Chromosome-Level Analysis of the Pelochelys cantorii Genome Provides Insights to Its Immunity, Growth and Longevity

Abstract

The Asian giant soft-shelled turtle, Pelochelys cantorii (Trionychidae), is one of the largest aquatic turtles in China and was designated as a First-Grade Protected Animal in China in 1989. Previous investigation based on a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies acquired a high-quality chromosome-level genome of Pc. cantorii. In this study, comparative genomic analysis between Pc. cantorii and 16 other vertebrate genomes indicated that turtles separated from the ancestor of archosaurians approximately 256.6 (95% highest posterior density interval, 263.6–251.9) million years ago (Mya) (Upper Permian to Triassic) and that Pc. cantorii separated from the ancestor of Pd. sinensis and R. swinhoei approximately 59.3 (95% highest posterior density interval, 64.3–54.3) Mya. Moreover, several candidate genes, such as VWA5A, ABCG2, A2M and IGSF1, associated with tumor suppression, growth and age were expanded, implicating their potential roles in the exceptional longevity of turtles. This new chromosome-level assembly has important scientific value in the study of conservation of Pc. cantorii and also enriches the evolutionary investigation of turtle species.

Cross-species genomic survey reveals a single origin of the soft-shelled turtles

“…sinensis , combining Oxford Nanopore sequencing, Illumina, and Hi-C technologies, with the genome size of 2.36 Gb and the scaffold N50 124.95 Mb, which is larger than the reported Trionychidae species P . sinensis (Wang et al ., 2013), A. spinifera (Gessler et al, 2023), R. swinhoei (Ren et al ., 2022), and P. cantorii (Liu et al, 2023) genomes and even other hard-shelled turtles including Trachemys scripta (Brian Simison et al, 2020), Chelonia mydas , and Dermochelys coriacea , providing an invaluable genetic resource for the origin and evolution of Trionychidae. The assembled P .…”

“…Additionally, it also signifies that we have constructed the first sex chromosomes in Trionychidae. Although the chromosome-level genome was also possessed in R. swinhoei and P. cantorii , the complete sex chromosomes have not been assembled (Liu et al ., 2023; Ren et al ., 2022). Moreover, P .…”

“…Furthermore, a female-specific sex marker developed in A. spinifera allowed for cross-species sex identification for P. sinensis (Literman et al, 2017). By constructing the chromosome-level genome of R. swinhoei and P. cantorii , the clues that they have a ZW sex-determination system have also been discovered (Liu et al ., 2023; Ren et al ., 2022). Collectively, these species encompass 9 of the 13 genera in Trionychidae (Shine, 2013); therefore, we have sufficient evidences and confidences to believe that there is a conserved ZW-type sex determination system in Trionychidae species.…”