Genome features and GC content in prokaryotic genomes in connection with environmental evolution

Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

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Variation of the Virus-Related Elements within Syntenic Genomes of the Hyperthermophilic Archaeon Aeropyrum

Applied and Environmental Microbiology ◽

10.1128/aem.01089-13 ◽

2013 ◽

Vol 79 (19) ◽

pp. 5891-5898 ◽

Cited By ~ 2

Author(s):

Takashi Daifuku ◽

Takashi Yoshida ◽

Takayuki Kitamura ◽

Satoshi Kawaichi ◽

Takahiro Inoue ◽

...

Keyword(s):

Gc Content ◽

Adaptation Strategy ◽

Hyperthermophilic Archaea ◽

Orthologous Genes ◽

Entire Genome ◽

Content Type ◽

Aeropyrum Pernix ◽

System A ◽

Genome Features ◽

Short Palindromic Repeat

ABSTRACTThe increasing number of genome sequences of archaea and bacteria show their adaptation to different environmental conditions at the genomic level.Aeropyrumspp. are aerobic and hyperthermophilic archaea.Aeropyrum caminiwas isolated from a deep-sea hydrothermal vent, andAeropyrum pernixwas isolated from a coastal solfataric vent. To investigate the adaptation strategy in each habitat, we compared the genomes of the two species. Shared genome features were a small genome size, a high GC content, and a large portion of orthologous genes (86 to 88%). The genomes also showed high synteny. These shared features may have been derived from the small number of mobile genetic elements and the lack of a RecBCD system, a recombinational enzyme complex. In addition, the specialized physiology (aerobic and hyperthermophilic) ofAeropyrumspp. may also contribute to the entire-genome similarity. Despite having stable genomes, interference of synteny occurred with two proviruses,A. pernixspindle-shaped virus 1 (APSV1) andA. pernixovoid virus 1 (APOV1), and clustered regularly interspaced short palindromic repeat (CRISPR) elements. Spacer sequences derived from theA. caminiCRISPR showed significant matches with protospacers of the two proviruses infectingA. pernix, indicating thatA. caminiinteracted with viruses closely related to APSV1 and APOV1. Furthermore, a significant fraction of the nonorthologous genes (41 to 45%) were proviral genes or ORFans probably originating from viruses. Although the genomes ofA. caminiandA. pernixwere conserved, we observed nonsynteny that was attributed primarily to virus-related elements. Our findings indicated that the genomic diversification ofAeropyrumspp. is substantially caused by viruses.

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Sequencing of the Litchi Downy Blight Pathogen Reveals It Is a Phytophthora Species With Downy Mildew-Like Characteristics

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-16-0056-r ◽

2016 ◽

Vol 29 (7) ◽

pp. 573-583 ◽

Cited By ~ 21

Author(s):

Wenwu Ye ◽

Yang Wang ◽

Danyu Shen ◽

Delong Li ◽

Tianhuizi Pu ◽

...

Keyword(s):

Downy Mildew ◽

Gc Content ◽

Specific Protein ◽

Phytophthora Species ◽

Effector Proteins ◽

Morphological Development ◽

Downy Mildews ◽

Genome Features ◽

Genomic Adaptation ◽

Species Specific

On the basis of its downy mildew–like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently, however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLR, 30 necrosis-and-ethylene-inducing protein-like, and 14 crinkler proteins. The typical motifs, phylogenies, and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preferences of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew–like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens.

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Genome survey sequencing of common vetch (Vicia sativa L.) and genetic diversity analysis of Chinese germplasm with genomic SSR markers

Molecular Biology Reports ◽

10.1007/s11033-021-06875-z ◽

2021 ◽

Author(s):

Lin Ma ◽

Xiao Wang ◽

Min Yan ◽

Fang Liu ◽

Shuxing Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Sequence Data ◽

Gc Content ◽

Vicia Sativa ◽

Whole Genome ◽

Common Vetch ◽

High Genetic Diversity ◽

Genome Survey ◽

Genome Features ◽

High Quality Sequence

Abstract Background Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. Methods and results In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1568 Mbp, 0.4345 and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. Conclusion This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.

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An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

10.1101/153213 ◽

2017 ◽

Cited By ~ 1

Author(s):

Ulrich Omasits ◽

Adithi R. Varadarajan ◽

Michael Schmid ◽

Sandra Goetze ◽

Damianos Melidis ◽

...

Keyword(s):

Gene Prediction ◽

Bartonella Henselae ◽

Prokaryotic Genome ◽

Gc Content ◽

Laboratory Strain ◽

Open Reading Frames ◽

General Applicability ◽

Protein Coding ◽

Prokaryotic Genomes ◽

Coding Potential

AbstractAccurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations.Our strategy towards accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources,ab initiogene prediction algorithms andin silicoORFs in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensiveBartonella henselaeproteomics dataset against such an iPtgxDB allowed us to unambiguously identify novel ORFs uniquely predicted by each resource, including lipoproteins, differentially expressed and membrane-localized proteins, novel start sites and wrongly annotated pseudogenes. Most novelties were confirmed by targeted, parallel reaction monitoring mass spectrometry, including unique ORFs and variants identified in a re-sequenced laboratory strain that are not present in its reference genome. We demonstrate the general applicability of our strategy for genomes with varying GC content and distinct taxonomic origin, and release iPtgxDBs forB. henselae,Bradyrhozibium diazoefficiensandEscherichia colias well as the software to generate such proteogenomics search databases for any prokaryote.

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Genomic GC content drifts slowly downward in most bacterial genomes

10.1101/2020.07.19.211128 ◽

2020 ◽

Author(s):

Bert Ely

Keyword(s):

Gene Conversion ◽

Gc Content ◽

Bacterial Genomes ◽

Base Pairs ◽

Wide Range ◽

Biased Gene Conversion ◽

Prokaryotic Genomes ◽

Genome Content ◽

Genomic Gc Content ◽

Eukaryotic Genomes

AbstractIn every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is slowly declining in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing at a slow rate. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genome content as well.

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Linking high GC content to the repair of double strand breaks in prokaryotic genomes

PLoS Genetics ◽

10.1371/journal.pgen.1008493 ◽

2019 ◽

Vol 15 (11) ◽

pp. e1008493 ◽

Cited By ~ 4

Author(s):

Jake L. Weissman ◽

William F. Fagan ◽

Philip L. F. Johnson

Keyword(s):

Gc Content ◽

Double Strand Breaks ◽

Strand Breaks ◽

Prokaryotic Genomes

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Genomic GC content drifts downward in most bacterial genomes

PLoS ONE ◽

10.1371/journal.pone.0244163 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0244163

Author(s):

Bert Ely

Keyword(s):

Gene Conversion ◽

Gc Content ◽

Bacterial Genomes ◽

Evolutionary Time ◽

Base Pairs ◽

Wide Range ◽

Biased Gene Conversion ◽

Prokaryotic Genomes ◽

Genomic Gc Content ◽

Eukaryotic Genomes

In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is drifting downward in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genomic GC content as well.

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Genome Survey Sequencing of Common Vetch (Vicia Sativa L.) and Genetic Diversity Analysis of Chinese Germplasm with Genomic SSR Markers

10.21203/rs.3.rs-832190/v1 ◽

2021 ◽

Author(s):

lin ma ◽

Xiao Wang ◽

Min Yan ◽

Fang Liu ◽

Xuemin Wang

Keyword(s):

Genetic Diversity ◽

Sequence Data ◽

Gc Content ◽

Vicia Sativa ◽

Whole Genome ◽

Common Vetch ◽

High Genetic Diversity ◽

Genome Survey ◽

Genome Features ◽

High Quality Sequence

Abstract Common vetch (Vicia sativa L.) is an annual legume with excellent suitability in cold and dry regions. Despite its great applied potential, the genomic information regarding common vetch currently remains unavailable. In the present study, the whole genome survey of common vetch was performed using the next-generation sequencing (NGS). A total of 79.84 Gbp high quality sequence data were obtained and assembled into 3,754,145 scaffolds with an N50 length of 3,556 bp. According to the K-mer analyses, the genome size, heterozygosity rate and GC content of common vetch genome were estimated to be 1,568 Mbp, 0.4345% and 35%, respectively. In addition, a total of 76,810 putative simple sequence repeats (SSRs) were identified. Among them, dinucleotide was the most abundant SSR type (44.94%), followed by Tri- (35.82%), Tetra- (13.22%), Penta- (4.47%) and Hexanucleotide (1.54%). Furthermore, a total of 58,175 SSR primer pairs were designed and ten of them were validated in Chinese common vetch. Further analysis showed that Chinese common vetch harbored high genetic diversity and could be clustered into two main subgroups. This is the first report about the genome features of common vetch, and the information will help to design whole genome sequencing strategies. The newly identified SSRs in this study provide basic molecular markers for germplasm characterization, genetic diversity and QTL mapping studies for common vetch.

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Aerobiosis is not associated with GC content and G to T mutations are not the signature of oxidative stress in prokaryotic evolution

10.1101/154534 ◽

2017 ◽

Author(s):

Sidra Aslam ◽

Xin-Ran Lan ◽

Bo-Wen Zhang ◽

Zheng-Lin Chen ◽

Deng-Ke Niu

Keyword(s):

Oxidative Stress ◽

Oxidative Dna Damage ◽

Gc Content ◽

Opposite Pattern ◽

Guanine Oxidation ◽

Prokaryotic Genomes ◽

Shared Ancestry ◽

Widespread Belief ◽

The Relationship ◽

Prokaryotic Evolution

AbstractBackground: Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines result in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results.Results: We retrieved 70 aerobe-anaerobe pairs of prokaryotes, and members of each pair were adjacent on the phylogenetic tree. Pairwise comparisons of either whole-genome GC content or the GC content at 4-fold degenerate sites of orthologous genes among these 70 pairs did not show significant differences between aerobes and anaerobes. The signature of guanine oxidation on GC content evolution has not been detected even after extensive controlling of other influencing factors. Furthermore, the anaerobes were not different from the aerobes in the rate of either G to T, C to A, or other directions of substitutions. The presence of the enzymes responsible for guanine oxidation in anaerobic prokaryotes provided additional evidence that guanine oxidation might be prevalent in anaerobic prokaryotes. In either aerobes or anaerobes, the rates of G:C to T:A mutations were not significantly higher than the reverse mutations.Conclusions: The previous counterintuitive results on the relationship between oxygen requirement and GC content should be attributed to the methodological artefact resulting from phylogenetically non-independence among the analysed samples. Our results showed that aerobiosis does not increase or decrease GC content in evolution. Furthermore, our study challenged the widespread belief that abundant G:C to T:A transversions are the signature of oxidative stress in prokaryotic evolution.

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