Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12310%2F23%3A43906706" target="_blank" >RIV/60076658:12310/23:43906706 - isvavai.cz</a>

Result on the web

<a href="https://www.mdpi.com/1422-0067/24/17/13167" target="_blank" >https://www.mdpi.com/1422-0067/24/17/13167</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3390/ijms241713167" target="_blank" >10.3390/ijms241713167</a>

Result language

angličtina

Original language name

Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish

Original language description

The organization of the genome nucleotide (AT/GC) composition in vertebrates remains poorly understood despite the numerous genome assemblies available. Particularly, the origin of the AT/GC heterogeneity in amniotes, in comparison to the homogeneity in anamniotes, is controversial. Recently, several exceptions to this dichotomy were confirmed in an ancient fish lineage with mammalian AT/GC heterogeneity. Hence, our current knowledge necessitates a reevaluation considering this fact and utilizing newly available data and tools. We analyzed fish genomes in silico with as low user input as possible to compare previous approaches to assessing genome composition. Our results revealed a disparity between previously used plots of GC% and histograms representing the authentic distribution of GC% values in genomes. Previous plots heavily reduced the range of GC% values in fish to comply with the alleged AT/GC homogeneity and AT-richness of their genomes. We illustrate how the selected sequence size influences the clustering of GC% values. Previous approaches that disregarded chromosome and genome sizes, which are about three times smaller in fish than in mammals, distorted their results and contributed to the persisting confusion about fish genome composition. Chromosome size and their transposons may drive the AT/GC heterogeneity apparent on mammalian chromosomes, whereas far less in fishes.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/LM2018131" target="_blank" >LM2018131: Czech National Infrastructure for Biological Data</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

International Journal of Molecular Sciences

ISSN

1422-0067

e-ISSN

1422-0067

Volume of the periodical

24

Issue of the periodical within the volume

17

Country of publishing house

CH - SWITZERLAND

Number of pages

14

Pages from-to

—

UT code for WoS article

001062707800001

EID of the result in the Scopus database

2-s2.0-85170250648