GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional Cytogenomics

Abstract

The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.

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

“…This pattern is in line with early observations of some badly reproducible banding patterns on less spiralized chromosomes [53][54][55][56]. The insufficient cytogenetic resolution in small-sized fish chromosomes can be augmented by the homogenizing effect of repetitive elements [46] that can be highly expanded in fish chromosomes, particularly in lineages with an additional whole-genome duplication [57]. The role of genome size can also be seen in the fact that in gar and other fishes and fish-like species with a rather larger genome (e.g., bowfin, lamprey, reedfish, sturgeon), at least four isofamilies could be identified with the sliding window size 100 kb (Figure 1 and Appendix B).…”

“…However, the mammalian-like AT/GC heterogeneity in the cold-blooded ancient gars excludes both these directions because (1) according to the gBGC, the significantly smaller chromosome size should result in higher GC% values in fishes because of the stronger recombination, and (2) gars are cold-blooded vertebrates with their body temperature dependent on the environment (discussed in detail by [5]). Hence, an alternative to the two traditional groups of hypotheses was introduced-the AT/GC homogenizing effect of transposons in genomes of anamniotes [45,46]. This alternative hypothesis involves a substantially larger genome fraction in contrast to exons-the repeats and, particularly, transposons-and it utilizes the currently available tools and genome assemblies.…”

“…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]. Such fluctuations in the GC% are not detectable by cytogenetics on densely spiralized small chromosomes that sometimes do not allow for distinguishing their morphology [50][51][52].…”

Why Do Some Vertebrates Have Microchromosomes?

“…Recently, these isochores have also been identified in teleost genomes with similar characteristics. Researchers [ 135 , 137 , 138 ] analyzed the GC-content of exonic third codon positions (GC3) of more than 6000 expressed sequence tags (ESTs) in the American alligator ( Alligator mississippiensis , Daudin, 1802) [ 139 ] and mentioned that the alligator genome has a certain level of GC heterogeneity suggesting the presence of GC-rich isochore in ancestors of archosaurs (birds and crocodilians). The GC content of alligator and crocodile assembled genomes was examined, and a higher average GC content was observed compared to many other vertebrates [ 140 ].…”

Fish Cytogenetics: Present and Future

“…Finally, two papers used the cytogenomic approach, providing new perspectives on genome evolution in vertebrates. The first one investigates at a fine scale AT/GC organization in fish genomes and understands the contribution of repeats to the total GC% [ 28 ]. As GC% is associated with gene density and chromatin structure, the results could explain the inability to produce G-banding with traditional cytogenetic methods: in some species, it might provide an alternative occasional banding pattern along the chromosomes.…”