Genomic insights into the evolution of the critically endangered soft-shelled turtle Rafetus swinhoei.

The 2019 death of the female Swinhoes soft-shelled turtle (Rafetus swinhoei) individual in China put this species in a dire conservation state. To avoid the loss of genetic information from the female individual and facilitate the protection and preservation of R. swinhoei, we sequenced and assembled its draft chromosome-level genome by combining BGISEQ short reads, Nanopore long reads, and Hi-C sequencing reads. We characterized its potential ZZ/ZW sex determination system. Phylogeny and divergence time analyses indicated that R. swinhoei has a close relationship with Pelodiscus sinensis, and they shared a common ancestor ~54.4 Ma. Population history analyses indicated that R. swinhoei has the lowest heterozygosity among all turtles examined, and its population size has declined dramatically over the past 10 million years. Many core genes involved in autophagy and DNA damage response, such as Rab5a and Parp1, were under positive selection and/or evolving rapidly, and these genes may make important contributions to the long lifespan and evolutionary adaptation of R. swinhoei. The loss of several tooth-related genes in turtle genomes explains the genetic basis of their toothless phenotype. This study not only provides a genomic resource for scientists to study the species using the strategy of comparative genomics, but also provides a data basis for us to find more potential R. swinhoei individuals in the wild.

Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes.

In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.