Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Abstract

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four-and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

“…We then performed the RepeatMasker 65 to mask the assembly, using the combined RepBase library. Usually, Repeat elements take a substantial part of the genome and contribute as important events to genome evolution 61,66,67 . In this study, by the combination of de novo and homology-based searching, 153 Mbp repeat elements were finally identified for the male FAW, and accounting for 28.24% the FAW genomes.…”

A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution

“…For greater resolution at shorter timescales, we used the recently sequenced M. pahari genome (Thybert et al 2018) to compile a younger phylostratum, using Ensembl's orthology annotation (Herrero et al 2016) to find homologs in M. musculus. Of the 789 putative proteins excluded in Wilson et al (2017) as being unique to M. musculus, 155 also had homologs in M. pahari.…”

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

“…Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes [130].…”

“…These advances have allowed researchers to perform clade genomics, producing assemblies for multiple members of a species or clade [130,131], and are required for the ambitious goals of projects such as Genome 10K [42] which aim to produce thousands of assemblies of diverse organisms. In addition, efforts are growing to produce de-novo assemblies of individual humans to evaluate the human health implications of structural variation and variation within regions not currently accessible with reference assisted approaches [132,133,134].…”