Chromosome-level genome assembly of the Chinese three-keeled pond turtle (Mauremys reevesii) provides insights into freshwater adaptation.

Mauremys reevesii is an endangered freshwater turtle that symbolizes longevity in Chinese culture. Despite its importance, genetic studies of this species remain limited, with no genomic sequence reported to date. Here, we report a high-quality, chromosome-level genomic sequence of M. reevesii obtained using a combination of Nanopore and Hi-C sequencing technologies. The 2.37 Gb of M. reevesii genome was assembled from a total of ~226.80 Gb Nanopore sequencing data. The M. reevesii genome contig N50 is 34.73 Mb, the highest value in published turtle genomes. In total 18,238 genes were functionally annotated. The contigs were clustered and ordered onto 27 pseudochromosomes covering approximately 96.55 % of the genome assembled with Hi-C data. To explore the genome evolution, synteny analysis was performed between M. reevesii (freshwater turtle) and G. evgoodei (terrestrial turtle) genomes. In general, each chromosome of M. reevesii corresponded to one chromosome of G. evgoodei, but some inter-chromosomal rearrangements occurred between the two species based on the assembled genomes. These inter-chromosomal rearrangements were further confirmed by mapping of the long-read nanopore data to the assembly. The reconstructed demographic history showed varied effective population size among freshwater, marine, and terrestrial turtles. We also discovered expansion of genes related to innate immune system in M. reevesii that may provide defense against freshwater pathogens. The high-quality genomic sequence provides a valuable genetic resource for further studies of genetics and genome evolution in turtles.