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Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

Matthew A. Conte, Rajesh Joshi, Emily C. Moore, Sri Pratima Nandamuri, William J. Gammerdinger, Reade B. Roberts, Karen L. Carleton, Sigbjørn Lien, Thomas D. Kocher
doi: https://doi.org/10.1101/383992
Matthew A. Conte
1Department of Biology, University of Maryland, College Park, MD 20742, USA
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Rajesh Joshi
2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Emily C. Moore
3Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, USA
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Sri Pratima Nandamuri
1Department of Biology, University of Maryland, College Park, MD 20742, USA
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William J. Gammerdinger
1Department of Biology, University of Maryland, College Park, MD 20742, USA
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Reade B. Roberts
3Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, USA
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Karen L. Carleton
1Department of Biology, University of Maryland, College Park, MD 20742, USA
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Sigbjørn Lien
2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Thomas D. Kocher
1Department of Biology, University of Maryland, College Park, MD 20742, USA
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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 understand 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 developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes.

Large intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (< 10Mbp total). Placement of the centromeres within 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 reductions in 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 (TE) insertions compared to O. niloticus, suggesting that several TE 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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 03, 2018.
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Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
Matthew A. Conte, Rajesh Joshi, Emily C. Moore, Sri Pratima Nandamuri, William J. Gammerdinger, Reade B. Roberts, Karen L. Carleton, Sigbjørn Lien, Thomas D. Kocher
bioRxiv 383992; doi: https://doi.org/10.1101/383992
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Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
Matthew A. Conte, Rajesh Joshi, Emily C. Moore, Sri Pratima Nandamuri, William J. Gammerdinger, Reade B. Roberts, Karen L. Carleton, Sigbjørn Lien, Thomas D. Kocher
bioRxiv 383992; doi: https://doi.org/10.1101/383992

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