Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (GigaScience)
Abstract
Background
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.
Results
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.
Conclusion
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.
Article activity feed
-
Now published in GigaScience doi: 10.1093/gigascience/giz030
Matthew A. Conte 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRajesh Joshi 2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NorwayFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEmily C. Moore 3Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSri Pratima Nandamuri 1Department of Biology, University of Maryland, College Park, MD …
Now published in GigaScience doi: 10.1093/gigascience/giz030
Matthew A. Conte 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRajesh Joshi 2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NorwayFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEmily C. Moore 3Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSri Pratima Nandamuri 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWilliam J. Gammerdinger 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteReade B. Roberts 3Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKaren L. Carleton 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSigbjørn Lien 2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NorwayFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteThomas D. Kocher 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz030 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101604 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101605
-
-
