scholarly journals Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shanshan Liu ◽  
Zhen Wang ◽  
Yingjuan Su ◽  
Ting Wang
Keyword(s):  
Large Scale ◽  
Structural Evolution ◽  
Genomic Analysis ◽  
Structural Features ◽  
Comparative Genomic ◽  
Insertion Sequences ◽  
Strand Breaks ◽  
Genomic Structural Variation ◽  
Organizational Stability ◽  
Dispersed Repeats

Abstract Background Comparative chloroplast genomics could shed light on the major evolutionary events that established plastomic diversity among closely related species. The Polypodiaceae family is one of the most species-rich and underexplored groups of extant ferns. It is generally recognized that the plastomes of Polypodiaceae are highly notable in terms of their organizational stability. Hence, no research has yet been conducted on genomic structural variation in the Polypodiaceae. Results The complete plastome sequences of Neolepisorus fortunei, Neolepisorus ovatus, and Phymatosorus cuspidatus were determined based on next-generation sequencing. Together with published plastomes, a comparative analysis of the fine structure of Polypodiaceae plastomes was carried out. The results indicated that the plastomes of Polypodiaceae are not as conservative as previously assumed. The size of the plastomes varies greatly in the Polypodiaceae, and the large insertion fragments present in the genome could be the main factor affecting the genome length. The plastome of Selliguea yakushimensis exhibits prominent features including not only a large-scale IR expansion exceeding several kb but also a unique inversion. Furthermore, gene contents, SSRs, dispersed repeats, and mutational hotspot regions were identified in the plastomes of the Polypodiaceae. Although dispersed repeats are not abundant in the plastomes of Polypodiaceae, we found that the large insertions that occur in different species are mobile and are always adjacent to repeated hotspot regions. Conclusions Our results reveal that the plastomes of Polypodiaceae are dynamic molecules, rather than constituting static genomes as previously thought. The dispersed repeats flanking insertion sequences contribute to the repair mechanism induced by double-strand breaks and are probably a major driver of structural evolution in the plastomes of Polypodiaceae.

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 Comparative genomic analysis identifies structural features of CRISPR-Cas systems in Riemerella anatipestifer

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
De-Kang Zhu ◽  
Xue-Qin Yang ◽  
Yang He ◽  
Wang-Shu Zhou ◽  
Xiao-Heng Song ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Structural Features ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Riemerella Anatipestifer

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.

scholarly journals In SilicoTyping and Comparative Genomic Analysis of IncFIIKPlasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles

2018 ◽  
Vol 62 (10) ◽  
Author(s):  
Dexi Bi ◽  
Jiayi Zheng ◽  
Jun-Jie Li ◽  
Zi-Ke Sheng ◽  
Xingchen Zhu ◽  
...  
Keyword(s):  
Large Scale ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Epidemiological Studies ◽  
Genome Comparison ◽  
Comparative Genomic ◽  
Content Type ◽  
Bacterial Plasmid ◽  
Phylogeny And Evolution ◽  
Sequence Types

ABSTRACTIncFIIKplasmids are associated with the acquisition and dissemination of multiple-antimicrobial resistance inKlebsiella pneumoniaeand often encountered in clinical isolates of this species. Since the phylogeny and evolution of IncFIIKplasmids remain unclear, here we performed large-scalein silicotyping and comparative analysis of these plasmids in publicly available bacterial/plasmid genomes. IncFIIKplasmids are prevalent inK. pneumoniae, being found in 69% of sequenced genomes, covering 66% of sequenced STs (sequence types), but sparse in otherEnterobacteriaceae. IncFIIKreplicons have three lineages. One IncFIIKallele could be found in distinctK. pneumoniaeSTs, highlighting the lateral genetic flow of IncFIIKplasmids. A set of 77 IncFIIKplasmids with full sequences were further analyzed. A pool of 327 antibiotic resistance genes or remnants were annotated in 75.3% of these plasmids. Plasmid genome comparison reiterated that they often contain other replicons belonging to IncFIA, IncFIB, IncFIIYp, IncFIIpCRY, IncR, IncL, and IncN groups and that they share a conserved backbone featuring an F-like conjugation module that has divergent components responsible for regulation and mating pair stabilization. Further epidemiological studies of IncFIIKplasmids are required due to the sample bias ofK. pneumoniaegenomes in public databases. This study provides insights into the evolution and structures of IncFIIKplasmids.

scholarly journals The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data

2015 ◽  
Author(s):  
Sandeep J. Joseph ◽  
Ben Li ◽  
Robert A. Petit ◽  
Zhaohui S. Qin ◽  
Lyndsey A. Darrow ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Large Scale ◽  
Pathogen Detection ◽  
Geographic Distance ◽  
Human Microbiome ◽  
Genomic Analysis ◽  
Single Species ◽  
Metagenomic Data ◽  
Comparative Genomic ◽  
Genome Coverage

AbstractMetagenome shotgun sequence projects offer the potential for large scale biogeographic analysis of microbial species. In this project we developed a method for detecting 33 common subtypes of the pathogenic bacterium Staphylococcus aureus. We used a binomial mixture model implemented in the binstrain software and the coverage counts at > 100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of each subtype in metagenome samples. Using this pipeline we were able to obtain > 87% sensitivity and > 94% specificity when testing on low genome coverage samples of diverse S. aureus strains (0.025X). We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S. aureus at genome coverage > 0.025. In both projects, CC8 and CC30 were the most common S. aureus subtypes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are risk factors for S. aureus but there was limited power to find factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city. We argue that pathogen detection in metagenome samples requires the use of subtypes based on whole species population genomic analysis rather than using ad hoc collections of reference strains.

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 whale shark genome reveals how genomic and physiological properties scale with body size

2020 ◽  
Vol 117 (34) ◽  
pp. 20662-20671 ◽  
Author(s):  
Jessica A. Weber ◽  
Seung Gu Park ◽  
Victor Luria ◽  
Sungwon Jeon ◽  
Hak-Min Kim ◽  
...  
Keyword(s):  
Body Size ◽  
Metabolic Rate ◽  
Large Scale ◽  
Gc Content ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Traits ◽  
Whale Shark ◽  
Gene Length ◽  
Genetic Features

The endangered whale shark (Rhincodon typus) is the largest fish on Earth and a long-lived member of the ancient Elasmobranchii clade. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 83 animals and yeast. We examined the scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Among animals, increased lifespan is positively correlated to body size and metabolic rate. Several genomic traits also significantly correlated with body size, including intron and gene length. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: Guanine and cytosine (GC) content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. Focusing on the whale shark genome, we identified multiple features that significantly correlate with lifespan. Among these were very long gene length, due to introns being highly enriched in repetitive elements such as CR1-like long interspersed nuclear elements, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. The whale shark genome also has the second slowest evolutionary rate observed in vertebrates to date. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan and showed that the whale shark is a promising model for studies of neural architecture and lifespan.

scholarly journals Integrated exome and RNA sequencing of dedifferentiated liposarcoma

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Makoto Hirata ◽  
Naofumi Asano ◽  
Kotoe Katayama ◽  
Akihiko Yoshida ◽  
Yusuke Tsuda ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Clinical Features ◽  
Large Scale ◽  
Genomic Analysis ◽  
Dedifferentiated Liposarcoma ◽  
Comparative Genomic ◽  
Sequencing Analysis ◽  
Genomic Alterations ◽  
Whole Exome ◽  
Well Differentiated

AbstractThe genomic characteristics of dedifferentiated liposarcoma (DDLPS) that are associated with clinical features remain to be identified. Here, we conduct integrated whole exome and RNA sequencing analysis in 115 DDLPS tumors and perform comparative genomic analysis of well-differentiated and dedifferentiated components from eight DDLPS samples. Several somatic copy-number alterations (SCNAs), including the gain of 12q15, are identified as frequent genomic alterations. CTDSP1/2-DNM3OS fusion genes are identified in a subset of DDLPS tumors. Based on the association of SCNAs with clinical features, the DDLPS tumors are clustered into three groups. This clustering can predict the clinical outcome independently. The comparative analysis between well-differentiated and dedifferentiated components identify two categories of genomic alterations: shared alterations, associated with tumorigenesis, and dedifferentiated-specific alterations, associated with malignant transformation. This large-scale genomic analysis reveals the mechanisms underlying the development and progression of DDLPS and provides insights that could contribute to the refinement of DDLPS management.

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