A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations

The western painted turtle, Chrysemys picta bellii, has the greatest tolerance to anoxia of any tetrapod studied to date. These turtles reside in the northern United States and southern Canada, and survive months of anoxia while submerged in ice-locked ponds and bogs. Reference genomes provide an important resource for elucidating the molecular bases for such unique physiological traits. The initial reference genome for this species, published in 2013, is highly fragmented, thereby limiting downstream analyses and biological interpretation. We created a new and improved assembly by combining PacBio HiFi, 10 × Genomics Chromium, Hi-C sequence data and Bionano optical mapping derived from a single individual to generate a new haplotype-resolved chromosome-level reference assembly for C. picta bellii: "SLU_Cpb5.0". The genome size of the primary assembly is 2.372 Gb with a scaffold N50 of 133.6 Mb, a 6.5-fold improvement over the previous assembly. Annotation of SLU_Cpb5.0 revealed 12,242 novel genes compared to previous assemblies. PacBio Iso-Seq RNA sequencing using twelve tissues identified more than 100,000 novel transcript isoforms and 3,910 novel genes not previously annotated. This new genome assembly and annotation will support future comparative genomics studies, and the distinct patterns of tissue-specific isoform expression create a robust foundation for future characterization of the functions of these genes. Furthermore, to better understand the genetic basis of C. picta bellii's extreme physiological adaptations and other aspects of its biology, we utilize existing RNA-seq data to identify dozens of novel, differentially expressed genes in the heart and brain of anoxic painted turtles.