DOI: 10.1101/473710Nov 24, 2018Paper

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

BioRxiv : the Preprint Server for Biology
Luca Penso DolfinFederica Di-Palma

Abstract

African Lakes Cichlids are one of the most impressive example of 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) to speciation events (through a reduction of gene flow) and adaptation to different ecological niches. Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in five cichlid species (Astatotilapia burtoni, Metriaclima zebra, Neolamprologus brichardi, Pundamilia nyererei and Oreochromis niloticus). We investigate the patterns of gain/loss evolution across the phylogeny for each SV type enabling the identification of both lineage specific events and a set of conserved SVs, common to all four species in the radiation. Both deletion and inversion events show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA ...Continue Reading

Related Concepts

Antigens
Base Sequence
Cichlids
Biological Evolution
Gene Deletion
Gene Duplication
Genes
Oreochromis niloticus
Skeletal Bone
Adaptation

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