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Abstract Transposable elements (TEs), despite generally being considered deleterious, represent a substantial portion of most eukaryotic genomes. Specific genomic regions, such as telomeres and pericentromeres, are often densely populated with TEs. In these regions, which tend to be gene-poor, reduced recombination shelters the genome from the deleterious effects of TEs. Here, we describe unusually large and continuous pericentromeric transposable element-rich regions in all chromosomes of the genome assembly of Pegoscapus hoffmeyeri sp. A (511.79 Mbp), a Neotropical fig wasp that is the obligate pollinator of Ficus obtusifolia. The identified pericentromeric transposable element-rich regions span nearly half (46%) of the genome, and harbor over 40% of all annotated genes, including 30% of conserved Benchmarking Universal Single-Copy Orthologs genes. We present evidence that low recombination in these transposable element-rich regions generates strong bimodal molecular evolution patterns genome-wide. Patterns of nucleotide diversity and protein-coding gene evolution in transposable element-rich regions are consistent with a reduced efficiency of selection and suggestive of strong Hill–Robertson effects. A significant reduction in third codon position GC content (GC3) in transposable element-rich regions emerged as the most distinctive gene feature differentiating genes in transposable element-rich regions from those in the rest of the genome, a pattern that likely results from the absence of GC-biased gene conversion. This remarkable bimodal compartmental genome organization in the genome of P. hoffmeyeri provides a unique example of how genome organization with compartmental transposable element distribution can lead to context-dependent gene evolution shaped by common evolutionary forces. 

Abstract Cichlid fishes have undergone an extraordinary diversification in East Africa. They also have a high rate of sex chromosome turnover. This clade provides an opportunity to study the rates and patterns of sex chromosome turnover, and the interactions of sex chromosome turnover with adaptation and speciation. Here we investigate the evolution sex chromosomes in the tribes Tilapiini, Coptodonini, Heterotilapiini, Gobiocichlini, Pelmatolapiini and Oreochromini. We assembled chromosome-scale genomes of male and female Pelmatotilapia mariae. We then mapped pooled sequencing reads for males and females of P. mariae and 12 additional species on several genome assemblies to identify sex chromosomes. Tilapia sparrmanii and Oreochromis aureus share a ZW system on LG3 that overlaps the ZW system identified in P. mariae. Heterotilapia buettikoferi, T. brevimanus and Coptodon bakossiorum share an XY system mapping to another region of LG3. Coptodon zilli, Sarotherodon galilaeus, S. melanotheron and O. niloticus share an XY system on LG1. Finally, O. mossambicus and O. shiranus share an XY system on LG14 and we find evidence of an XY system on LG20 in Danakilia sp. ‘shukoray’. The phylogenetic distribution of these sex determination systems suggests a long period of polymorphism for the systems on LG1 and LG3 and a generally lower rate of sex chromosome turnover in these lineages compared to the lacustrine lineages of the East African radiation. Our data is not consistent with the recent suggestion of figla and banf2 as candidate genes for the LG1XY and LG3ZW systems. We suggest a possible role for ubiquitination in the XY systems on LG3.