scholarly journals Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont

2017 ◽  
Author(s):  
Ian Goodhead ◽  
Frances Blow ◽  
Philip Brownridge ◽  
Margaret Hughes ◽  
John Kenny ◽  
...  
Keyword(s):  
Single Molecule ◽  
Translational Control ◽  
Large Scale ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Proteome Analysis ◽  
Comparative Genomic ◽  
Intracellular Bacteria ◽  
Evolutionary Trajectory ◽  
Sodalis Glossinidius

AbstractThe majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic strategies, combining: Illumina and Pacific Biosciences Single-Molecule Real Time DNA-sequencing and annotation; stranded RNA-sequencing; and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53% and 74% of the Sodalis transcriptome remains active in cell-free culture. Mean sense transcription from Coding Domain Sequences (CDS) is four-times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40% of the 2,729 genes in the core genome, suggesting that they are stable and/or Sodalis is a recent introduction across the Glossina genus as a facultative symbiont. These data further shed light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics give a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.ImportanceBacterial genes are generally 1Kb in length, organized efficiently (i.e. with few gaps between genes or operons), and few open reading frames (ORFs) lack any predicted function. Intracellular bacteria have been removed from extracellular selection pressures acting on pathways of declining importance to fitness and thus, these bacteria tend to delete redundant genes in favour of smaller functional repertoires. In the genomes of endosymbionts with a recent evolutionary relationship with their host, however, this process of genome reduction is not complete; Genes and pathways may be at an intermediate stage, undergoing mutation linked to reduced selection and small population numbers being vertically transmitted from mother to offspring in their hosts, resulting in an increase in abundance of pseudogenes and reduced coding capacities. A greater knowledge of the genomic architecture of persistent pseudogenes, with respect to their DNA structure, mRNA transcription and even putative translation to protein products, will lead to a better understanding of the evolutionary trajectory of endosymbiont genomes, many of which have important roles in arthropod ecology.

scholarly journals The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

2013 ◽  
Vol 79 (15) ◽  
pp. 4620-4634 ◽  
Author(s):  
Noha H. Youssef ◽  
M. B. Couger ◽  
Christopher G. Struchtemeyer ◽  
Audra S. Liggenstoffer ◽  
Rolf A. Prade ◽  
...  
Keyword(s):  
Single Molecule ◽  
Crop Residues ◽  
Plant Biomass ◽  
Consolidated Bioprocessing ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Evolutionary Trajectory ◽  
Content Type ◽  
Gene Acquisition ◽  
Intergenic Regions

ABSTRACTAnaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate,Orpinomycessp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production.

scholarly journals Complete Genome Sequence of Escherichia Coli Strain S9922 Isolated from Meningitis in Calf and Comparative Genomic Analysis with Other E. Coli Pathotypes

2021 ◽  
Author(s):  
Beibei Li ◽  
Jingjing Ren ◽  
Xun Ma ◽  
Qian Qin ◽  
Xinyu Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cluster Analysis ◽  
Large Scale ◽  
Virulent Strain ◽  
Evolutionary Relationship ◽  
Intestinal Flora ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
E Coli ◽  
Wide Range

Abstract Background: Extraintestinal pathogenic Escherichia coli (ExPEC) exists in the normal intestinal flora, but can invade and colonize extraintestinal sites and cause a wide range of infections. Genomic analysis of ExPEC has mainly focused on isolates of human, poultry and pig. In recent years, some large-scale dairy farms in Xinjiang broke out cases characterized by neurological symptoms and acute death in newborn calves. To better understand the genomic attributes underlying the pathogenicity of bovine-source ExPEC, a highly virulent strain, which named E. coli S9922 was isolated from cerebral effusion in a calf that died of meningitis, was sequenced and analyzed.Results: Using single-molecule sequencing technology on PacBio and then assembled, the genes were predicted and annotated. The whole genome of E.coli S9922 was consisted of a chromosome and three plasmids containing 5055 genes, and the total length was 5269374 bp and the average G+C content was 50.82%. In addition, 291 host-, 204 virulence-, and 185 resistance-related genes, and 182 T3SS effector proteins were found by comparison with related databases. Comparison of this genome to 16 representative strains of pathogenic E.coli genomic sequences showed that E.coli S9922 had the greatest co-linearity with E.coli 90-9272. In addition, Core genes obtained by cluster analysis of E.coli S9922 homologous genes were classified, a total of 2570, 2780, and 2188 genes were obtained via COG, KEGG, and GO comparisons, respectively. The unique genes identified by homologous cluster analysis were classified 204, 550, 239 genes in COG, KEGG, and GO comparisons, respectively. Evolutionary tree analysis revealed a close evolutionary relationship between E.coli S9922 and E.coli 90-9272, and a distant relationship between E.coli S9922 and UTI89.Conclusions: The study provide dgenomics of E.coli S9922 strain from the cattle that had died of meningitis. It enriched the genome data of E.coli and laid a theoretical foundation for further experimental study of ExPEC. Comparative genomics analysis showed that E.coli S9922 had a close evolutionary relationship with E.coli 90-9272, but far from that of UTI89.

scholarly journals Multiple origins of obligate nematode and insect symbionts by a clade of bacteria closely related to plant pathogens

2020 ◽  
Vol 117 (50) ◽  
pp. 31979-31986
Author(s):  
Vincent G. Martinson ◽  
Ryan M. R. Gawryluk ◽  
Brent E. Gowen ◽  
Caitlin I. Curtis ◽  
John Jaenike ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Pathogenic Bacteria ◽  
Plant Pathogens ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Intracellular Bacteria ◽  
Multiple Origins ◽  
Severe Reduction ◽  
Insect Symbionts ◽  
Erosion Characteristic

Obligate symbioses involving intracellular bacteria have transformed eukaryotic life, from providing aerobic respiration and photosynthesis to enabling colonization of previously inaccessible niches, such as feeding on xylem and phloem, and surviving in deep-sea hydrothermal vents. A major challenge in the study of obligate symbioses is to understand how they arise. Because the best studied obligate symbioses are ancient, it is especially challenging to identify early or intermediate stages. Here we report the discovery of a nascent obligate symbiosis in Howardula aoronymphium, a well-studied nematode parasite of Drosophila flies. We have found that H. aoronymphium and its sister species harbor a maternally inherited intracellular bacterial symbiont. We never find the symbiont in nematode-free flies, and virtually all nematodes in the field and the laboratory are infected. Treating nematodes with antibiotics causes a severe reduction in fly infection success. The association is recent, as more distantly related insect-parasitic tylenchid nematodes do not host these endosymbionts. We also report that the Howardula nematode symbiont is a member of a widespread monophyletic group of invertebrate host-associated microbes that has independently given rise to at least four obligate symbioses, one in nematodes and three in insects, and that is sister to Pectobacterium, a lineage of plant pathogenic bacteria. Comparative genomic analysis of this group, which we name Candidatus Symbiopectobacterium, shows signatures of genome erosion characteristic of early stages of symbiosis, with the Howardula symbiont’s genome containing over a thousand predicted pseudogenes, comprising a third of its genome.

scholarly journals Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Courtney M. Thomas ◽  
Najwa Taib ◽  
Simonetta Gribaldo ◽  
Guillaume Borrel
Keyword(s):  
Gut Microbiota ◽  
Large Scale ◽  
Genomic Analysis ◽  
Host Adaptation ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Methyl Branch ◽  
Mechanisms Of Adaptation ◽  
Hydrogenotrophic Methanogens ◽  
Almost All

AbstractOther than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood–Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.

scholarly journals Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus”

mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Marian Dominguez-Mirazo ◽  
Rong Jin ◽  
Joshua S. Weitz
Keyword(s):  
Causative Agent ◽  
De Novo ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Prediction Approach

ABSTRACT Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen “Candidatus Liberibacter asiaticus” is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of “Ca. Liberibacter asiaticus” has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available “Ca. Liberibacter asiaticus” genomes and are classified into three prophage types. Here, we reexamined all 15 “Ca. Liberibacter asiaticus” genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the “Ca. Liberibacter asiaticus” genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 “Ca. Liberibacter asiaticus” strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and “Ca. Liberibacter asiaticus” pathogenicity. IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.”

Comparative genomic analysis ofAcidithiobacillus ferrooxidansstrains using theA. ferrooxidansATCC 23270 whole-genome oligonucleotide microarray

2009 ◽  
Vol 55 (5) ◽  
pp. 587-598 ◽  
Author(s):  
Hailang Luo ◽  
Li Shen ◽  
Huaqun Yin ◽  
Qian Li ◽  
Qijiong Chen ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Oligonucleotide Microarray ◽  
Open Reading Frames ◽  
Genomic Diversity ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Mining Areas ◽  
Main Factor

Acidithiobacillus ferrooxidans is an important microorganism used in biomining operations for metal recovery. Whole-genomic diversity analysis based on the oligonucleotide microarray was used to analyze the gene content of 12 strains of A. ferrooxidans purified from various mining areas in China. Among the 3100 open reading frames (ORFs) on the slides, 1235 ORFs were absent in at least 1 strain of bacteria and 1385 ORFs were conserved in all strains. The hybridization results showed that these strains were highly diverse from a genomic perspective. The hybridization results of 4 major functional gene categories, namely electron transport, carbon metabolism, extracellular polysaccharides, and detoxification, were analyzed. Based on the hybridization signals obtained, a phylogenetic tree was built to analyze the evolution of the 12 tested strains, which indicated that the geographic distribution was the main factor influencing the strain diversity of these strains. Based on the hybridization signals of genes associated with bioleaching, another phylogenetic tree showed an evolutionary relationship from which the co-relation between the clustering of specific genes and geochemistry could be observed. The results revealed that the main factor was geochemistry, among which the following 6 factors were the most important: pH, Mg, Cu, S, Fe, and Al.

scholarly journals Single-molecule analysis reveals widespread structural variation in multiple myeloma

2015 ◽  
Vol 112 (25) ◽  
pp. 7689-7694 ◽  
Author(s):  
Aditya Gupta ◽  
Michael Place ◽  
Steven Goldstein ◽  
Deepayan Sarkar ◽  
Shiguo Zhou ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Tumor Progression ◽  
Single Molecule ◽  
Large Scale ◽  
Structural Variation ◽  
Plasma Cells ◽  
Optical Mapping ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Whole Genome Analysis

Multiple myeloma (MM), a malignancy of plasma cells, is characterized by widespread genomic heterogeneity and, consequently, differences in disease progression and drug response. Although recent large-scale sequencing studies have greatly improved our understanding of MM genomes, our knowledge about genomic structural variation in MM is attenuated due to the limitations of commonly used sequencing approaches. In this study, we present the application of optical mapping, a single-molecule, whole-genome analysis system, to discover new structural variants in a primary MM genome. Through our analysis, we have identified and characterized widespread structural variation in this tumor genome. Additionally, we describe our efforts toward comprehensive characterization of genome structure and variation by integrating our findings from optical mapping with those from DNA sequencing-based genomic analysis. Finally, by studying this MM genome at two time points during tumor progression, we have demonstrated an increase in mutational burden with tumor progression at all length scales of variation.

scholarly journals Functional and comparative genomic analysis of integrated prophage-like sequences in Candidatus Liberibacter asiaticus

2019 ◽  
Author(s):  
Marian Dominguez-Mirazo ◽  
Rong Jin ◽  
Joshua S. Weitz
Keyword(s):  
De Novo ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Prediction Approach

AbstractHuanglongbing (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen Candidatus Liberibacter asiaticus (CLas) is an alphapro-teobacterium of the Rhizobiaceae family that has been identified as the cause. The virulence of CLas has been attributed, in part, to prophage encoded genes. Prophage and prophage like elements have been identified in 12 of the 15 CLas available genomes, and are classified into three prophage types. Here, we re-examined all 15 CLas genomes using a de novo prediction approach and expanded the number of prophage like elements from 16 to 33. Further, we find that all CLas contain at least one prophage-like sequence. Comparative analysis reveals a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 CLas strain that had previously been reported as lacking prophages. Our findings provide both a resource and new insights into the evolutionary relationship between phage and CLas pathogenicity.

scholarly journals A large scale, multiple genome comparison of acidophilic Archaea (pH ≤ 5.0) extends our understanding of oxidative stress responses in polyextreme environments

2021 ◽  
Author(s):  
Gonzalo Neira ◽  
Eva Vergara ◽  
Diego Nahuel Cortez ◽  
David S. Holmes
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Large Scale ◽  
Genomic Analysis ◽  
Low Ph ◽  
Genome Comparison ◽  
Comparative Genomic ◽  
Acidophilic Bacteria ◽  
Acidophilic Archaea ◽  
Oxidative Stress Responses

Acidophilic Archaea thrive in anaerobic and aerobic low pH environments (<pH 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2·−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic Archaea with sequenced genomes. These organisms can be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what can this tell us about the evolution of these mechanisms in acidophilic Archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic Archaea and between acidophilic Archaea and acidophilic Bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in Archaea and possible Horizontal Gene Transfer (HGT) events.

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