Insights on macrosynteny, 'rebel' genes, and a new sex-linked region in anurans from comparative genomics and a new chromosome-level genome for the western chorus frog

Abstract

Amphibians have unique genome characteristics including slow karyotypic evolution and cytogenetically undifferentiated sex chromosomes. Yet our understanding of amphibian genomes has not kept pace with that of mammals and birds, partially due to scarce genomic resources and challenges associated with large genome sizes and high repetitiveness. We assembled and annotated a chromosome-level genome for the western chorus frog (Pseudacris triseriata), a species of conservation concern and importance in evolutionary research. Comparison of our new genome with other chromosome-level frog genomes reveals exceptionally conserved evolution of 13 chromosomal elements and gene orders across over 200 million years of anuran evolution. We uncovered rebel Benchmarking Universal Single-Copy Orthologs (BUSCO) genes that have been duplicated in almost all frog species, have been transposed, and showed lineage-specific synteny patterns - possibly relating to key traits such as frog advertisement calls and mitochondrial genome evolution. We also assembled a complete mitochondrial genome and found heteroplasmy of both point polymorphisms and length variation in the tandem repeat arrays in the control region. Double-digest restriction-site associated DNA sequencing analysis indicates that the western chorus frog has an XY sex system and the sex-linked region involved an [~]1Mb indel structural variant. Overall, our study provides important genomic resources for treefrogs and other anurans, documents highly conserved chromosomal evolution and gene orders in anurans, identifies rebel genes that might be important for frog evolution, and reveals a new sex-linked region with indel structural variants in anurans.