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

Abstract

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.

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

“…Fish genomes, while being comparably GC-rich as mammals, are about two to three times smaller than mammalian ones despite the additional teleost-specific genome duplication [37]. Hence, the resolution of analytical tools may play a major role in assessing the genome compositional heterogeneity in smaller genomes with smaller chromosomes [49]. To test this, the only user input in our computational analyses was the setting of the sequence size expressed by the sliding window size used to scan the genome assembly for the GC%.…”

“…Due to these larger sizes in mammals, the sliding window size has been traditionally set to 100 kb to produce GC% profiles of a reasonable size. In fish, such a large window size obviously hinders identifying fluctuations in the GC% [49]. There are indeed small(er)-scale fluctuations in the GC% in fish; however, they are detectable by bioinformatics only when using smaller window sizes, 1 kb or 3 kb [46].…”