The Spotted Turtle (Rafetus swinhoei) is the largest surviving turtle species on Earth, with a dorsal carapace length of up to 1.5 meters and a weight of up to 115 kg. In addition, the spotted turtle is currently the most endangered turtle species in the world. At the beginning of 2019, only 4 individual turtles have been clearly recorded worldwide (1 female and 1 male in China; 2 in Vietnam, gender unknown). However, on April 13, 2019, the unexpected death of female individuals on the mainland (which was also the only female spotted turtle individual in the world at that time to determine sex) was very regrettable.
In order to avoid the permanent loss of genetic information in the female turtle genome, and in order to promote the continuation of the investigation and protection of the turtle, with the support of the Changsha Ecological Zoo, the researchers collected tissue samples of the individual during the pathological anatomy of the female dead turtle. By combining sequencing data such as Nanopoore long read long sequences, BGI-seq short read long sequences, and chromosomal conformation capture technology (Hi-C), the researchers successfully assembled a high-quality reference genome sequence at the chromosomal level of the individual. The assembled genome size is 2.24Gb and the Scaffold N50 is 131.98Mb long. 26,646 high-quality protein-coding genes were successfully predicted by combining de novo prediction, homologous comparison, and transcript-assisted annotation. In addition, the researchers defined their sex-determining system for ZZ/ZW by analyzing their chromosomes.
Based on multiple datasets and algorithms for building phylogenous trees, the researchers found that the spotted turtle is closely related to the Chinese turtle (Pelodiscus sinensis), but began to part ways 54.4 million years ago. Population history analysis shows that the effective population of the spotted turtle has shown a continuous downward trend historically, which is consistent with its low genetic heterozygosity and genetic diversity. Comparative genomics analysis shows that some of the core genes associated with autophagy, DNA damage response, and growth-related processes are undergoing positive selection or rapid evolution, suggesting that they have important functions in processes such as the long lifespan and large size of the spotted turtle. In addition, the researchers found that some genes associated with tooth formation are missing in the turtle genome, which partly explains the genetic basis of their toothless phenotype.
The analysis and analysis of the whole genome genetic information of the spotted turtle not only retains the whole genome information for the species (especially the ZW heterozygomic genetic information of the female turtle), but also has great significance for the field investigation, search and protection of the spotted turtle in the future (the successful analysis of the whole genome sequence of the spotted turtle helps to design a more sensitive and specific and effective genetic molecular probe, which is conducive to the use of environmental DNA methods to quickly detect, find, discover and identify more potential wild spotted turtle individuals in the field investigation).
The study was jointly completed by the Kunming Institute of Zoology of the Chinese Academy of Sciences and the Changsha Ecological Zoo, and published in the international journal Molecular Ecology Resources in March, with Ren Yandong, a doctoral student from kunming zoological institute, and Zhang Qiang from Changsha Ecological Zoo as co-first authors, and Rao Dingqi, associate researcher of Kunming Institute of Zoology, and Li Yongxin, a graduated doctoral student, as co-corresponding authors.
Article link: https://doi.org/10.1111/1755-0998.13596
Fig. 1 Spotted turtle (Rafetus swinhoei) (female individual) Lü Shunqing
Fig. 2 Assembly and comparative analysis of the turtle genome
Figure 3 Genetic differences behind similar body types in turtles and tortoises
Figure 4 Population status of the spotted turtle
Extend:
In April 2019, the death of the only female turtle in the world at that time to determine the sex of the turtle, which put the conservation, breeding and rescue of the species almost in a desperate situation, and the future and sustainable survival of the turtle were widely concerned at home and abroad. Although the discovery of a female turtle in Vietnam at the end of 2020 rekindled hopes for the recovery of the species population, the status quo of the turtle on the verge of extinction still exists, and the turtle population in the lower Yangtze River - Taihu Lake Basin has actually declared its biological extinction after the death of the only surviving female turtle, and the turtle population in the Red River Basin has only been identified in Vietnam with 3 (including 1 female individual). At present, the search for surviving spotted turtles in the wild is still difficult, which is the key to saving the spotted turtles, and the Kunming Institute of Zoology of the Chinese Academy of Sciences, together with Huangshan University, Hainan Normal University and the International Wildlife Conservation Society (WCS), has been sparing no effort to explore the possible survival of the spotted turtles in the wild in the Red River Basin in Yunnan Province, and continues to seek cooperation with Vietnam.
Tips: This article is transferred from "iPlants", the article reprinted only for academic dissemination, no commercial use, the copyright belongs to the original author, such as infringement issues, please contact us, we will modify or delete in time.
TOPSCI-TOPS IS CREATED BY THE PHD TEAM OF WORLD-RENOWNED UNIVERSITIES TO CREATE SCIENTIFIC RESEARCH ACADEMIC SHARING, SCI PAPER EDITING/ SCI JOURNAL ANALYSIS/ SCI PAPER WRITING SKILLS GUIDANCE/ SCIENTIFIC RESEARCH TOOL APPLICATION/ TRANSFORMATION OF SCIENTIFIC RESEARCH ACHIEVEMENTS.