scholarly journals Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses

2016 ◽  
Vol 90 (17) ◽  
pp. 7920-7933 ◽  
Author(s):  
Jennifer A. Dill ◽  
Alvin C. Camus ◽  
John H. Leary ◽  
Francesca Di Giallonardo ◽  
Edward C. Holmes ◽  
...  
Keyword(s):  
Hepatitis B ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Surface Proteins ◽  
Comparative Genomic ◽  
Structural Constraints ◽  
Metagenomic Sequencing ◽  
Diverse Range ◽  
Core Proteins ◽  
History Of

ABSTRACTHepadnaviruses (hepatitis B viruses [HBVs]) are the only animal viruses that replicate their DNA by reverse transcription of an RNA intermediate. Until recently, the known host range of hepadnaviruses was limited to mammals and birds. We obtained and analyzed the first amphibian HBV genome, as well as several prototype fish HBVs, which allow the first comprehensive comparative genomic analysis of hepadnaviruses from four classes of vertebrates. Bluegill hepadnavirus (BGHBV) was characterized from in-house viral metagenomic sequencing. The African cichlid hepadnavirus (ACHBV) and the Tibetan frog hepadnavirus (TFHBV) were discovered usingin silicoanalyses of the whole-genome shotgun and transcriptome shotgun assembly databases. Residues in the hydrophobic base of the capsid (core) proteins, designated motifs I, II, and III, are highly conserved, suggesting that structural constraints for proper capsid folding are key to capsid protein evolution. Surface proteins in all vertebrate HBVs contain similar predicted membrane topologies, characterized by three transmembrane domains. Most striking was the fact that BGHBV, ACHBV, and the previously described white sucker hepadnavirus did not form a fish-specific monophyletic group in the phylogenetic analysis of all three hepadnaviral genes. Notably, BGHBV was more closely related to the mammalian hepadnaviruses, indicating that cross-species transmission events have played a major role in viral evolution. Evidence of cross-species transmission was also observed with TFHBV. Hence, these data indicate that the evolutionary history of the hepadnaviruses is more complex than previously realized and combines both virus-host codivergence over millions of years and host species jumping.IMPORTANCEHepadnaviruses are responsible for significant disease in humans (hepatitis B virus) and have been reported from a diverse range of vertebrates as both exogenous and endogenous viruses. We report the full-length genome of a novel hepadnavirus from a fish and the first hepadnavirus genome from an amphibian. The novel fish hepadnavirus, sampled from bluegills, was more closely related to mammalian hepadnaviruses than to other fish viruses. This phylogenetic pattern reveals that, although hepadnaviruses have likely been associated with vertebrates for hundreds of millions of years, they have also been characterized by species jumping across wide phylogenetic distances.

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 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 genomics sheds light on niche differentiation and the evolutionary history of comammoxNitrospira

2017 ◽  
Author(s):  
Alejandro Palomo ◽  
Anders G Pedersen ◽  
S Jane Fowler ◽  
Arnaud Dechesne ◽  
Thomas Sicheritz-Pontén ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Nitrite Reduction ◽  
Ammonium Uptake ◽  
Comparative Genomic ◽  
Ammonium Oxidation ◽  
Low Oxygen ◽  
Oxidation Pathway ◽  
History Of

AbstractThe description of comammoxNitrospiraspp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria (β-AOB) in the environment, call into question the metabolic potential of comammoxNitrospiraand the evolutionary history of their ammonium oxidation pathway. We report four new comammoxNitrospiragenomes, constituting two novel species, and the first comparative genomic analysis on comammoxNitrospira.ComammoxNitrospirahas lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizingNitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to otherNitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to β-AOB, comammoxNitrospiragenomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammoxNitrospiraseems attuned to oligotrophy and hypoxia compared to β-AOB.β-AOBs are the clear origin of the ammonium oxidation pathway in comammoxNitrospira: reconciliation analysis indicates two separate earlyamoAgene transfer events from β-AOB to an ancestor of comammoxNitrospira, followed by clade specific losses. ForhaoA, one early transfer from β-AOB to comammoxNitrospirais predicted – followed by intra-clade transfers. We postulate that the absence of comammox genes in mostNitrospiragenomes is the result of subsequent loss.SignificanceThe recent discovery of comammox bacteria - members of theNitrospiragenus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammoxNitrospiraand related nitrifiers. Ammonium oxidation genes in comammoxNitrospirahad a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

New perspectives on the evolutionary history of hepatitis B virus genotype F

2011 ◽  
Vol 59 (1) ◽  
pp. 114-122 ◽  
Author(s):  
Carolina Torres ◽  
Flavia Guadalupe Piñeiro y Leone ◽  
Silvana Claudia Pezzano ◽  
Viviana Andrea Mbayed ◽  
Rodolfo Héctor Campos
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Evolutionary History ◽  
Virus Genotype ◽  
B Virus ◽  
History Of ◽  
Genotype F

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.

scholarly journals Genomic Analysis of an Attenuated Chlamydia abortus Live Vaccine Strain Reveals Defects in Central Metabolism and Surface Proteins

2009 ◽  
Vol 77 (9) ◽  
pp. 4161-4167 ◽  
Author(s):  
L. S. Burall ◽  
A. Rodolakis ◽  
A. Rekiki ◽  
G. S. A. Myers ◽  
P. M. Bavoil
Keyword(s):  
Pyruvate Kinase ◽  
Vaccine Strain ◽  
Genomic Analysis ◽  
Live Vaccine ◽  
Surface Proteins ◽  
Comparative Genomic ◽  
Temperature Sensitive ◽  
Nucleotide Polymorphisms ◽  
Chlamydia Abortus ◽  
Virulence Attenuation

ABSTRACT Comparative genomic analysis of a wild-type strain of the ovine pathogen Chlamydia abortus and its nitrosoguanidine-induced, temperature-sensitive, virulence-attenuated live vaccine derivative identified 22 single nucleotide polymorphisms unique to the mutant, including nine nonsynonymous mutations, one leading to a truncation of pmpG, which encodes a polymorphic membrane protein, and two intergenic mutations potentially affecting promoter sequences. Other nonsynonymous mutations mapped to a pmpG pseudogene and to predicted coding sequences encoding a putative lipoprotein, a sigma-54-dependent response regulator, a PhoH-like protein, a putative export protein, two tRNA synthetases, and a putative serine hydroxymethyltransferase. One of the intergenic mutations putatively affects transcription of two divergent genes encoding pyruvate kinase and a putative SOS response nuclease, respectively. These observations suggest that the temperature-sensitive phenotype and associated virulence attenuation of the vaccine strain result from disrupted metabolic activity due to altered pyruvate kinase expression and/or alteration in the function of one or more membrane proteins, most notably PmpG and a putative lipoprotein.

scholarly journals Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostocsp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Caroline Chénard ◽  
Jennifer F. Wirth ◽  
Curtis A. Suttle
Keyword(s):  
Dna Polymerase ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Filamentous Cyanobacteria ◽  
Evolutionary Trajectory ◽  
Crispr Array ◽  
History Of ◽  
Pcc 7120

ABSTRACT  Here we present the first genomic characterization of viruses infectingNostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infectNostocsp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids ofCyanothecesp. strain PCC 7424,Nostocsp. strain PCC 7120, andAnabaena variabilisATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome ofNostocsp. strain PCC 7524. TheNostoccyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.IMPORTANCEFilamentous cyanobacteria belonging to the genusNostocare widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.

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’.

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