteria, and (iii) the spread of several viral hallmark genes, which encode proteins with key functions in viral replication and morphogenesis, among numerous and extremely diverse groups of viruses, in contrast to their absence in cellular life forms. Under the viral model of pre-cellular evolution, the key elements of cells including the replication apparatus, membranes, molecular complexes involved in membrane transport and translocation, and others originated as components of virus-like entities. This model alleviates, at least in part, the challenge of the emergence of the immensely complex organization of modern cells.

scholarly journals Six de novo assemblies from pathogenic and non-pathogenic strains of Fusarium oxysporum f. sp. niveum

2021 ◽  
Author(s):  
James Fulton ◽  
Jeremy Brawner ◽  
Jose Huguet-Tapia ◽  
Katherine E Smith ◽  
Randy Fernandez ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
De Novo ◽  
Citrullus Lanatus ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Soilborne Disease ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Reference Quality ◽  
History Of

Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon), is a soilborne disease which significantly limits yield in watermelon (Citrullus lanatus) and occasionally causes the loss of an entire year’s harvest. Reference-quality de novo genomic assemblies of pathogenic and non-pathogenic strains were generated using a combination of next-generation and third-generation sequencing technologies. Chromosomal-level genomes were produced with representatives from all Fon races facilitating comparative genomic analysis and the identification of chromosomal structural variation . Syntenic analysis between isolates allowed differentiation of the core and lineage-specific portions of their genomes. This research will support future efforts to refine the scientific understanding of the molecular and genetic factors underpinning the Fon host range, develop diagnostic assays for each of the four races, and decipher the evolutionary history of race 3.

scholarly journals Characterization of a blaNDM-1-Bearing IncHI5-Like Plasmid From Klebsiella pneumoniae of Infant Origin

2021 ◽  
Vol 11 ◽  
Author(s):  
Ziyi Liu ◽  
Ruifei Chen ◽  
Poshi Xu ◽  
Zhiqiang Wang ◽  
Ruichao Li
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Genetic Composition ◽  
Carbapenem Resistant ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
History Of ◽  
Core Genes

The spread of plasmid-mediated carbapenem-resistant clinical isolates is a serious threat to global health. In this study, an emerging NDM-encoding IncHI5-like plasmid from Klebsiella pneumoniae of infant patient origin was characterized, and the plasmid was compared to the available IncHI5-like plasmids to better understand the genetic composition and evolution of this emerging plasmid. Clinical isolate C39 was identified as K. pneumoniae and belonged to the ST37 and KL15 serotype. Whole genome sequencing (WGS) and analysis revealed that it harbored two plasmids, one of which was a large IncHI5-like plasmid pC39-334kb encoding a wide variety of antimicrobial resistance genes clustered in a single multidrug resistance (MDR) region. The blaNDM-1 gene was located on a ΔISAba125-blaNDM-1-bleMBL-trpF-dsbC structure. Comparative genomic analysis showed that it shared a similar backbone with four IncHI5-like plasmids and the IncHI5 plasmid pNDM-1-EC12, and these six plasmids differed from typical IncHI5 plasmids. The replication genes of IncHI5-like plasmids shared 97.06% (repHI5B) and 97.99% (repFIB-like) nucleotide identity with those of IncHI5 plasmids. Given that pNDM-1-EC12 and all IncHI5-like plasmids are closely related genetically, the occurrence of IncHI5-like plasmid is likely associated with the mutation of the replication genes of pNDM-1-EC12-like IncHI5 plasmids. All available IncHI5-like plasmids harbored 262 core genes encoding replication and maintenance functions and carried distinct MDR regions. Furthermore, 80% of them (4/5) were found in K. pneumoniae from Chinese nosocomial settings. To conclude, this study expands our knowledge of the evolution history of IncHI5-like plasmids, and more attention should be paid to track the evolution pathway of them among clinical, animal, and environmental settings.

scholarly journals Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the GenusAcidithiobacillus

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Delong Meng ◽  
Xueduan Liu ◽  
Xing Li ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Resistance Genes ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Purifying Selection ◽  
Metal Resistance ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
History Of

ABSTRACTMembers of the genusAcidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genusAcidithiobacillusto answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes inAcidithiobacillusspp. The results showed that the evolutionary history of metal resistance genes inAcidithiobacillusspp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes inAcidithiobacillusspp. were acquired by early HGT events from species that shared habitats withAcidithiobacillusspp., such asAcidihalobacter,Thiobacillus,Acidiferrobacter, andThiomonasspecies. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizingAcidithiobacillus ferridurans,Acidithiobacillus ferrivorans, andAcidithiobacillus ferrooxidansand were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability ofAcidithiobacillusspp. to adapt to harsh environments. Altogether, the results suggested thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes inAcidithiobacillusspp.IMPORTANCEHorizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT inAcidithiobacillusspecies in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved inAcidithiobacillusare still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies ofAcidithiobacillusspp.

scholarly journals Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Open Biology ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 170184 ◽  
Author(s):  
Guy Leonard ◽  
Aurélie Labarre ◽  
David S. Milner ◽  
Adam Monier ◽  
Darren Soanes ◽  
...  
Keyword(s):  
Draft Genome ◽  
Genomic Analysis ◽  
Filamentous Growth ◽  
Cellular Systems ◽  
Complex Life Cycle ◽  
Comparative Genomic ◽  
Genetic Features ◽  
History Of ◽  
Eukaryotic Microbes ◽  
Genome Comparisons

Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium catenoides . Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.

scholarly journals Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

2020 ◽  
Author(s):  
Laura A. Zinke ◽  
Paul N. Evans ◽  
Alena L. Schroeder ◽  
Donovan H. Parks ◽  
Ruth K. Varner ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
New Order ◽  
Hydrogen Metabolism ◽  
Metabolic Potential ◽  
Conventional View ◽  
Sedimentary Environments ◽  
History Of ◽  
Subarctic Lake ◽  
Globally Distributed

AbstractRecent discoveries of mcr and mcr-like complexes in genomes from diverse archaeal lineages suggest that methane (and more broadly alkane) metabolism is an ancient pathway with complicated evolutionary histories. The conventional view is that methanogenesis is an ancestral metabolism of the archaeal class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs), we show that these microorganisms do not encode the genes required for methanogenesis, which suggests that this metabolism may have been laterally acquired by an ancestor of the order Methanomassiliicoccales. These MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG (95% complete) that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, such as heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two of these lineages are globally widespread among anoxic, sedimentary environments, with the exception of Ca. Lunaplasma lacustris, which has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide new insights into the evolutionary history of methanogenesis within the Thermoplasmata.

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