Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

Penso-Dolfin, Luca, Man, Angela, Mehta, Tarang, Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X and Di Palma, Federica (2020) Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes. BMC Evolutionary Biology, 20 (1). ISSN 1471-2148

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Abstract

Background: East African lake cichlids are one of the most impressive examples of an adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) in the evolution of adaptive traits across the three Great Lakes of East Africa. Results: Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei. We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with "antigen processing and presentation"and other immune related categories. Our pipeline and results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events. Conclusions: Altogether, we provide the first comprehensive overview of rearrangement evolution in East African cichlids, and some important insights into their likely contribution to adaptation.

Item Type: Article
Additional Information: Funding Information: We thank the funding bodies for supporting this research project. Publisher Copyright: © 2020 The Author(s).
Uncontrolled Keywords: adaptation,genome evolution,structural variants,ecology, evolution, behavior and systematics ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Science
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 15 Sep 2022 14:30
Last Modified: 23 Sep 2022 02:58
URI: https://ueaeprints.uea.ac.uk/id/eprint/88315
DOI: 10.1186/s12862-020-01629-0

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