An Isochore-Like Structure in the Genome of the Flatworm<i>Schistosoma mansoni</i>

Lamolle, Guillermo; Protasio, Anna V.; Iriarte, Andrés; Jara, Eugenio; Simón, Diego; Musto, Héctor

doi:10.1093/gbe/evw170

Cited by 8 publications

(3 citation statements)

References 26 publications

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“…Further analysis in larger sets of genes showed that codon bias was not uniformly distributed between genes introducing the possibility of isochores (regions that differ in GC content) in the genomes of flatworms (Ellis and Morrison, 1995; Ellis et al, 1995). In agreement, a more recent compositional analysis of the S. mansoni genome reported an isochore-like organization (Lamolle et al, 2016). Early studies analyzing the forces behind codon bias found evidences of both mutational pressure (Musto et al, 1998) in S. mansoni and selection (Fernandez et al, 2001) in Echinococcus spp.…”

Section: Introductionsupporting

confidence: 74%

Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes

et al. 2019

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In the present work, we performed a comparative genome-wide analysis of 22 species representative of the main clades and lifestyles of the phylum Platyhelminthes. We selected a set of 700 orthologous genes conserved in all species, measuring changes in GC content, codon, and amino acid usage in orthologous positions. Values of 3rd codon position GC spanned over a wide range, allowing to discriminate two distinctive clusters within freshwater turbellarians, Cestodes and Trematodes respectively. Furthermore, a hierarchical clustering of codon usage data differs remarkably from the phylogenetic tree. Additionally, we detected a synonymous codon usage bias that was more dramatic in extreme GC-poor or GC-rich genomes, i.e., GC-poor Schistosomes preferred to use AT-rich terminated synonymous codons, while GC-rich M. lignano showed the opposite behavior. Interestingly, these biases impacted the amino acidic usage, with preferred amino acids encoded by codons following the GC content trend. These are associated with non-synonymous substitutions at orthologous positions. The detailed analysis of the synonymous and non-synonymous changes provides evidence for a two-hit mechanism where both mutation and selection forces drive the diverse coding strategies of flatworms.

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Section: Introductionsupporting

confidence: 74%

Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes

et al. 2019

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“…But on the contrary, (iv) vertebrate genomes (mainly those of mammals and birds) display large contiguous regions characterized by very similar GC content which are termed isochores ( Bernardi et al, 1985 ; Eyre-Walker and Hurst, 2001 ; Costantini and Musto, 2017 ), and each of these isochores display a particular and very similar pattern of codon usage ( Costantini et al, 2009 ) and amino acid frequencies ( Sabbia et al, 2007 ), although intragenic GC content heterogeneity has been noted in birds ( Khrustalev et al, 2014 ). Among unicellular eukaryotes, it has been shown that most of them are compositionally heterogeneous ( Costantini et al, 2013 ) as is the case in some flatworms ( Lamolle et al, 2016 ). Therefore, from the study of the genomic composition important features like diNs frequencies and codon usage have been derived, and helped us to understand important biological properties, like patterns of synonymous and non-synonymous substitutions, and the relative effects of neutral and selective forces driving these changes ( Pracana et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts

2021

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The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.

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“…This study demonstrated that a small, non-overlapping sliding window size of 1000 bp was able to yield GC% profiles with a sufficient resolution to identify hitherto hidden fluctuations in nucleotide composition in two teleost genomes. The standard window size is of 100,000 bp (100 kb) and is routinely used not only in mammals [31], but also in far smaller genomes of invertebrates [32]. However, this window size is unsuitable for fish genomes, which can be two to three times smaller.…”

Section: Discussionmentioning

confidence: 99%

Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies

Vohnoutová

Žifčáková

Symonová

2023

Fishes

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Fish chromosomes are considered homogeneous in their AT/GC nucleotide composition, and banding patterns enabling identification of homologs are largely missing. While cytogenomic approaches try to compensate for this issue by virtual karyotyping, they rely on the quality of genome assemblies available. Recently, soft-masked genome assemblies combining costly and arduous long- and short-read sequencing and new generation assemblers became available for two teleost fish species, climbing perch (Anabas testudineus) and channel bull blenny (Cottoperca gobio). Soft-masking turns repetitive sequences in a genome assembly into lower case letters, leaving unique sequences in upper case. This enables investigators to assess the proportion of guanine and cytosine nucleotides (GC%) of transposable elements as an indicator of AT/GC homogenisation in fish. We have developed a new version of our Python tool Evan, which utilises chromosome-level genome assemblies and combines the profiles of GC% and the proportion of repeats (rep%) along chromosomes. Our profiles of both of those fishes showed clear and abrupt but small-scale fluctuations in GC% along otherwise compositionally homogenised sequences. Our study also highlights the key role of the sliding window size in determining the resolution of GC% profiling. While the quality of the genome assemblies appeared to be sufficient for GC%/rep% profiling, more effective repeat masking is necessary to better distinguish to what extent repeats compositionally homogenize fish genomes.

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An Isochore-Like Structure in the Genome of the FlatwormSchistosoma mansoni

Cited by 8 publications

References 26 publications

Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes

Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes

Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts

Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies

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