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

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.

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

“…We investigated the possibility of differential evolutionary patterns between inverted and non- (Conte, et al 2018). The authors compared the genome structure of the two species at the chromosome scale, taking advantage of the high quality of these references.…”

Bayesian genomic models boost prediction accuracy for resistance againstStreptococcus agalactiaein Nile tilapia (Oreochromus nilioticus)

“…In “only LG” sub-set, only the SNPs assigned to specific linkage groups [31] were used. That is, the SNPs not assigned to any linkage groups, and those assigned to the mitochondrial genome [48], were removed. Further, these SNPs on “only LG” subset were pruned based on different LD values in PLINKv1.90b6.7 [49].…”

Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real‐time PCR analyses

“…TruSeq adapters and low‐quality reads and bases were trimmed using trimmomatic version 0.32 (Bolger, Lohse, & Usadel, ). Reads were mapped to the Nile tilapia ( Oreochromis niloticus , version “O_niloticus_UMD_NMBU”) reference genome (Conte, Gammerdinger, Bartie, Penman, & Kocher, ; Conte et al, ) using tophat2 version 2.0.13 (Kim et al, ) with the Metriaclima zebra UMD2a gene annotations (Conte et al,). Gene expression was quantified as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) using cufflinks version 2.2.1 (Trapnell et al, ).…”