Abstract
Deer species has both scientific research and economic value, and half of these species, however, are listed as endangered animals. For the conservation purpose, we designed a novel universal deer-specific PCR primer pair based on an evolutionarily conservative coding sequence (i.e., CEP295NL gene) across some deer species. This primer pair was successfully amplified and sequenced, showing around ~ 540 bp in cervids. Validation results showed that it can be utilized to develop a reliable and simple diagnostic tool for distinguishing other closely related species, as well as possibly interspecific identification amongst cervids.
References
Abernethy K (2008) The establishment of a hybrid zone between red and sika deer (genus Cervus). Mol Ecol 3:551–562
Ba H et al (2020) Chromosome-level genome assembly of Tarim red deer Cervus elaphus yarkandensis. Sci Data 7:187. https://doi.org/10.1038/s41597-020-0537-0
Bana NA et al (2018) The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes. Mol Genet Genomics 293:665–684. https://doi.org/10.1007/s00438-017-1412-3
Bartos L, Bubenik G (2011) Relationships between rank-related behaviour, antler cycle timing and antler growth in deer behavioural aspects. Anim Prod Sci 51:303–310
Blix AS (2016) Adaptations to polar life in mammals and birds. J Exp Biol 219:1093–1105. doi:https://doi.org/10.1242/jeb.120477
Chen L et al (2019) Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science. https://doi.org/10.1126/science.aav6202
de Jong MJ, Li Z, Qin Y, Quemere E, Baker K, Wang W, Hoelzel AR (2020) Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene. Mol Ecol. https://doi.org/10.1111/mec.15450
Derr JN, Hale DW, Ellsworth DL, Bickham JW (1991) Fertility in an F1 male hybrid of white-tailed deer (Odocoileus virginianus) × mule deer (O. hemionus. J Reprod Fertil 93:111–117. https://doi.org/10.1530/jrf.0.0930111
Frank K, Barta E, Bana NA, Nagy J, Horn P, Orosz L, Steger V (2016) Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae. Acta Biol Hung 67:133–147. https://doi.org/10.1556/018.67.2016.2.2
Geist V (1998) Deer of the world, their evolution, behavior, and ecology. Stackpole Books, Mechanicsburg
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174. https://doi.org/10.1007/BF02101694
Hassanin A et al (2012) Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C R Biol 335:32–50. https://doi.org/10.1016/j.crvi.2011.11.002
Kaltenbrunner M, Hochegger R, Cichna-Markl M (2018) Development and validation of a fallow deer (Dama dama)-specific TaqMan real-time PCR assay for the detection of food adulteration. Food Chem 243:82–90. https://doi.org/10.1016/j.foodchem.2017.09.087
Kaltenbrunner M, Hochegger R, Cichna-Markl M (2018) Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products. Sci Rep 8:7236. https://doi.org/10.1038/s41598-018-25299-7
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948
Li C, Yang F, Sheppard A (2009) Adult stem cells and mammalian epimorphic regeneration-insights from studying annual renewal of deer antlers. Curr Stem Cell Res Ther 4:237–251
Li Z et al (2017) Draft genome of the reindeer (Rangifer tarandus). Gigascience 6:1–5. https://doi.org/10.1093/gigascience/gix102
Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS (2020) Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. Commun Biol 3:480. https://doi.org/10.1038/s42003-020-1096-9
Qiao J, Yang W, Gao X (2006) Natural diet and food habitat use of the Tarim red deer, Cervus elaphus yarkandensis. Chin Sci Bull 51:147–152
Randi E, Mucci N, Pierpaoli M, Douzery E (1998) New phylogenetic perspectives on the Cervidae (Artiodactyla) are provided by the mitochondrial cytochrome b gene. Proc Biol Sci 265:793–801. https://doi.org/10.1098/rspb.1998.0362
Russell T, Cullingham C, Kommadath A, Stothard P, Herbst A, Coltman D (2019) Development of a novel mule deer genomic assembly and species-diagnostic SNP panel for assessing introgression in mule deer, white-tailed deer, and their interspecific. hybrids. G3 (Bethesda) 9:911–919. https://doi.org/10.1534/g3.118.200838
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S (2012) Estimating divergence times in large molecular phylogenies. J Proc Nat Acad Sci 109:19333–19338. https://doi.org/10.1073/pnas.1213199109
Wang W et al (2019) The sequence and de novo assembly of hog deer genome. Sci Data 6:180305. https://doi.org/10.1038/sdata.2018.305
Yang Y et al (2020) Rapid identification of cervus antlers by species-specific PCR assay. Nat Prod Res 34:1315–1319. https://doi.org/10.1080/14786419.2018.1560285
Zhang C et al (2018) Draft genome of the milu (Elaphurus davidianus). Gigascience. https://doi.org/10.1093/gigascience/gix130
Acknowledgements
This work was funded by National Natural Science Foundation of China (No. 31402035) and Science and Technology Foundation of Jilin Province of China (No. 20200602013ZP). We wish to thank Dr. Zhipeng Li for his deer DNA samples.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no competing interests.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Electronic supplementary material 1 (PDF 330 kb)
Figure S1 Design of a universal PCR primer pair across 12 deer species on CEP295NL gene. WL: white-lipped; PD: Pere David's; BM: black muntjac; RM: Reeves muntjac; EE: Eurasian elk; CW: Chinese water; WT: white-tailed
Rights and permissions
About this article
Cite this article
Xie, L., Deng, Y., Shao, X. et al. Design of a universal primer pair for the identification of deer species. Conservation Genet Resour 13, 9–12 (2021). https://doi.org/10.1007/s12686-020-01176-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-020-01176-2