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Molecular divergence and genomic composition of B chromosomes in the fish Cyphocharax modestus (Characiformes, Curimatidae).

Natalia Dos Santos·Francisco de Menezes Cavalcante Sassi·Rodrigo Zeni Dos Santos·Caio Augusto Gomes Goes·Renata Luiza Rosa de Moraes·Fabio Porto-Foresti·Thomas Liehr·Marcelo de Bello Cioffi·Ricardo Utsunomia
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Abstract

B chromosomes are supernumerary elements that evolve from standard A chromosomes and are primarily composed of repetitive DNAs, yet their origin, diversification, and molecular composition remain poorly understood in most vertebrates. We investigated two allopatric populations of Cyphocharax modestus (Curimatidae) combining classical cytogenetics, comparative genomic hybridization (CGH), and comparative satellitomics to characterize the repetitive DNA landscape of its B chromosomes. While both populations exhibited a conserved karyotype of 2n=54 biarmed chromosomes, five individuals from the Batalha River (BR) carried supernumerary chromosomes, comprising two distinct variants: a C-positive B1 and an C-negative B2. Comparative satellitome analysis between 3B-carrying and B-lacking individuals identified 116 satellite DNAs (CmoSatDNAs), with the 3B library showing higher abundances of specific sequences. Fluorescence in situ hybridization (FISH) revealed that both B variants share two centromeric satellites (CmoSat01-192 and CmoSat02-108) with the A complement, while CmoSat58-47 was exclusively to B2. Minimum spanning tree analysis of CmoSat58-47 revealed B-exclusive haplotypes alongside haplotypes shared with B-lacking individuals, suggesting a recent origin for these chromosomes. CGH experiments further confirm the sequence sharing between the A and B chromosomes, supporting an intraspecific origin, and revealing substantial genomic differentiation among B variants.

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AnimalsCharaciformesChromosomesKaryotypeIn Situ Hybridization, FluorescenceComparative Genomic HybridizationDNA, SatelliteEvolution, MolecularKaryotypingGenetic VariationGenomicsGenomePhylogenyComparative genomic hybridizationCytogenomicRepetitive DNAsSatellitomeSupernumerary chromosomessatDNAsJournal ArticleResearch Support, Non-U.S. Gov't

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Natalia Dos Santos, Francisco de Menezes Cavalcante Sassi, Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, Renata Luiza Rosa de Moraes, Fabio Porto-Foresti, Thomas Liehr, Marcelo de Bello Cioffi, Ricardo Utsunomia. 2026-09-09. Molecular divergence and genomic composition of B chromosomes in the fish Cyphocharax modestus (Characiformes, Curimatidae).. https://doi.org/10.1038/s41598-026-66448-7

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