Genome composition of asymmetric hybrids in relation to the phylogenetic distance between the parents. Nucleus-chloroplast interaction

1992 ◽  
Vol 84-84 (7-8) ◽  
pp. 930-940 ◽  
Author(s):  
F. H. M. Derks ◽  
J. C. Hakkert ◽  
W. H. J. Verbeek ◽  
C. M. Colijn-Hooymans
Keyword(s):  
Phylogenetic Distance ◽  
Genome Composition ◽  
Asymmetric Hybrids

scholarly journals SARS-CoV-2 and other human coronavirus show genome patterns previously associated to reduced viral recognition and altered immune response

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giovanni Franzo
Keyword(s):  
Immune Response ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Rna Degradation ◽  
Codon Usage Pattern ◽  
Interferon Production ◽  
Genome Composition ◽  
Coding Sequences ◽  
Spike Coding ◽  
Viral Recognition

AbstractA new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia. Initial evidence suggests that dysregulation of the immune response could contribute to the pathogenesis, as previously demonstrated for SARS-CoV. The presence of genome composition features involved in delaying viral recognition is herein investigated for human coronaviruses (HCoVs), with a special emphasis on SARS-CoV-2. A broad collection of HCoVs polyprotein, envelope, matrix, nucleocapsid and spike coding sequences was downloaded and several statistics representative of genome composition and codon bias were investigated. A model able to evaluate and test the presence of a significant under- or over-representation of dinucleotide pairs while accounting for the underlying codon bias and protein sequence was also implemented. The study revealed the significant under-representation of CpG dinucleotide pair in all HcoV, but especially in SARS-CoV and even more in SARS-CoV-2. The presence of forces acting to minimize CpG content was confirmed by relative synonymous codon usage pattern. Codons containing the CpG pair were severely under-represented, primarily in the polyprotein and spike coding sequences of SARS-CoV-2. Additionally, a significant under-representation of the TpA pair was observed in the N and S region of SARS-CoV and SARS-CoV-2. Increasing experimental evidence has proven that CpG and TpA are targeted by innate antiviral host defences, contributing both to RNA degradation and RIG-1 mediated interferon production. The low content of these dinucleotides could contribute to a delayed interferon production, dysregulated immune response, higher viral replication and poor outcome. Significantly, the RIG-1 signalling pathway was proven to be defective in elderlies, suggesting a likely interaction between limited viral recognition and lower responsiveness in interferon production that could justify the higher disease severity and mortality in older patients.

scholarly journals Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giovanni Franzo ◽  
Claudia Maria Tucciarone ◽  
Matteo Legnardi ◽  
Mattia Cecchinato
Keyword(s):  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Accessory Proteins ◽  
Effective Number ◽  
Genome Composition ◽  
Infectious Bronchitis ◽  
Selective Forces ◽  
Effective Number Of Codons

Abstract Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.

scholarly journals Hemoglobin Richmond, a Human Hemoglobin Which Forms Asymmetric Hybrids with Other Hemoglobins

1969 ◽  
Vol 244 (22) ◽  
pp. 6105-6116
Author(s):  
G.D. Efremov ◽  
T.H.J. Huisman ◽  
Linda L. Smith ◽  
J.B. Wilson ◽  
Janice L. Kitchens ◽  
...  
Keyword(s):  
Human Hemoglobin ◽  
Asymmetric Hybrids

scholarly journals Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

2021 ◽  
Author(s):  
Lina Kloub ◽  
Sean Gosselin ◽  
Matthew Fullmer ◽  
Joerg Graf ◽  
J Peter Gogarten ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Families ◽  
Microbial Evolution ◽  
Phylogenetic Distance ◽  
Secretion Systems ◽  
Type Iii Secretion Systems ◽  
A Genome ◽  
Conserved Gene

Abstract Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale dataset of over 22000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the observed relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

scholarly journals Fecal Microbiota Transplant in Two Ulcerative Colitis Pediatric Cases: Gut Microbiota and Clinical Course Correlations

2020 ◽  
Vol 8 (10) ◽  
pp. 1486
Author(s):  
Andrea Quagliariello ◽  
Federica Del Chierico ◽  
Sofia Reddel ◽  
Alessandra Russo ◽  
Andrea Onetti Muda ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Fecal Microbiota Transplantation ◽  
Fecal Microbiota ◽  
Clinical Effects ◽  
Phylogenetic Distance ◽  
Fecal Microbiota Transplant ◽  
Inflammatory Bowel ◽  
Clinical Conditions ◽  
And Control

Fecal microbiota transplantation (FMT) is a promising strategy in the management of inflammatory bowel disease (IBD). The clinical effects of this practice are still largely unknown and unpredictable. In this study, two children affected by mild and moderate ulcerative colitis (UC), were pre- and post-FMT monitored for clinical conditions and gut bacterial ecology. Microbiota profiling relied on receipts’ time-point profiles, donors and control cohorts’ baseline descriptions. After FMT, the improvement of clinical conditions was recorded for both patients. After 12 months, the mild UC patient was in clinical remission, while the moderate UC patient, after 12 weeks, had a clinical worsening. Ecological analyses highlighted an increase in microbiota richness and phylogenetic distance after FMT. This increase was mainly due to Collinsella aerofaciens and Eubacterium biforme, inherited by respective donors. Moreover, a decrease of Proteus and Blautia producta, and the increment of Parabacteroides, Mogibacteriaceae, Bacteroides eggerthi, Bacteroides plebeius, Ruminococcus bromii, and BBacteroidesovatus were associated with remission of the patient’s condition. FMT results in a long-term response in mild UC, while in the moderate form there is probably need for multiple FMT administrations. FMT leads to a decrease in potential pathogens and an increase in microorganisms correlated to remission status.

scholarly journals Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan

2010 ◽  
Vol 60 (3) ◽  
pp. 603-609 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova
Keyword(s):  
Sea Of Japan ◽  
Sequence Similarity ◽  
Fatty Acid Analysis ◽  
Phenotypic Characterization ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
The Novel ◽  
Bacterial Strains ◽  
Separate Branch

Two bacterial strains, KMM 3891T and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink–reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C17 : 1 ω6c, C17 : 0, C16 : 0 and C16 : 1 ω7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891T was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891T and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891T and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891T (=NRIC 0753T =JCM 15738T).

scholarly journals Old and new challenges in using species diversity for assessing biodiversity

2011 ◽  
Vol 366 (1576) ◽  
pp. 2426-2437 ◽  
Author(s):  
Alessandro Chiarucci ◽  
Giovanni Bacaro ◽  
Samuel M. Scheiner
Keyword(s):  
Species Diversity ◽  
Quantitative Measurement ◽  
Phylogenetic Distance ◽  
Existing Problems ◽  
Species Abundances ◽  
Species Lists ◽  
Assessment And Monitoring ◽  
New Challenges ◽  
Patterns And Processes ◽  
Conservation And Management

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.

scholarly journals Comparison of Silks from Pseudoips prasinana and Bombyx mori Shows Molecular Convergence in Fibroin Heavy Chains but Large Differences in Other Silk Components

2021 ◽  
Vol 22 (15) ◽  
pp. 8246
Author(s):  
Michal Rindos ◽  
Lucie Kucerova ◽  
Lenka Rouhova ◽  
Hana Sehadova ◽  
Michal Sery ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Silk Gland ◽  
Amino Acid Sequences ◽  
Phylogenetic Distance ◽  
Rna Seq ◽  
Chain Molecules ◽  
Heavy Chains ◽  
Lepidopteran Larvae ◽  
Crystalline Domains

Many lepidopteran larvae produce silk feeding shelters and cocoons to protect themselves and the developing pupa. As caterpillars evolved, the quality of the silk, shape of the cocoon, and techniques in forming and leaving the cocoon underwent a number of changes. The silk of Pseudoips prasinana has previously been studied using X-ray analysis and classified in the same category as that of Bombyx mori, suggesting that silks of both species have similar properties despite their considerable phylogenetic distance. In the present study, we examined P. prasinana silk using ‘omics’ technology, including silk gland RNA sequencing (RNA-seq) and a mass spectrometry-based proteomic analysis of cocoon proteins. We found that although the central repetitive amino acid sequences encoding crystalline domains of fibroin heavy chain molecules are almost identical in both species, the resulting fibers exhibit quite different mechanical properties. Our results suggest that these differences are most probably due to the higher content of fibrohexamerin and fibrohexamerin-like molecules in P. prasinana silk. Furthermore, we show that whilst P. prasinana cocoons are predominantly made of silk similar to that of other Lepidoptera, they also contain a second, minor silk type, which is present only at the escape valve.

scholarly journals Short Communication Microsatellite usefulness is independent of phylogenetic distance in Tyrant flycatchers (Aves: Tyrannidae): a test using two globally threatened species

2013 ◽  
Vol 12 (3) ◽  
pp. 2966-2972 ◽  
Author(s):  
B. Mahler ◽  
A.R.R. Schneider ◽  
A.S. Di Giacomo ◽  
A.G. Di Giacomo ◽  
J.C. Reboreda ◽  
...  
Keyword(s):  
Threatened Species ◽  
Short Communication ◽  
Phylogenetic Distance ◽  
Tyrant Flycatchers

scholarly journals Variability of NOR patterns in European water frogs of different genome composition and ploidy level

2017 ◽  
Vol 11 (2) ◽  
pp. 249-266 ◽  
Author(s):  
Anna Zaleśna ◽  
Maria Florek ◽  
Mariusz Rybacki ◽  
Maria Ogielska
Keyword(s):  
Ploidy Level ◽  
Genome Composition ◽  
European Water ◽  
Water Frogs ◽  
European Water Frogs
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