Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.

Area of Science:

• Evolutionary biology
• Genomics
• Bioinformatics

Background:

• Cichlid fishes exhibit remarkable phenotypic diversity, yet previous studies using single-nucleotide polymorphism (SNP) analysis showed low sequence divergence (0.1%-0.25%) between species.
• SNP-based studies relied on linear reference genomes and overlooked the impact of large-scale structural variants (SVs) on genomic diversity.

Purpose of the Study:

• To investigate the genomic diversity of East African cichlid fishes using pangenome methods.
• To uncover novel sequences and structural variants (SVs) missed by traditional reference-based approaches.
• To understand the role of SVs, particularly transposable elements (TEs), in cichlid evolution.

Main Methods:

• Construction of a pangenome graph integrating eight long-read genome assemblies (six new, two existing) of Lake Malawi haplochromine cichlids.
• Analysis of complex and nested genomic variations within the pangenome graph.
• Quantification of SVs and their contribution to overall genome size and interspecies divergence.

Main Results:

• The pangenome graph revealed substantial extra sequence (33.1% longer than a single genome) across seven species.
• Estimated interspecies structural variation ranged from 4.73% to 9.86% of assembly lengths, indicating significant underappreciated genomic diversity.
• A large proportion of SVs were identified as transposable element (TE) insertions (DNA, LINE, LTR), particularly outside conserved coding regions.

Conclusions:

• Pangenome analysis significantly expands the understanding of cichlid genomic diversity, highlighting the importance of SVs.
• Transposable elements play a major role in shaping the cichlid genome through large-scale alterations.
• Future research should integrate both small-nucleotide mutations and TE-derived SVs to fully elucidate cichlid evolutionary processes.