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bioRxiv · 10.1101/2025.08.05.668687

Genome Assembly of Astatotilapia latifasciata Uncovers B Chromosome Linked Chromatin Reorganization

Jehangir, M.·Ahmad, S. F.·Oliveira, J. I. N.·Cardoso, A. L.·Wolf, I. R.·Valente, G. T.·Srikulnath, K.·Martins, C.
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Abstract

B chromosomes (Bs) are supernumerary genomic elements found in many eukaryotes, yet their full sequence composition, functional potential, and regulatory impact on the host genome remain unclear. Here, we present a chromosome-level genome assembly of the cichlid fish Astatotilapia latifasciata, integrating PacBio long reads, Illumina short reads, and Hi-C chromatin contact maps to resolve both A and B chromosomes. The 0.93 Gb assembly (N50 = 36.2 Mb) includes a 34 Mb B chromosome containing 789 predicted protein-coding genes and a markedly higher density of transposable elements (TEs), especially long terminal repeats (LTR) retrotransposons. Transcriptome profiling revealed that B-linked genes are predominantly transcriptionally repressed relative to their A chromosome paralogs. Hi-C based chromatin modeling uncovered distinct 3D structural configurations associated with the B chromosome, including fewer topologically associating domains (TADs), reduced loop formation, and altered compartmentalization. These changes are linked to long-range chromatin interactions and genomic rearrangements, suggesting that the B chromosome reshapes the nuclear architecture of the host genome. Our study proposes a potential regulatory role of Bs in genome and provides a genomic resource for investigating chromosome evolution in cichlids.

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Jehangir, M., Ahmad, S. F., Oliveira, J. I. N., Cardoso, A. L., Wolf, I. R., Valente, G. T., Srikulnath, K., Martins, C.. 2025-08-07. Genome Assembly of Astatotilapia latifasciata Uncovers B Chromosome Linked Chromatin Reorganization. https://doi.org/10.1101/2025.08.05.668687

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