Hidden compositional heterogeneity of fish chromosomes in the era of polished genome assemblies

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F23%3A00583822" target="_blank" >RIV/60077344:_____/23:00583822 - isvavai.cz</a>

Alternative codes found

RIV/60076658:12310/23:43906429

Result on the web

<a href="https://doi.org/10.3390/fishes8040185" target="_blank" >https://doi.org/10.3390/fishes8040185</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3390/fishes8040185" target="_blank" >10.3390/fishes8040185</a>

Result language

angličtina

Original language name

Hidden compositional heterogeneity of fish chromosomes in the era of polished genome assemblies

Original language description

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.

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

10620 - Other biological topics

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

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

Name of the periodical

Fishes

ISSN

2410-3888

e-ISSN

2410-3888

Volume of the periodical

8

Issue of the periodical within the volume

4

Country of publishing house

CH - SWITZERLAND

Number of pages

15

Pages from-to

185

UT code for WoS article

000978025900001

EID of the result in the Scopus database

2-s2.0-85156193027