scholarly journals Comparative Genomics Unveils Regionalized Evolution of the Faustovirus Genomes

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 577 ◽  
Author(s):  
Khalil Geballa-Koukoulas ◽  
Hadjer Boudjemaa ◽  
Julien Andreani ◽  
Bernard La Scola ◽  
Guillaume Blanc
Keyword(s):  
Genomic Analysis ◽  
Nucleotide Composition ◽  
Death Process ◽  
Comparative Genomic ◽  
Type I ◽  
Homing Endonucleases ◽  
Bacterial Genomes ◽  
Phylogenetic Groups ◽  
Genome Wide ◽  
Dna Replication Origin

Faustovirus is a recently discovered genus of large DNA virus infecting the amoeba Vermamoeba vermiformis, which is phylogenetically related to Asfarviridae. To better understand the diversity and evolution of this viral group, we sequenced six novel Faustovirus strains, mined published metagenomic datasets and performed a comparative genomic analysis. Genomic sequences revealed three consistent phylogenetic groups, within which genetic diversity was moderate. The comparison of the major capsid protein (MCP) genes unveiled between 13 and 18 type-I introns that likely evolved through a still-active birth and death process mediated by intron-encoded homing endonucleases that began before the Faustovirus radiation. Genome-wide alignments indicated that despite genomes retaining high levels of gene collinearity, the central region containing the MCP gene together with the extremities of the chromosomes evolved at a faster rate due to increased indel accumulation and local rearrangements. The fluctuation of the nucleotide composition along the Faustovirus (FV) genomes is mostly imprinted by the consistent nucleotide bias of coding sequences and provided no evidence for a single DNA replication origin like in circular bacterial genomes.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus

2020 ◽  
Vol 8 (3) ◽  
pp. 366
Author(s):  
Jarred Yasuhara-Bell ◽  
Mohammad Arif ◽  
Grethel Y. Busot ◽  
Rachel Mann ◽  
Brendan Rodoni ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
The United States ◽  
Grass Species ◽  
Comparative Genomic ◽  
Underrepresented Populations ◽  
System A ◽  
Genome Wide ◽  
The Family ◽  
Study Support ◽  
Genomic Regions

Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.

scholarly journals Discovery and comparative genomic analysis of elk circovirus (ElkCV), a novel circovirus species and the first reported from a cervid host

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mathew Fisher ◽  
Thomas M. R. Harrison ◽  
Michelle Nebroski ◽  
Peter Kruczkiewicz ◽  
Jamie L. Rothenburger ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Analysis ◽  
Rocky Mountain ◽  
International Committee ◽  
Comparative Genomic Analysis ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Stem Loop ◽  
Genome Wide ◽  
Replication Region

Abstract The complete genome sequence of a novel circovirus (elk circovirus (ElkCV) Banff/2019) was determined via high throughput sequencing of liver tissue from a euthanized Rocky Mountain elk (Cervus canadensis nelsoni) from Alberta, Canada. The genome is circular and 1,787 nucleotides long, with two major ORFs encoding predicted proteins. Comparative genomic analysis to 4,164 publicly available complete and near complete circovirus genomes showed that ElkCV shares approximately 65% pairwise genome-wide nucleotide identity with the most closely related circovirus species, porcine circoviruses (PCV) 1 and 2 and bat-associated circovirus (BatACV) 11. ElkCV features a stem-loop within the origin of replication region characteristic of circoviruses. However, it differs from those found in PCV1, PCV2 and BatACV11 since it has a longer stem and contains hexamer repeats that overlap the stem in opposing orientations. Interestingly, stem-loop structures of similar length featuring repeats in a similar position and orientation are also seen in some avian circoviruses. Based on the demarcation threshold established by the International Committee on Taxonomy of Viruses (ICTV) for members of Circoviridae (80% pairwise genome-wide nucleotide identity), ElkCV represents a novel species and is the first complete circovirus genome reported from a cervid host.

scholarly journals Searching for a “Hidden” Prophage in a Marine Bacterium

2009 ◽  
Vol 76 (2) ◽  
pp. 589-595 ◽  
Author(s):  
Yanlin Zhao ◽  
Kui Wang ◽  
Hans-Wolfgang Ackermann ◽  
Rolf U. Halden ◽  
Nianzhi Jiao ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Genomic Analysis ◽  
Bioinformatic Analysis ◽  
Open Reading Frames ◽  
Careful Examination ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Genomic Analyses ◽  
Experimental Laboratory ◽  
Bacterial Genes

ABSTRACT Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-pro1) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this “hidden” prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-pro1 open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-pro1-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium.

scholarly journals Comparative Genomic Analysis Provides Insights into the Evolution and Genetic Diversity of Community-Genotype Sequence Type 72 Staphylococcus aureus Isolates

mSystems ◽  
2021 ◽  
Author(s):  
Wangxiao Zhou ◽  
Ye Jin ◽  
Yanzi Zhou ◽  
Yuan Wang ◽  
Luying Xiong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Staphylococcus Aureus ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Health Issues ◽  
Content Type ◽  
Genome Wide Analysis ◽  
Genome Wide

Understanding the evolution and dissemination of community-genotype ST72 Staphylococcus aureus isolates is important, as isolates of this lineage have rapidly spread into hospital settings and caused serious health issues. In this study, we first carried out genome-wide analysis of 107 global ST72 isolates to characterize the evolution and genetic diversity of the ST72 lineage.

scholarly journals Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M Integrated in the Chromosome

2017 ◽  
Vol 61 (7) ◽  
Author(s):  
Weihua Huang ◽  
Guiqing Wang ◽  
Robert Sebra ◽  
Jian Zhuge ◽  
Changhong Yin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
De Novo ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Type I ◽  
Content Type ◽  
Antimicrobial Resistance Genes

ABSTRACT The extended-spectrum-β-lactamase (ESBL)- and Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae represent serious and urgent threats to public health. In a retrospective study of multidrug-resistant K. pneumoniae, we identified three clinical isolates, CN1, CR14, and NY9, carrying both bla CTX-M and bla KPC genes. The complete genomes of these three K. pneumoniae isolates were de novo assembled by using both short- and long-read whole-genome sequencing. In CR14 and NY9, bla CTX-M and bla KPC were carried on two different plasmids. In contrast, CN1 had one copy of bla KPC-2 and three copies of bla CTX-M-15 integrated in the chromosome, for which the bla CTX-M-15 genes were linked to an insertion sequence, ISEcp1, whereas the bla KPC-2 gene was in the context of a Tn4401a transposition unit conjugated with a PsP3-like prophage. Intriguingly, downstream of the Tn4401a-bla KPC-2-prophage genomic island, CN1 also carried a clustered regularly interspaced short palindromic repeat (CRISPR)-cas array with four spacers targeting a variety of K. pneumoniae plasmids harboring antimicrobial resistance genes. Comparative genomic analysis revealed that there were two subtypes of type I-E CRISPR-cas in K. pneumoniae strains and suggested that the evolving CRISPR-cas, with its acquired novel spacer, induced the mobilization of antimicrobial resistance genes from plasmids into the chromosome. The integration and dissemination of multiple copies of bla CTX-M and bla KPC from plasmids to chromosome depicts the complex pandemic scenario of multidrug-resistant K. pneumoniae. Additionally, the implications from this study also raise concerns for the application of a CRISPR-cas strategy against antimicrobial resistance.

scholarly journals Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs

2019 ◽  
Author(s):  
Rachel C. Williams ◽  
Marina B. Blanco ◽  
Jelmer W. Poelstra ◽  
Kelsie E. Hunnicutt ◽  
Aaron A. Comeault ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genomic Analysis ◽  
Population Level ◽  
Comparative Genomic ◽  
Effective Population ◽  
High Coverage ◽  
Genome Wide ◽  
Conservation Concern ◽  
Genomic Regions ◽  
Dwarf Lemur

AbstractMadagascar’s biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar’s dwarf lemurs (genus Cheirogaleus), the only obligate hibernating primate. We here apply comparative genomic approaches to generate the first genome-wide estimates of genetic diversity within dwarf lemurs. We generate a reference genome for the fat-tailed dwarf lemur, Cheirogaleus medius, and use this resource to facilitate analyses of high-coverage (~30x) genome sequences for wild-caught individuals representing species: C. sp. cf. medius, C. major, C. crossleyi and C. sibreei. This study represents the largest contribution to date of novel genomic resources for Madagascar’s lemurs. We find concordant phylogenetic relationships among the four lineages of Cheirogaleus across most of the genome, and yet detect a number of discordant genomic regions consistent with ancient admixture. We hypothesized that these regions could have resulted from adaptive introgression related to hibernation, indeed finding that genes associated with hibernation are present, though most significantly, that gene ontology categories relating to transcription are over-represented. We estimate levels of heterozygosity and find particularly low levels in an individual sampled from an isolated population of C. medius that we refer to as C. sp. cf. medius. Results are consistent with a recent decline in effective population size, which is evident across species. Our study highlights the power of comparative genomic analysis for identifying species and populations of conservation concern, as well as for illuminating possible mechanisms of adaptive phenotypic evolution.

Genome-wide assessment ofMycobacterium tuberculosisconditionally essential metabolic pathways

2019 ◽  
Author(s):  
Yusuke Minato ◽  
Daryl M Gohl ◽  
Joshua M. Thiede ◽  
Jeremy M. Chacón ◽  
William R. Harcombe ◽  
...  
Keyword(s):  
Functional Genomics ◽  
In Silico ◽  
Metabolic Pathways ◽  
Genomic Analysis ◽  
Essential Genes ◽  
Comparative Genomic ◽  
Cellular Functions ◽  
Flux Balance ◽  
Genome Wide ◽  
Balance Analysis

AbstractBetter understanding of essential cellular functions in pathogenic bacteria is important for the development of more effective antimicrobial agents. We performed a comprehensive identification of essential genes inMycobacterium tuberculosis, the major causative agent of tuberculosis, using a combination of transposon insertion sequencing (Tn-seq) and comparative genomic analysis. To identify conditional essential genes by Tn-seq, we used media with different nutrient composition. Although many conditional gene essentialities were affected by the presence of relevant nutrient sources, we also found that the essentiality of genes in a subset of metabolic pathways was unaffected by metabolites. Comparative genomic analysis revealed that not all essential genes identified by Tn-seq were fully conserved within theM. tuberculosiscomplex including some existing anti-tubercular drug target genes. In addition, we utilized an availableM. tuberculosisgenome-scale metabolic model, iSM810, to predictM. tuberculosisgene essentialityin silico. Comparing the sets of essential genes experimentally identified by Tn-seq to those predictedin silicoreveals the capabilities and limitations of gene essentiality predictions highlighting the complexity ofM. tuberculosisessential metabolic functions. This study provides a promising platform to study essential cellular functions inM. tuberculosis.Author SummaryMycobacterium tuberculosiscauses 10 million cases of tuberculosis (TB) each year resulting in over one million deaths. TB therapy is challenging because it requires a minimum of six months of treatment with multiple drugs. Protracted treatment times and the emergent spread of drug resistant TB necessitate the identification of novel targets for drug discovery to curb this global health threat. Essential functions, defined as those indispensable for growth and/or survival, are potential targets for new antimicrobial drugs. In this study, we aimed to define gene essentialities ofM. tuberculosison a genome-wide scale to comprehensively identify potential targets for drug discovery. We utilized a combination of experimental (functional genomics) andin silicoapproaches (comparative genomics and flux balance analysis). Our functional genomics approach identified sets of genes whose essentiality was affected by nutrient availability. Comparative genomics revealed that not all essential genes were fully conserved within theM. tuberculosiscomplex. Comparing sets of essential genes identified by functional genomics to those predicted by flux balance analysis highlighted gaps in current knowledge regardingM. tuberculosismetabolic capabilities. Thus, our study identifies numerous potential anti-tubercular drug targets and provides a comprehensive picture of the complexity ofM. tuberculosisessential cellular functions.

Genome-wide identification and analyses of bHLH family genes in Brassica napus

2019 ◽  
Vol 99 (5) ◽  
pp. 589-598 ◽  
Author(s):  
Wei Shen ◽  
Xin Cui ◽  
Hui Li ◽  
Rui-Min Teng ◽  
Yong-Xin Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Oilseed Crop ◽  
Plant Growth And Development ◽  
The Third ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
Binding Type

The bHLH (basic/helix-loop-helix) protein is one of the largest transcription factors (TFs) that is essential in regulating plant growth and development. Although the bHLH family has been identified in some organisms, a systemic study has not been performed in Brassica napus, which is the third most important oilseed crop worldwide. In the present study, a total of 460 bHLH TFs were identified from the genome of B. napus and clustered into 25 subfamilies. Structural analysis was used to identify the DNA binding type and conserved amino residues of the identified sequence in the bHLH domain. In addition, a comparative genomic analysis of B. napus and its progenitors (Brassica rapa and Brassica oleracea) and two basal angiosperms (Amborella trichopoda and Vitis vinifera) was performed to trace the change during expansion and evolution of the bHLH family. The bHLH TFs in leaves and roots showed various expression patterns. The homologs of the AA-subgenome and CC-subgenome exhibited similar expression patterns, but were more divergent between the homologs caused from other duplicate events.

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