The dynamics of genome size and GC contents evolution in genus Nicotiana

Abstract Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one’s (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.

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Genome size and base composition of seven Quercus species: inter- and intra-population variation

Genome ◽

10.1139/g98-006 ◽

1998 ◽

Vol 41 (2) ◽

pp. 162-168 ◽

Cited By ~ 23

Author(s):

V Zoldos ◽

D Papes ◽

S C Brown ◽

O Panaud ◽

S Siljak-Yakovlev

Keyword(s):

Genome Size ◽

Dna Content ◽

Base Composition ◽

Gc Content ◽

Population Variation ◽

French Population ◽

Content Variation ◽

Quercus Species ◽

Dna Content Variation ◽

Two Populations

Seven Quercus species, four deciduous (Q. cerris, Q. petraea, Q. pubescens, andQ. robur) and three evergreen (Q. coccifera, Q. ilex, andQ. suber), were assessed for DNA content. Their genome sizes ranged from 1.88 to 2.00 pg/2C, namely an interspecific DNA content variation of 6%. In addition, the DNA content of several populations of Q. petraea andQ. robur with different geographical origins, French and Croatian, was estimated. DNA content did not vary among four populations of Q. robur, but did differ between two populations of Q. petraea, the French population having a higher 2C DNA value than the Croatian. The genome size of this French population showed important dispersion among 10 measured individuals. This was in accordance with subsequent cytogenetic data that revealed extra chromosomes in some individuals from this population. The percent GC varied little between the species; a GC content of 39.9% is established as typical for oak.Key words: Quercus, flow cytometry, genome size, GC percent, DNA content variations, extra chromosomes.

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Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab076 ◽

2021 ◽

Author(s):

Andreina I Castillo ◽

Rodrigo P P Almeida

Keyword(s):

Plant Pathogen ◽

Geographic Origin ◽

Gc Content ◽

Nucleotide Composition ◽

Plant Host ◽

Mixed Effect ◽

Genomic Changes ◽

Evolutionary Forces ◽

Multiple Variables ◽

Vector Borne

Abstract Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, Core vs. Accessory, and Recombinant vs. Non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs. natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.

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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Nature Genetics ◽

10.1038/ng.807 ◽

2011 ◽

Vol 43 (5) ◽

pp. 476-481 ◽

Cited By ~ 566

Author(s):

Tina T Hu ◽

Pedro Pattyn ◽

Erica G Bakker ◽

Jun Cao ◽

Jan-Fang Cheng ◽

...

Keyword(s):

Genome Size ◽

Genome Sequence ◽

Size Change ◽

Arabidopsis Lyrata

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Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

BMC Biology ◽

10.1186/s12915-021-01134-w ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

C. P. Stelzer ◽

J. Blommaert ◽

A. M. Waldvogel ◽

M. Pichler ◽

B. Hecox-Lea ◽

...

Keyword(s):

Genome Size ◽

Satellite Dna ◽

Gc Content ◽

Size Variation ◽

Isolated Populations ◽

Genome Size Variation ◽

Variable Regions ◽

Geographic Population ◽

Genome Size Evolution ◽

Size Evolution

Abstract Background Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. Results Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Conclusions By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

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Evolution of Nucleotide Composition in the SARS-CoV-2 Lineage: Implications for Vaccine Design

10.20944/preprints202006.0250.v1 ◽

2020 ◽

Author(s):

Sankar Subramanian

Keyword(s):

Base Composition ◽

Scientific Community ◽

Significant Positive Correlation ◽

Gc Content ◽

Nucleotide Composition ◽

Reverse Direction ◽

Novel Coronavirus ◽

Near Future ◽

Systematic Reduction ◽

Gc Contents

The worldwide outbreak of a novel coronavirus, SARS-CoV-2 has caused a pandemic of respiratory disease. Due to this emergency, researchers around the globe have been investigating the evolution of the genome of SARS-CoV-2 in order to design vaccines. Here I examined the evolution of GC content of SARS-CoV-2 by comparing the genomes of the members of the group Betacoronavirus. The results of this investigation revealed a highly significant positive correlation between the GC contents of betacoronaviruses and their divergence from SARS-CoV-2. The betacoronaviruses that are distantly related to SARS-CoV-2 have much higher GC contents than the latter. Conversely, the closely related ones have low GC contents, which are only slightly higher than that of SARS-CoV-2. This suggests a systematic reduction in the GC content in the SARS-CoV-2 lineage over time. The declining trend in this lineage predicts a much-reduced GC content in the coronaviruses that will descend/evolve from SARS-CoV-2 in the future. Due to the three consecutive outbreaks (MERS-CoV, SARS-CoV and SARS-CoV-2) caused by the members of the SARS-CoV-2, the scientific community is emphasizing the need for universal vaccines that are effective across many strains including those, that will inevitably emerge in the near future. The reduction in GC contents implies an increase in the rate of GC→AT mutations than that the mutational changes in the reverse direction. Therefore, understanding the evolution of base composition and mutational patterns of SARS-CoV-2 could be useful in designing broad-spectrum vaccines that could identify and neutralize the present and future strains of this virus.

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GPRED-GC: a Gene PREDiction model accounting for 5 ′- 3′ GC gradient

BMC Bioinformatics ◽

10.1186/s12859-019-3047-3 ◽

2019 ◽

Vol 20 (S15) ◽

Cited By ~ 1

Author(s):

Prapaporn Techa-Angkoon ◽

Kevin L. Childs ◽

Yanni Sun

Keyword(s):

Ab Initio ◽

Gene Annotation ◽

Gene Prediction ◽

Source Code ◽

Gc Content ◽

Prediction Tools ◽

Homologous Sequences ◽

Manual Intervention ◽

Grass Genomes ◽

Gc Contents

Abstract Background Gene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tools and they have been widely used for gene annotation for various species. However, existing tools are not optimized for identifying genes with highly variable GC content. In addition, some genes in grass genomes exhibit a sharp 5 ′- 3′ decreasing GC content gradient, which is not carefully modeled by available gene prediction tools. Thus, there is still room to improve the sensitivity and accuracy for predicting genes with GC gradients. Results In this work, we designed and implemented a new hidden Markov model (HMM)-based ab initio gene prediction tool, which is optimized for finding genes with highly variable GC contents, such as the genes with negative GC gradients in grass genomes. We tested the tool on three datasets from Arabidopsis thaliana and Oryza sativa. The results showed that our tool can identify genes missed by existing tools due to the highly variable GC contents. Conclusions GPRED-GC can effectively predict genes with highly variable GC contents without manual intervention. It provides a useful complementary tool to existing ones such as Augustus for more sensitive gene discovery. The source code is freely available at https://sourceforge.net/projects/gpred-gc/.

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An evolutionary correlate of genome size change in plethodontid salamanders

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.1997.0085 ◽

1997 ◽

Vol 264 (1381) ◽

pp. 597-604 ◽

Cited By ~ 52

Author(s):

Elizabeth L. Jockusch

Keyword(s):

Genome Size ◽

Size Change ◽

Plethodontid Salamanders

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Marsupial chromosome DNA content and genome size assessed from flow karyotypes: invariable low autosomal GC content

Royal Society Open Science ◽

10.1098/rsos.171539 ◽

2018 ◽

Vol 5 (8) ◽

pp. 171539 ◽

Cited By ~ 3

Author(s):

Fumio Kasai ◽

Patricia C. M. O'Brien ◽

Jorge C. Pereira ◽

Malcolm A. Ferguson-Smith

Keyword(s):

Genome Size ◽

Dna Content ◽

Chromosome Painting ◽

Gc Content ◽

Tammar Wallaby ◽

Individual Chromosome ◽

Tasmanian Devil ◽

Marsupial Species ◽

Cross Species Chromosome Painting ◽

High Level

Extensive chromosome homologies revealed by cross-species chromosome painting between marsupials have suggested a high level of genome conservation during evolution. Surprisingly, it has been reported that marsupial genome sizes vary by more than 1.2 Gb between species. We have shown previously that individual chromosome sizes and GC content can be measured in flow karyotypes, and have applied this method to compare four marsupial species. Chromosome sizes and GC content were calculated for the grey short-tailed opossum (2 n = 18), tammar wallaby (2 n = 16), Tasmanian devil (2 n = 14) and fat-tailed dunnart (2 n = 14), resulting in genome sizes of 3.41, 3.31, 3.17 and 3.25 Gb, respectively. The findings under the same conditions allow a comparison between the four species, indicating that the genomes of these four species are 1–8% larger than human. We show that marsupial genomes are characterized by a low GC content invariable between autosomes and distinct from the higher GC content of the marsupial × chromosome.

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Draft Genome Sequence of Rummeliibacillus sp. Strain TYF005, a Physiologically Recalcitrant Bacterium with High Ethanol and Salt Tolerance Isolated from Spoilage Vinegar

Microbiology Resource Announcements ◽

10.1128/mra.00244-19 ◽

2019 ◽

Vol 8 (31) ◽

Author(s):

Min Li ◽

Yao Li ◽

Xiaojun Fan ◽

Yuhong Qin ◽

Yongji He ◽

...

Keyword(s):

Salt Tolerance ◽

Genome Size ◽

Genome Sequence ◽

Draft Genome ◽

Gc Content ◽

Thermophilic Bacterium ◽

Draft Genome Sequence ◽

Content Type ◽

High Ethanol

Rummeliibacillus sp. strain TYF005 is a thermophilic bacterium with high ethanol (8% vol/vol) and salt (13% wt/vol) tolerance that was isolated from spoilage vinegar. Here, we report the draft genome sequence of this strain, which has 117 scaffolds with a total genome size of 3.7 Mb and a 34.4% GC content.

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