Abstract
Restriction site-associated DNA sequencing (RAD-seq) was used to develop single nucleotide polymorphisms (SNP) marker for the Pelodiscus sinensis, which is a commercially important species in China. A total of 105 high-quality SNP markers were identified. The genetic statistics showed that the minor allele frequency varied from 0.0571 to 0.3382 and the observed heterozygosity and the expected heterozygosity ranged from 0.1143 to 0.6765 and 0.1078 to 0.4477, respectively. These novel SNP markers will serve as a valuable genetic tool for future conservation and population genetics studies for P. sinensis.
Data availability
The RAD-seq data are openly available in NCBI at https://www.ncbi.nlm.nih.gov/sra, PRJNA680995.
Code availability
Not applicable.
References
Bu X, Liu L, Nie L (2014) Genetic diversity and population differentiation of the Chinese soft-shelled turtle (Pelodiscus sinensis) in three geographical populations. Biochem Syst Ecol 54:279–284. https://doi.org/10.1016/j.bse.2014.02.022
Cordeiro IR, Yu R, Tanaka M (2020) Regulation of the limb shape during the development of the Chinese softshell turtles. Evol Dev. https://doi.org/10.1111/ede.12352
Danecek P et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158. https://doi.org/10.1093/bioinformatics/btr330
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510. https://doi.org/10.1038/nrg3012
Haitao S, Parham JF, Zhiyong F, Meiling H, Feng Y (2008) Evidence for the massive scale of turtle farming in China. Oryx 42:147–150. https://doi.org/10.1017/S0030605308000562
Kruck NC, Innes DI, Ovenden JR (2013) New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus). Mol Ecol Resour 13:715–725. https://doi.org/10.1111/1755-0998.12112
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Liang HW, Wang LH, Sha H, Zou GW (2019) Development and validation of sex-specific markers in Pelodiscus sinensis using restriction site-associated DNA sequencing. Genes. https://doi.org/10.3390/genes10040302
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. https://doi.org/10.1093/bioinformatics/btq033
Wang Z et al (2013) The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet 45:701-+ https://doi.org/10.1038/ng.2615
Xiong G, Wang X-Q, Zhou X-W, Zeng D, Chen Z-N, Wang P, Kang L (2019) Genetic variation in the Chinese soft-shell turtles (Pelodiscus spp.) revealed by sequences of mitochondrial Cytb gene. Mitochondrial DNA A 30:874–879. https://doi.org/10.1080/24701394.2019.1693551
Xiong L, Nie L, Li X, Liu X (2010) Comparison research and phylogenetic implications of mitochondrial control regions in four soft-shelled turtles of Trionychia (Reptilia, Testudinata). Genes Genomics 32:291–298. https://doi.org/10.1007/s13258-010-0015-8
You FM et al (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinform 9:253. https://doi.org/10.1186/1471-2105-9-253
Zhu L, Li Z, Li J, Feng X, Xie N (2012) Genetic diversity of farmed Chinese soft-shelled turtle (Pelodiscus sinensis) evaluated from microsatellite analysis. J Anim Vet Adv 11:1217–1222
Acknowledgements
We thank Yang Li for providing computer resources.
Funding
This work was supported by the Hefei Independent Innovation Policy ‘loan to supplement’ project (No. J2019G37) and Fishery Industrial System of Anhui Province, China, No. [2021] 711.
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QX and SS conceived of the presented idea. QX and FL experimented. QX developed the theory and performed the computations. JZ and XL verified the analytical methods. QX wrote the manuscript with support from FL, JZ, and XL. GF and RM provided the experiment samples. SS supervised the findings of this work. All authors discussed the results and contributed to the final manuscript.
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This study was followed by the ethical standard of China (GB/T 35892-2018).
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12686_2021_1238_MOESM1_ESM.docx
Supplementary file1 (DOCX 732 kb) The detailed process of data analysis and genetic information of 105 SNP markers can be found in Supplementary Materials 1 and 2.
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Xie, Q., Liu, F., Zhang, J. et al. Development of 105 SNP markers in endangered turtle species Pelodiscus sinensis using RAD-seq. Conservation Genet Resour 14, 27–30 (2022). https://doi.org/10.1007/s12686-021-01238-z
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DOI: https://doi.org/10.1007/s12686-021-01238-z