scholarly journals Evolution of linkage and genome expansion in protocells: The origin of chromosomes

PLoS Genetics ◽  
2020 ◽  
Vol 16 (10) ◽  
pp. e1009155
Author(s):  
András Szilágyi ◽  
Viktor Péter Kovács ◽  
Eörs Szathmáry ◽  
Mauro Santos
Keyword(s):  
Genome Size ◽  
Marked Reduction ◽  
Deleterious Mutations ◽  
Remarkable Feature ◽  
Intragenomic Conflict ◽  
Size Number ◽  
Added Benefit ◽  
Chromosome Formation ◽  
Selection Of ◽  
Chromosome Level

Chromosomes are likely to have assembled from unlinked genes in early evolution. Genetic linkage reduces the assortment load and intragenomic conflict in reproducing protocell models to the extent that chromosomes can go to fixation even if chromosomes suffer from a replicative disadvantage, relative to unlinked genes, proportional to their length. Here we numerically show that chromosomes spread within protocells even if recurrent deleterious mutations affecting replicating genes (as ribozymes) are considered. Dosage effect selects for optimal genomic composition within protocells that carries over to the genic composition of emerging chromosomes. Lacking an accurate segregation mechanism, protocells continue to benefit from the stochastic corrector principle (group selection of early replicators), but now at the chromosome level. A remarkable feature of this process is the appearance of multigene families (in optimal genic proportions) on chromosomes. An added benefit of chromosome formation is an increase in the selectively maintainable genome size (number of different genes), primarily due to the marked reduction of the assortment load. The establishment of chromosomes is under strong positive selection in protocells harboring unlinked genes. The error threshold of replication is raised to higher genome size by linkage due to the fact that deleterious mutations affecting protocells metabolism (hence fitness) show antagonistic (diminishing return) epistasis. This result strengthens the established benefit conferred by chromosomes on protocells allowing for the fixation of highly specific and efficient enzymes.

scholarly journals Evolution of linkage and genome expansion in protocells

2019 ◽  
Author(s):  
András Szilágyi ◽  
Viktor Péter Kovács ◽  
Eörs Szathmáry ◽  
Mauro Santos
Keyword(s):  
Marked Reduction ◽  
Genetic Linkage ◽  
Deleterious Mutations ◽  
Remarkable Feature ◽  
Intragenomic Conflict ◽  
Size Number ◽  
Added Benefit ◽  
Chromosome Formation ◽  
Selection Of ◽  
Chromosome Level

AbstractChromosomes are likely to have followed unlinked genes in early evolution. Genetic linkage reduces the assortment load and intragenomic conflict in reproducing protocell models to the extent that chromosomes can go to fixation even if chromosomes suffer from a replicative disadvantage, relative to unlinked genes, proportional to their length. Here we show that chromosomes spread within protocells even if recurrent deleterious mutations affecting replicating genes (as ribozymes) are taken into account. Dosage effect selects for optimal genomic composition within protocells that carries over to the genic composition of emerging chromosomes. Lacking an accurate segregation mechanism protocells continue to benefit from the stochastic corrector principle (group selection of early replicators), but now at the chromosome level. A remarkable feature of this process is the appearance of multigene families (in optimal genic proportions) on chromosomes. An added benefit of chromosome formation is an increase in the selectively maintainable genome size (number of different genes), primarily due to the marked reduction of the assortment load. This result complements the established benefit conferred by chromosomes on protocells allowing for the fixation of highly specific and efficient enzymes.

scholarly journals Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Rui Zhang ◽  
Chang Li ◽  
Mengjun Yu ◽  
Xiaoyun Huang ◽  
Mengqi Zhang ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Phylogenetic Tree ◽  
Genome Size ◽  
Genome Assembly ◽  
Teleost Fish ◽  
Common Ancestor ◽  
Biological Features ◽  
Repeat Sequences ◽  
Genomic Resource ◽  
Chromosome Level

The humpback puffer, Tetraodon palembangensis, is a poisonous freshwater pufferfish species mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we report the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb, with a contig N50 value of ∼1.78 Mb and a scaffold N50 value of ∼15.8 Mb. Based on this genome assembly, ∼61.5 Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and the function of 90.01% of these genes could be predicted. Finally, a phylogenetic tree of ten teleost fish species was constructed. This analysis suggests that the humpback puffer and T. nigroviridis share a common ancestor 18.1 million years ago (MYA), and diverged from T. rubripes 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.

scholarly journals Dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis revealed by its hologenome

2020 ◽  
Author(s):  
Yi Lan ◽  
Jin Sun ◽  
Chong Chen ◽  
Yanan Sun ◽  
Yadong Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Snail Host ◽  
Bacterial Symbionts ◽  
Mutualistic Relationship ◽  
Genomic Studies ◽  
Similar Depth ◽  
Selection Of ◽  
Chromosome Level

AbstractAnimals endemic to deep-sea hydrothermal vents often form obligatory relationships with bacterial symbionts, maintained by intricate host-symbiont interactions. Endosymbiosis with more than one symbiont is uncommon, and most genomic studies focusing on such ‘dual symbiosis’ systems have not investigated the host and the symbionts to a similar depth simultaneously. Here, we report a novel dual symbiosis among the peltospirid snail Gigantopelta aegis and its two Gammaproteobacteria endosymbionts – one being a sulphur oxidiser and the other a methane oxidiser. We assembled high-quality genomes for all three parties of this holobiont, with a chromosome-level assembly for the snail host (1.15 Gb, N50 = 82 Mb, 15 pseudo-chromosomes). In-depth analyses of these genomes reveal an intimate mutualistic relationship with complementarity in nutrition and metabolic codependency, resulting in a system highly versatile in transportation and utilisation of chemical energy. Moreover, G. aegis has an enhanced immune capability that likely facilitates the possession of more than one type of symbiont. Comparisons with Chrysomallon squamiferum, another chemosymbiotic snail in the same family but only with one sulphur-oxidising endosymbiont, show that the two snails’ sulphur-oxidising endosymbionts are phylogenetically distant, agreeing with previous results that the two snails have evolved endosymbiosis independently and convergently. Notably, the same capabilities of biosynthesis of specific nutrition lacking in the host genome are shared by the two sulphur-oxidising endosymbionts of the two snail genera, which may be a key criterion in the selection of symbionts by the hosts.

scholarly journals Antibiotic usage rates in bacterial versus nonbacterial diseases: a new way to monitor hospital-acquired infections in children: a retrospective case analysis

2020 ◽  
Vol 7 (11) ◽  
pp. 2176
Author(s):  
Jayendra R. Gohil ◽  
Chintu C. Chaudary ◽  
Sheena D. Sivanandan
Keyword(s):  
Antibiotic Usage ◽  
Retrospective Case ◽  
Hospital Acquired Infections ◽  
Group A ◽  
Added Benefit ◽  
Reduction Of Mortality ◽  
Group B ◽  
The Cost ◽  
Hospital Acquired ◽  
Selection Of

Background: While treating children, the selection of antibiotics, when indicated, should be from the point of its effectiveness, safety, suitability, and cost. However, this flow of action does not take place in all cases. Aim of the study was to assess the antibiotic usage in admitted children and mortality.Methods: The case records between January to July 2012 in children wards was evaluated for the use of antibiotics. Patients were grouped into; group A- ‘must use' antibiotic in all, and group B- where antibiotics are not indicated.Results: There were 1852 admissions, including 719 Thalassemia cases. Antibiotic usage was 63% in 1133 cases after excluding thalassemia. Out of 1133 cases, 423 were in group A and 710 cases were in group B. In group B the antibiotic usage was 41%. The mortality was 6.6% and 4.8% in group A and B. Inside group B, mortality was 5.9% versus 4.0% in those administered versus not administered, antibiotics.Conclusions: There was no increase in mortality in patients in whom antibiotics were not prescribed, and no added benefit of prescribing antibiotics was observed in nonbacterial group B disease patients. The mortality was similar in both the groups. In nonbacterial group B, the antibiotics did not offer any advantage in the reduction of mortality, but increased the cost of the treatment, and possibly the chance of development of drug resistance and adverse events. When analysing the hospital antibiotic usage, only the nonbacterial diseases should be considered to get a true picture of the inappropriate prescription of antibiotics.

Selection of flood-resistant and susceptible seedlings of Populustrichocarpa Torr. & Gray

1988 ◽  
Vol 18 (2) ◽  
pp. 271-275 ◽  
Author(s):  
Barbara A. Smit
Keyword(s):  
Leaf Area ◽  
Marked Reduction ◽  
Branch Length ◽  
Stomatal Resistance ◽  
Growth And Survival ◽  
Seed Collection ◽  
Individual Leaf ◽  
Total Branch Length ◽  
Collection Sites ◽  
Selection Of

To identify Populustrichocarpa plants with contrasting levels of resistance to flooding, seedlings from five diverse riparian sites were evaluated for growth and survival under flooding conditions. All seedlings survived 6 or 8 weeks of flooding. Total branch length and leaf number were reduced in all flooded plants relative to nonflooded controls. There was also a marked reduction in individual leaf area and increased stomatal resistance of flooded plants compared with nonflooded controls. Growth of flooded and nonflooded plants was highly variable within populations and no significant trends were found among populations. Therefore differential responses to flooding can be selected for within any of the seed collection sites. Plants that were rated as particularly resistant or susceptible fo flooding were selected for further study.

Clinical correlates of response to anti-PD-1 (aPD1)-based therapy in patients (pts) with metastatic melanoma (MM).

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e21000-e21000
Author(s):  
Elizabeth J. Davis ◽  
Shilin Zhao ◽  
Fei Ye ◽  
Katherine Rappazzo ◽  
Jeffrey Alan Sosman ◽  
...  
Keyword(s):  
Performance Status ◽  
Progression Free Survival ◽  
Clinical Predictors ◽  
Ecog Performance Status ◽  
Free Survival ◽  
Size Number ◽  
Multivariable Analyses ◽  
Status Number ◽  
Univariate Analyses ◽  
Selection Of

e21000 Background: aPD1, alone or in combination with ipilimumab (IPI), produces durable responses in a subset of MM. Tumor features that correlate with treatment response, including size, number, and location of metastases (mets) are not well defined. Methods: We collected clinical data from mm pts treated at one center who received aPD1 (n = 185) or aPD1 + IPI (n = 42). We correlated number of mets, size of largest tumor, and organ involvement with response rate (RR), progression-free survival (PFS) and overall survival (OS). Results: Among all pts, RR was 67% for aPD1 + IPI and 41% for aPD1 alone. In univariate analyses, responders to aPD1 had lower diameter of largest tumor (4cm vs. 5.5cm; p = 0.02) whereas aPD1 + IPI had equivalent largest tumor diameters (p = 0.65). Regarding sites of mets, liver mets were associated with lower RR in aPD1 treated pts (26% vs. 46%), lower PFS (median 138 vs. 326 days, p = 0.02), and lower OS (median 334 vs. 1080 days, p < 0.01). No associations with RR, PFS, or OS were observed with liver mets in aPD1 + IPI treated pts. We also did not observe any differences between pts who did or did not have lung, lymph node, or brain mets for either aPD1 or aPD1 + IPI. Interestingly, superior RR to aPD1 + IPI was observed in pts with bone mets compared to those without bone mets (91% vs. 58%, p = 0.048). Regarding number of sites, RR to aPD1 was greater in pts with ≤10 mets compared with those with > 10 (46% vs. 28%, p = 0.02), although no consistent relationship was observed at lower cutoffs. In multivariable analyses, diameter of largest tumor (tumor bulk) was independently associated with PFS (OR, 1.11, p < 0.001) and OS (OR 1.08, p < 0.001) whereas AJCC stage, lactate dehydrogenase, liver mets, ECOG performance status, number of mets, and prior therapies were not significant. Tumor bulk and other risk factors were not associated with PFS or OS in aPD1 + IPI. Conclusions: Tumor bulk was strongly and independently associated with clinical outcomes in aPD1 but not IPI + aPD1. Other associations with disease sites (liver and bone) need further validation. In conjunction with molecular biomarkers, clinical predictors may help guide selection of aPD1 or aPD1 + IPI.

scholarly journals In Vitro and In Vivo Stability a Cryptococcus neoformans Glucuronoxylomannan Epitope That Elicits Protective Antibodies

1999 ◽  
Vol 67 (6) ◽  
pp. 3096-3107 ◽  
Author(s):  
Wendy Cleare ◽  
Robert Cherniak ◽  
Arturo Casadevall
Keyword(s):  
Cryptococcus Neoformans ◽  
Parent Strain ◽  
Marked Reduction ◽  
Murine Models ◽  
Clear Trend ◽  
Agglutination Assay ◽  
Protective Antibodies ◽  
Selection Of

ABSTRACT The monoclonal antibody (MAb) 2H1 defines an epitope inCryptococcus neoformans capsular glucuronoxylomannan (GXM) that can elicit protective antibodies. In murine models of cryptococcosis, MAb 2H1 administration prolongs survival and reduces fungal burden but seldom clears the infection. The mechanism by whichC. neoformans persists and escape antibody-mediated clearance is not understood. One possibility is that variants that do not bind MAb 2H1 emerge in the course of infection. Using an agglutination-sedimentation protocol, we recovered a variant of strain 24067 that did not agglutinate, could not be serotyped, and had marked reduction in GXM O-acetyl groups. Binding of MAb 2H1 to 24067 variant cells produced a different immunofluorescence pattern and lower fluorescence intensity relative to the parent 24067 cells. Addition of MAb 2H1 to 24067 variant cells had no effect on cell charge. Phagocytic assays demonstrated that MAb 2H1 was not an effective opsonin for the 24067 variant. The 24067 variant was less virulent than the 24067 parent strain in mice, and MAb 2H1 administration did not prolong survival in animals infected with the variant strain. To investigate whether variants which do not bind MAb 2H1 are selected in experimental infection, three C. neoformans strains were serially passaged in mice given either MAb 2H1 or no antibody. Analysis of passaged isolates by agglutination assay, flow cytometry, and indirect immunofluorescence revealed changes in MAb 2H1 epitope expression but no clear trend with regards to gain or loss of MAb 2H1 epitope. C. neoformans variants with reduced MAb 2H1 epitope content can be isolated in vitro, but persistence of infection in mice given MAb 2H1 does not appear to be a result of selection of escape variants that lack the MAb 2H1 epitope.

scholarly journals Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

2021 ◽  
Author(s):  
Stephanie H Chen ◽  
Maurizio Rossetto ◽  
Marlien van der Merwe ◽  
Patricia Lu-Irving ◽  
Jia-Yee S Yap ◽  
...  
Keyword(s):  
Genome Size ◽  
De Novo ◽  
New South ◽  
New South Wales ◽  
Single Copy ◽  
Size Estimation ◽  
De Novo Genome Assembly ◽  
South Wales ◽  
Long Reads ◽  
Chromosome Level

Background: Telopea speciosissima, the New South Wales waratah, is Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Findings: Here, we report the first chromosome-level reference genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 91.2 % of Embryophyta BUSCOs complete. We introduce a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering assembly scaffolds. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single copy orthologues and find that the assembly is 93.9 % of the estimated genome size. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. Our results indicate that the waratah genome is highly repetitive, with a repeat content of 62.3 %. Conclusions: The T. speciosissima genome (Tspe_v1) will accelerate waratah evolutionary genomics and facilitate marker assisted approaches for breeding. Broadly, it represents an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

scholarly journals The number of cell types, information content, and the evolution of complex multicellularity

2014 ◽  
Vol 83 (4) ◽  
pp. 337-347 ◽  
Author(s):  
Karl J. Niklas ◽  
Edward D. Cobb ◽  
A. Keith Dunker
Keyword(s):  
Genome Size ◽  
Information Content ◽  
Intrinsically Disordered Protein ◽  
Cell Types ◽  
Base Pairs ◽  
Protein Residues ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Size Number ◽  
Different Cell Types

The number of different cell types (NCT) characterizing an organism is often used to quantify organismic complexity. This method results in the tautology that more complex organisms have a larger number of different kinds of cells, and that organisms with more different kinds of cells are more complex. This circular reasoning can be avoided (and simultaneously tested) when NCT is plotted against different measures of organismic information content (e.g., genome or proteome size). This approach is illustrated by plotting the NCT of representative diatoms, green and brown algae, land plants, invertebrates, and vertebrates against data for genome size (number of base-pairs), proteome size (number of amino acids), and proteome functional versatility (number of intrinsically disordered protein domains or residues). Statistical analyses of these data indicate that increases in NCT fail to keep pace with increases in genome size, but exceed a one-to-one scaling relationship with increasing proteome size and with increasing numbers of intrinsically disordered protein residues. We interpret these trends to indicate that comparatively small increases in proteome (and not genome size) are associated with disproportionate increases in NCT, and that proteins with intrinsically disordered domains enhance cell type diversity and thus contribute to the evolution of complex multicellularity.

scholarly journals The salmon louse genome may be much larger than sequencing suggests

2022 ◽  
Author(s):  
Grace Wyngaard ◽  
Rasmus Skern-Mauritzen ◽  
Ketil Malde ◽  
Rachel Prendergast ◽  
Stefano Peruzzi
Keyword(s):  
Genome Size ◽  
North Atlantic ◽  
Single Copy ◽  
Bay Of Fundy ◽  
Lepeophtheirus Salmonis ◽  
The North ◽  
Salmon Lice ◽  
The North Atlantic ◽  
Genome Assemblies ◽  
Chromosome Level

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding over 92% of expected genes and transcriptome datasets routinely mapping over 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements in the range of 1.3 to 1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up approx. 60% of the genome assemblies.

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