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Complete mitochondrial genomes of fivesubspecies of the Eurasian magpie Pica pica,
obtained with Oxford Nanopore MinION, and theirinterpretation regarding intraspecific taxonomy
Alexey P. Kryukov , Liudmila N. Spiridonova , Alexey P. Tyunin , Kirill A.
Kryukov & Beatriz A. Dorda
To cite this article: Alexey P. Kryukov , Liudmila N. Spiridonova , Alexey P. Tyunin , Kirill
A. Kryukov & Beatriz A. Dorda (2020) Complete mitochondrial genomes of five subspeciesof the Eurasian magpie Pica�pica, obtained with Oxford Nanopore MinION, and theirinterpretation regarding intraspecific taxonomy, Mitochondrial DNA Part B, 5:3, 3810-3811, DOI:
10.1080/23802359.2020.1838354
To link to this article: https://doi.org/10.1080/23802359.2020.1838354© 2020 The Author(s). Published by Informa
UK Limited, trading as Taylor & FrancisGroup.

Published online: 20 Nov 2020.

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MITOCHONDRIAL DNA PART B
2020, VOL. 5, NO. 3, 3810–3811
https://doi.org/10.1080/23802359.2020.1838354

MITOGENOME ANNOUNCEMENT

Complete mitochondrial genomes of five subspecies of the Eurasian magpie Pica
pica, obtained with Oxford Nanopore MinION, and their interpretation regarding
intraspecific taxonomy
Alexey P. Kryukova
Beatriz A. Dordac, Liudmila N. Spiridonovaa, Alexey P. Tyunina, Kirill A. Kryukovbanda
Federal Scientific Center of the East Asia Terrestrial Biodiversity (FSCEATB), Far Eastern Branch of the Russian Academy of Sciences,Vladivostok, Russia; bNational Institute of Genetics, Mishima, Japan; cNational Museum of Natural Science (MNCN-CSIC), Madrid, Spain

ABSTRACTARTICLE HISTORY

The complete mitochondrial (mt) genomes of five subspecies of the Eurasian (Common) magpie Pica
pica were determined for the first time. Lengths of the circular genomes comprise 13 protein-coding
genes, two rRNA genes (for 12S rRNA and 16S rRNA), 22 tRNA genes, and the non-coding control
region (CR). Gene content and lengths of the genomes (16,936–16,945 bp) are similar to typical vertebrate mt genomes. The subspecies studied differs by several single substitutions and indels, especiallyin the CR. The phylogenetic tree based on complete mt genomes shows a deep divergence of the twogroups of subspecies which supports the proposed division into two distinct species: P. pica andP. serica.

Received 21 September 2020
Accepted 8 October 2020

Complete mitochondrial (mt) genomes are still rarely
explored in intraspecies systematics. Taxonomy, species borders, and intraspecies structure of the Eurasian (Common)
magpie Pica pica L. (Passeriformes, Corvidae) are a matter ofdebate. It is widespread in the Holarctic. For the Palearctictaxa, taxonomy varies from accepting a single species with
12 subspecies (Madge and Burn 1999; Kryukov et al. 2017) todivision into four species (Song et al. 2018). Only one complete mt genome of P. pica has been reported previously(GenBank HQ915867). Here, we describe the complete mt
genomes of five subspecies (sensu Kryukov et al. 2017) ofmagpie and use them for assessing intraspecies relationships.
Tissue (blood or feather) samples were collected: P. p.
camtschatica in Kamchatka Peninsula, Russia (54.30N,156.00E); P. p. jankowskii in Primorsky Krai, Russia (43.84N,131.86E); P. p. fennorum in Moscow region, Russia (55.75N,38.01E); P. p. leucoptera in Mongolia (48.45N, 115.35E); P. p.
melanotos in Buitrago del Lozoya, Spain (40.99N, 3.64W). The
samples are stored in the tissue and DNA collections of
FSCEATB, Russia (#2320 for camtschatica, #2205 for jankowskii, #1215 for fennorum, and #2385 for leucoptera), and
MNCN, Spain (#2804 for melanotos). DNA was extracted withDNeasy Blood and Tissue kit (Qiagen, Hilden, Germany). Twoprimer pairs were designed for the amplification of two overlapping fragments: mtPica-66F (GACAAAAGACTTAGTCC
TAACCTTACTGTT) and mtPica-7010R (GTGGTTTATGCGG
TTGGCTTGAA) for a 7-kb fragment; mtPica-5359F(CCTCTGTAAAAAGGACTACAGCCTA)
andmtPica-68R
CONTACT Alexey P. Kryukovalex.p.kryukov@gmail.com
Academy of Sciences, Vladivostok 690022, Russia

KEYWORDS

Mitochondrial genome;
Eurasian magpie; Pica pica;
Pica serica; Corvidae(AGTAAGGTTAGGACTAAGTCTTTTG) for a 11-kb fragment.
The amplicons obtained were individually tagged with barcode sequences and sequenced using the Oxford Nanopore
MinION with Flow Cell R10 and the protocol ‘1d-native-barcoding-genomic-dna-NBE_9065_v109_revI_23May2018.’ Thereads were aligned one by one to the reference genome
HQ915867 with AliView v. 1.17.1 (Larsson 2014) and consensus sequences were completed using Consensus Tool (http://kirr.dyndns.org/bio/consensus/). Annotation was performedwith MITOS (Bernt et al. 2013).
The assembled genomes are 16,936–16,945 bp in lengthand each contains 37 genes comprising 13 protein-coding
genes, two rRNA genes (for 12S rRNA and 16S rRNA), and 22
tRNA genes. The control region (CR) is located betweentRNA-Glu and tRNA-Phe genes and has a length of
1351–1362 bp. The H- and L-strands encode 28 and nine
genes, respectively. The gene arrangement is the same in all
genomes studied. GC content of the new genomes is43.3–43.5%. Proportions of A, T, C, and G in subspecies havethe following ranges (in %): 31–31.1, 25.4–25.6, 29.2–29.5,
and 14.0–14.1, respectively.
For illustrating phylogenetic relations of the complete mt
genomes obtained, we constructed a maximum-likelihood(ML) tree (Figure 1) using MEGA X (Kumar et al. 2018).
The western group of subspecies includes fennorum, melanotos, leucoptera, as well as geographically distant camtschatica. Jankowskii is nearly identical to HQ915867. The twoclades are well differentiated by p-distance of .039 onFederal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russianß 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,distribution, and reproduction in any medium, provided the original work is properly cited.

MITOCHONDRIAL DNA PART B

3811Funding
The study was partly supported by the Far East Basic Research Programof the Far Eastern Branch of the Russian Academy of Sciences, grant [No.
18-4-031].

ORCID
Figure 1. Maximum-likelihood phylogenetic tree for the five newly obtainedcomplete mitochondrial genomes of Pica pica s.l., and the previously determined sequence of Pica pica (GenBank HQ915867). Garrulus glandarius(JN018413) is used as outgroup. Numbers at nodes are bootstrap support values
in %.

average. In general, this is consistent with the previous
results obtained using individual genes: cytB and CR (Kryukov
et al. 2004, 2017; Haring et al. 2007); cytB, ND2, and twonuclear introns (Song et al. 2018). This degree of divergencesupports classifying the two clades as separate species.
The subspecies name of HQ915867 is not mentioned in its
GenBank entry. Its near identity to jankowskii suggests that it
could belong to jankowskii or a closely related subspecies,
such as serica or anderssoni. Kryukov et al. (2017) showedclose affinity of serica and jankowskii, while Song et al. (2018)
showed near identity of serica and anderssoni, and suggested
grouping them under Pica serica species. Based on our complete mt genome data, we support classifying Pica serica as aspecies, distinct from P. pica (the western clade). Pica serica
species may include jankowskii, serica, and anderssoni subspecies.
Continuation of genomic studies is necessary for clarifying
taxonomy of the remaining subspecies.

Acknowledgements
We are grateful for Elisabeth Haring for editing the manuscript. We arethankful to Yaroslav Redkin and Eugeny Lobkov for providing samples.

Disclosure statement
No potential conflicts of interest were reported by the author(s).

Alexey P. Kryukov
http://orcid.org/0000-0001-7010-7338
http://orcid.org/0000-0001-8712-9752
Liudmila N. Spiridonova
Alexey P. Tyunin
http://orcid.org/0000-0002-6467-8596
http://orcid.org/0000-0002-0286-0288
Kirill A. Kryukov
http://orcid.org/0000-0002-2741-1841
Beatriz A. Dorda

Data availability statement
The data that support the findings of this study are openly available in
the National Center for Biotechnology Information database (NCBI/GenBank) at https://www.ncbi.nlm.nih.gov/, reference numbers
MT792352, MT792353, MT792354, MT792355, and MT792356.

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