scholarly journals What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140331 ◽  
Author(s):  
Tyler A. Elliott ◽  
T. Ryan Gregory
Keyword(s):  
Genome Size ◽  
Developmental Rate ◽  
Rapid Expansion ◽  
Division Rate ◽  
Protein Coding ◽  
Genome Data ◽  
Pair Composition ◽  
A Genome ◽  
Wide Range ◽  
Size Diversity

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.

scholarly journals A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

2019 ◽  
Vol 11 (11) ◽  
pp. 3144-3157 ◽  
Author(s):  
Yutaka Satou ◽  
Ryohei Nakamura ◽  
Deli Yu ◽  
Reiko Yoshida ◽  
Mayuko Hamada ◽  
...  
Keyword(s):  
Genome Size ◽  
Inbred Line ◽  
Genome Assembly ◽  
Ciona Intestinalis ◽  
Type A ◽  
Chromosomal Evolution ◽  
Sequence Information ◽  
A Genome ◽  
Biological Studies ◽  
Wide Range

Abstract Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

scholarly journals Draft Genome Sequence of the UV-Resistant Antarctic Bacterium Sphingomonas sp. Strain UV9

2019 ◽  
Vol 8 (7) ◽  
Author(s):  
Juan J. Marizcurrena ◽  
Danilo Morales ◽  
Pablo Smircich ◽  
Susana Castro-Sowinski
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Antarctic Bacterium ◽  
A Genome ◽  
The Antarctic

We report the draft genome sequence of the Antarctic UV-resistant bacterium Sphingomonas sp. strain UV9. The strain has a genome size of 4.25 Mb, a 65.62% GC content, and 3,879 protein-coding sequences.

Characterization of Base Periodicities in Protein-Coding Genes

1998 ◽  
Vol 06 (01) ◽  
pp. 49-70 ◽  
Author(s):  
Julius H. Jackson ◽  
Roy George ◽  
Hezekiah O. Adeyemi ◽  
Michael A. Winrow ◽  
Patricia A. Herring ◽  
...  
Keyword(s):  
Quantitative Measure ◽  
Gene Families ◽  
Neural Nets ◽  
Protein Coding ◽  
Natural Systems ◽  
Protein Coding Genes ◽  
Genome Data ◽  
Codon Preference ◽  
A Genome ◽  
Density Analysis

A Fourier Transform of Equal Symbols (FTES) was applied as a spectral density analysis method to identify DNA bases that repeat at any frequency in selected protein-coding genes. The analysis especially focused on identification of bases responsible for the dominant signal at frequency f=1/3 found in all protein-coding genes. The study included homologous sequences from two gene families and multiple unrelated sequences from single organisms. No signal pattern or spectrum specifically characterized either gene family. However, the patterns of bases comprising the signal at f=1/3 suggested the presence of a genome-specific label for protein-coding genes from the same genome. Data suggest that three factors form the informational basis for the signal structure at f=1/3: (1) codon base positional bias; (2) codon preference; and (3) codon arrangement. Quantitative measure of the contribution of each base to the period-3 signal suggests a basis to distinguish protein-coding genes from different organisms. Application of the FTES analysis characterized genes from Escherichia coli as different from the genes from Pseudomonas aeruginosa. Preliminary analyses of genes from these and three other bacteria by artificial neural nets, using FTES parameters, support our suggestion that the period-3 informational structure contains labels for the genomic origins of protein-coding genes. FTES analysis alone or in combination with other informational measures may reveal pathways and processes of gene flow into and through natural systems of microbial cell populations.

Genome size is inversely correlated with relative brain size in parrots and cockatoos

Genome ◽  
2009 ◽  
Vol 52 (3) ◽  
pp. 261-267 ◽  
Author(s):  
Chandler B. Andrews ◽  
T. Ryan Gregory
Keyword(s):  
Metabolic Rate ◽  
Genome Size ◽  
Cognitive Abilities ◽  
Nuclear Dna ◽  
Brain Size ◽  
Nuclear Dna Content ◽  
Developmental Rate ◽  
Ecological Traits ◽  
Division Rate ◽  
Cell Division Rate

Genome size (haploid nuclear DNA content) has been found to correlate positively with cell size and negatively with cell division rate in a variety of taxa. These cytological relationships manifest in various ways at the organism level, for example, in terms of body size, metabolic rate, or developmental rate, depending on the biology of the organisms. In birds, it has been suggested that high metabolic rate and strong flight ability are linked to small genome size. However, it was also hypothesized that the exceptional cognitive abilities of birds may impose additional constraints on genome size through effects on neuron size and differentiation, as has been observed in amphibians. To test this hypothesis, a comparative analysis was made between genome size, cell (erythrocyte) size, and brain size in 54 species of parrots and cockatoos (order Psittaciformes, family Psittacidae). Relative brain volume, which is taken as an indicator of investment in brain tissue and is widely correlated with behavioural and ecological traits, was found to correlate inversely with genome size. Several possible and mutually compatible explanations for this relationship are described.

scholarly journals When Bigger Is Better: 3D RNA Profiling of the Developing Head in the Catshark Scyliorhinus canicula

2021 ◽  
Vol 9 ◽  
Author(s):  
Hélène Mayeur ◽  
Maxence Lanoizelet ◽  
Aurélie Quillien ◽  
Arnaud Menuet ◽  
Léo Michel ◽  
...  
Keyword(s):  
Neural Tube Closure ◽  
Digital Model ◽  
Model Organisms ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Rna Profiling ◽  
Scyliorhinus Canicula ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

We report the adaptation of RNA tomography, a technique allowing spatially resolved, genome-wide expression profiling, to a species occupying a key phylogenetic position in gnathostomes, the catshark Scyliorhinus canicula. We focused analysis on head explants at an embryonic stage, shortly following neural tube closure and of interest for a number of developmental processes, including early brain patterning, placode specification or the establishment of epithalamic asymmetry. As described in the zebrafish, we have sequenced RNAs extracted from serial sections along transverse, horizontal and sagittal planes, mapped the data onto a gene reference taking advantage of the high continuity genome recently released in the catshark, and projected read counts onto a digital model of the head obtained by confocal microscopy. This results in the generation of a genome-wide 3D atlas, containing expression data for most protein-coding genes in a digital model of the embryonic head. The digital profiles obtained for candidate forebrain regional markers along antero-posterior, dorso-ventral and left-right axes reproduce those obtained by in situ hybridization (ISH), with expected relative organizations. We also use spatial autocorrelation and correlation as measures to analyze these data and show that they provide adequate statistical tools to extract novel expression information from the model. These data and tools allow exhaustive searches of genes exhibiting any predefined expression characteristic, such a restriction to a territory of interest, thus providing a reference for comparative analyses across gnathostomes. This methodology appears best suited to species endowed with large embryo or organ sizes and opens novel perspectives to a wide range of evo-devo model organisms, traditionally counter-selected on size criterion.

scholarly journals Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

2018 ◽  
Author(s):  
Irma Lozada-Chávez ◽  
Peter F. Stadler ◽  
Sonja J. Prohaska
Keyword(s):  
Genome Size ◽  
Evolutionary Dynamics ◽  
Protein Coding ◽  
Specific Level ◽  
Spliceosomal Introns ◽  
Major Mechanism ◽  
Genome Wide ◽  
A Genome ◽  
Eukaryotic Gene ◽  
The Impact

AbstractThe impact of spliceosomal introns on genome and organismal evolution remains puzzling. Here, we investigated the correlative associations among genome-wide features of introns from protein-coding genes (e.g., size, density, genome-content, repeats), genome size and multicellular complexity on 461 eukaryotes. Thus, we formally distinguished simple from complex multicellular organisms (CMOs), and developed the program GenomeContent to systematically estimate genomic traits. We performed robust phylogenetic controlled analyses, by taking into account significant uncertainties in the tree of eukaryotes and variation in genome size estimates. We found that changes in the variation of some intron features (such as size and repeat composition) are only weakly, while other features measuring intron abundance (within and across genes) are not, scaling with changes in genome size at the broadest phylogenetic scale. Accordingly, the strength of these associations fluctuates at the lineage-specific level, and changes in the length and abundance of introns within a genome are found to be largely evolving independently throughout Eukarya. Thereby, our findings are in disagreement with previous estimations claiming a concerted evolution between genome size and introns across eukaryotes. We also observe that intron features vary homogeneously (with low repetitive composition) within fungi, plants and stramenophiles; but they vary dramatically (with higher repetitive composition) within holozoans, chlorophytes, alveolates and amoebozoans. We also found that CMOs and their closest ancestral relatives are characterized by high intron-richness, regardless their genome size. These patterns contrast the narrow distribution of exon features found across eukaryotes. Collectively, our findings unveil spliceosomal introns as a dynamically evolving non-coding DNA class and strongly argue against both, a particular intron feature as key determinant of eukaryotic gene architecture, as well as a major mechanism (adaptive or non-adaptive) behind the evolutionary dynamics of introns over a large phylogenetic scale. We hypothesize that intron-richness is a pre-condition to evolve complex multicellularity.

scholarly journals Introns structure patterns of variation in nucleotide composition in Arabidopsis thaliana and rice protein-coding genes

2014 ◽  
Author(s):  
Adrienne Ressayre ◽  
Sylvain Glemin ◽  
Pierre Montalent ◽  
Laurana Serres-Giardi ◽  
Christine Dillmann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Nucleotide Composition ◽  
Coding Region ◽  
Protein Coding ◽  
Plant Genomes ◽  
A Genome ◽  
Wide Range ◽  
Intron Number ◽  
Species Specific ◽  
Range Of Variation

Plant genomes are large, intron-rich and present a wide range of variation in coding region G+C content. Concerning coding regions, a sort of syndrome can be described in plants: the increase in G+C content is associated with both the increase in heterogeneity among genes within a genome and the increase in variation across genes. Taking advantage of the large number of genes composing plant genomes and the wide range of variation in gene intron number, we performed a comprehensive survey of the patterns of variation in G+C content at different scales from the nucleotide level to the genome scale in two species Arabidopsis thaliana and Oryza sativa, comparing the patterns in genes with different intron numbers. In both species, we observed a pervasive effect of gene intron number and location along genes on G+C content, codon and amino acid frequencies suggesting that in both species, introns have a barrier effect structuring G+C content along genes. In external gene regions (located upstream first or downstream last intron), species-specific factors are shaping G+C content while in internal gene regions (surrounded by introns), G+C content is constrained to remain within a range common to both species. In rice, introns appear as a major determinant of gene G+C content while in A. thaliana introns have a weaker but significant effect. The structuring effect of introns in both species is susceptible to explain the G+C content syndrome observed in plants.

scholarly journals Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

2021 ◽  
Author(s):  
Noé Cochetel ◽  
Andrea Minio ◽  
Mélanie Massonnet ◽  
Amanda M Vondras ◽  
Rosa Figueroa-Balderas ◽  
...  
Keyword(s):  
Single Molecule ◽  
Interleukin 1 ◽  
Plasmopara Viticola ◽  
Cabernet Sauvignon ◽  
Disease Resistance Gene ◽  
Chromosome Fusion ◽  
Protein Coding ◽  
Downy Mildews ◽  
A Genome ◽  
Muscadinia Rotundifolia

Abstract Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map of M. rotundifolia. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using Full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/ Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser for Trayshed, its annotation, and an associated Blast tool are available at .www.grapegenomics.com

scholarly journals PROTEIN POLYMORPHISMS, SEGREGATION IN GENETIC CROSSES AND GENETIC DISTANCES AMONG FISHES OF THE GENUS XIPHOPHORUS (POECILIIDAE)

Genetics ◽  
1982 ◽  
Vol 102 (3) ◽  
pp. 539-556
Author(s):  
Don C Morizot ◽  
Michael J Siciliano
Keyword(s):  
Goodness Of Fit ◽  
Inbred Strains ◽  
Interspecific Backcross ◽  
Genetic Distances ◽  
Rapid Expansion ◽  
Starch Gel Electrophoresis ◽  
Lower Vertebrate ◽  
Protein Coding ◽  
Group I ◽  
Starch Gel

ABSTRACT The products of 49 protein-coding loci were examined by starch gel electrophoresis for populational variation in six species of Xiphophorus fishes and/or segregation in intra- and interspecific backcross and intercross hybrids. Electrophoretic variation was observed for 29 of the 35 locus products in a survey of 42 population samples. The highest frequency of polymorphic loci observed in noninbred populations was 0.143. After ten or more generations of inbreeding, all loci studied were monomorphic. Inbred strains generally exhibited the commonest electrophoretic alleles of the population from which they were derived. An assessment of genetic distances among Xiphophorus populations reflected classical systematic relationships and suggested incipient subspeciation between X. maculatus from different drainages as well as several species groups. Thirty-three loci were analyzed with respect to segregation in hybrids. The goodness of fit of segregations to Mendelian expectations at all loci analyzed (except loci in linkage group I) is interpreted as evidence for high genetic compatibility of the genomes of Xiphophorus species. It is anticipated that these data will result in a rapid expansion of the assignment of protein-coding loci to linkage groups in these lower vertebrate species.

scholarly journals Ecofriendly Synthesis of Silver Nanoparticles by Terrabacter humi sp. nov. and Their Antibacterial Application against Antibiotic-Resistant Pathogens

2020 ◽  
Vol 21 (24) ◽  
pp. 9746
Author(s):  
Shahina Akter ◽  
Sun-Young Lee ◽  
Muhammad Zubair Siddiqi ◽  
Sri Renukadevi Balusamy ◽  
Md. Ashrafudoulla ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Spherical Shape ◽  
Optimal Growth ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Drug Resistant ◽  
Protein Coding ◽  
A Genome ◽  
The Fourier Transform

It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 °C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%–98.8%). Terrabacter humi MAHUQ-38T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38T was used for the eco-friendly and facile synthesis of AgNPs. The transmission electron microscopy (TEM) image showed the spherical shape of AgNPs with a size of 6 to 24 nm, and the Fourier transform infrared (FTIR) analysis revealed the functional groups responsible for the synthesis of AgNPs. The synthesized AgNPs exhibited strong anti-bacterial activity against multi-drug-resistant pathogens, Escherichia coli and Pseudomonas aeruginosa. Minimal inhibitory/bactericidal concentrations against E. coli and P. aeruginosa were 6.25/50 and 12.5/50 μg/mL, respectively. The AgNPs altered the cell morphology and damaged the cell membrane of pathogens. This study encourages the use of Terrabacter humi for the ecofriendly synthesis of AgNPs to control multi-drug-resistant microorganisms.

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