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First Evidence of Heteroplasmy in Grey Partridge (Perdix

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First Evidence of Heteroplasmy in Grey Partridge (Perdix Pizzirani et al. Avian Res (2020) 11:27 https://doi.org/10.1186/s40657-020-00213-w Avian Research LETTER TO THE EDITOR Open Access First evidence of heteroplasmy in Grey Partridge (Perdix perdix) Claudia Pizzirani1,2, Paolo Viola2, Federica Gabbianelli3, Anna Fagotti1, Francesca Simoncelli1, Ines Di Rosa1, Paolo Salvi4, Andrea Amici2 and Livia Lucentini1* Abstract We report for the frst time the occurrence of heteroplasmy in Grey Partridge (Perdix perdix) revealed by means of two mitochondrial fragments. The possible serious biological and management implications of this exception to unilateral inheritance of mtDNA were underlined. Keywords: Galliformes, Grey Partridge, Heteroplasmy, Hybridization, Perdix perdix Correspondence 2007; Barbanera et al. 2009) and Sanger sequencing Te Grey Partridge (Perdix perdix Linnaeus, 1758) is a was outsourced for both ends of amplicons to Eurofns polytypic Galliform species included in the Least Con- Genomics. cern (LC) category of the IUCN Red List of Treatened All sequences of 561 bp for D-loop and of 334 bp for Species at both global (Staneva and Burfeld 2017) and COI were screened manually looking for double peaks in national scale (Peronace et al. 2012). Considering that, order to evaluate the presence and to validate point het- to date, Grey Partridge’s population genetics is based eroplasmy (Ramos et al. 2013). We found out that, out of on mtDNA (Andersen and Kahlert 2012), and that het- 102 individuals, nine showed point heteroplasmy in the eroplasmy has been previously described specifcally D-loop fragment (Fig. 1A), and two in COI gene. Both in hybrids and other Galliform species (Barr et al. 2005; mutations are missense, causing in the frst case the sub- Gandolf et al. 2017), we decided to investigate the pres- stitution of an Isoleucine (AUU) by a Serine (AGU) while ence of this phenomenon in P. perdix. in the other case a Glycine (CAA) was substituted by an During this research, both wild and farm animals were Arginine (CGA). analyzed (102 samples, Additional fle 1); as concerns Diferent haplotypes were retrieved and deposited in wild animals, both present and historical (see Gandolf GenBank (Accession Numbers MN413488–MN413500, et al. 2017 for “historical” defnition), P. perdix samples MT649222–MT649228 for D-loop and MN480303– were characterized, whereas as to contemporary live MN480304, MT649229–MT649247 for COI). samples, non-invasive specimens belonged both to hus- Specimens presenting clear heteroplasmic D-loop sin- bandries or were sampled in nature (feather or faeces). gle mutation sites and others showing electropherograms DNA was extracted through a specifcally modifed suggesting D-loop heteroplasmy insertion/deletion, were protocol (Lucentini et al. 2010), and two mitochondrial cloned using pGEM-T Easy vector (Promega) following genes, Cytochrome Oxidase Subunit I (COI) and Con- the manufacturer’s instructions. Te analysis of clones trol Region (CR/D-loop), were amplifed (Kerr et al. strongly confrms the presence of heteroplasmy and the absence of any contamination. In fact, obtained clones, *Correspondence: [email protected] when sequenced, showed two diferent haplotypes, con- 1 Department of Chemistry, Biology and Biotechnologies (DCBB), frming the presence of more than one mtDNA in each University of Perugia, 06100 Perugia, Italy Full list of author information is available at the end of the article cloned sample (Fig. 1B). © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/ zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Pizzirani et al. Avian Res (2020) 11:27 Page 2 of 3 Fig. 1 A Example of D-loop heteroplasmy in Perdix samples. Example of polymorphic site (b) (GenBank MN413492), clearly showing mtDNA heteroplasmy compared with homoplasmic samples for this site (a) (GenBank MN413497) (c) (GenBank MN413494). B Electropherogram of one of the cloned samples and of two related clones (MN413488–MN413489) Furthermore, to rule out possible contaminations, Obtained related sequences were registered in GenBank 39 individuals, including the nine heteroplasmic ones, (MN442418–MN442421). were genotyped with a nuclear gene, the Oocyte matu- In conclusion, this study provides the frst evidence ration factor (c-mos) using both primers appropriately of mitochondrial heteroplasmy in Perdix perdix, a phe- designed for this purpose (CMOS2F; F5′-3′GCT GTG nomenon that can create some ambiguities in phyloge- AAG CAA GTG AAG AA; CMOS2 R; R5′-3′AGC CGA netic and evolutionary interpretations. In fact, paternal AGT CTC CAA TCT T) and those described by Shen mtDNA could lead to inaccurate estimates of divergence et al. (2014). Te analysis of this nuclear locus never times if the molecular clock is used, and could confuse showed any double peaks and/or signal superimposition, the putative haplogroup assignment. Furthermore, the thus excluding the presence of sample contamination. data obtained, suggesting the occurrence of hybridization in Perdix perdix, strongly underlined the importance of Pizzirani et al. Avian Res (2020) 11:27 Page 3 of 3 the rapid adoption of control measures aimed to prevent Consent for publication Not applicable. the introduction of genomes from diferent geographical areas and to avoid the concrete risk of an extinction vor- Competing interests tex to which the residual, small and isolated populations The authors declare that they have no competing interests. are segregated. Author details Further researches should focus to advance the knowl- 1 Department of Chemistry, Biology and Biotechnologies (DCBB), University 2 edge on the hybridization scheme of Perdix species and of Perugia, 06100 Perugia, Italy. Department of Agriculture and Forest Sci- ence (DAFNE), University of Tuscia, 01100 Viterbo, Italy. 3 Department for Inno- on the possible interfertile species, to better under- vation in Biological Agro-food and Forest Systems (DIBAF), University of Tuscia, stand the evolutionary history of the species and its 01100 Viterbo, Italy. 4 Parco Nazionale dei Monti Sibillini, 62039 Visso, MC, Italy. management. Received: 16 April 2020 Accepted: 22 July 2020 Supplementary information Supplementary information accompanies this paper at https ://doi. org/10.1186/s4065 7-020-00213 -w. References Andersen LW, Kahlert J. Genetic indications of translocated and stocked grey Additional fle 1. Data about samples used in this study. partridges (Perdix perdix): does the indigenous Danish grey partridge still exist? Biol J Linn Soc. 2012;105:694–710. Barbanera F, Guerrini M, Khan AA, Panayides P, Hadjigerou P, Sokos C, et al. Acknowledgements Human-mediated introgression of exotic chukar (Alectoris chukar, Gal- Authors would like to thank the Natural History Museum of the University of liformes) genes from East Asia into native Mediterranean partridges. Biol Pisa, the Civic Museum of Zoology of Rome, the Casalina’s Gallery of Natural Invas. 2009;11:333–48. History and the Natural History Museum of Fisiocritici of Siena. Barr CM, Neiman M, Taylor DR. Inheritance and recombination of mitochon- drial genomes in plants, fungi and animals: Research review. New Phytol. Authors’ contributions 2005;168:39–50. AA, PV and LL conceived and designed the research. PV, PS and AA acquired Gandolf A, Crestanello B, Fagotti A, Simoncelli F, Chiesa S, Girardi M, et al. New samples. CP, FG and LL performed the sample analysis. LL, AF and AA analyzed evidences of mitochondrial DNA heteroplasmy by putative paternal the data. PV, LL, CP, FS, IDR and AA conducted manuscript preparation, revis- leakage between the Rock Partridge (Alectoris graeca) and the Chukar ing and analysis of intellectual contents. LL and AA contributed equally to the Partridge (Alectoris chukar). PLoS ONE. 2017;12:e0170507. extent of this research. All authors read and approved the fnal manuscript. Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN. Compre- hensive DNA barcode coverage of North American birds. Mol Ecol Notes. Funding 2007;7:535–43. Not applicable. Lucentini L, Gigliarelli L, Puletti ME, Volpi L, Panara F. Comparison of conserva- tive DNA extraction methods for two Galliformes: grey partridge (Perdix Availability of data and materials perdix italica, Hartert 1917) and red-legged partridge (Alectoris rufa, Lin- Sample number and origin of each sample was reported. In particular a naeus 1758). Conserv Genet Resour. 2010;2:381–4. geographical origin or a museum/collection collocation was specifed, if appli- Peronace V, Cecere J, Gustin M, Rondinini C. Lista rossa degli uccelli nidifcanti cable. Furthermore, details about GenBank code on D-Loop, COI and c-mos in Italia. Avocetta. 2012;36:11–58. fragment were provided. Diferent haplotypes were retrieved and deposited in Ramos A, Santos C, Mateiu L, del Mar Gonzalez M, Alvarez L, Azevedo L, et al. GenBank (Accession Numbers MN413488–MN413500, MT649222–MT649228 Frequency and pattern of heteroplasmy in the complete human mito- for Dloop, MN480303–MN480304, MT649229–MT649247 for COI and chondrial genome. PLoS ONE. 2013;8:e74636. MN442418–MN442421 for c-mos). Shen Y-Y, Dai K, Cao X, Murphy RW, Shen X-J, Zhang Y-P. The updated phy- logenies of the Phasianidae based on combined data of nuclear and Ethics approval and consent to participate mitochondrial DNA.
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