2019 journal article
Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
GIGASCIENCE, 8(4).
author keywords: genome assembly; African cichlids; comparative genomics; genome rearrangements; chromosome evolution; karyotype; inversion; recombination; transposable elements; genetic maps
MeSH headings : Animals; Chromosome Mapping; Cichlids / genetics; Computational Biology / methods; DNA Transposable Elements; Diploidy; Evolution, Molecular; Genetic Linkage; Genome; Genomics / methods; Karyotype; Molecular Sequence Annotation; Recombination, Genetic; Repetitive Sequences, Nucleic Acid
open access via academic.oup.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Source: Web Of Science
Added: July 29, 2019
African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2–28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.