Sequence Capture of Mitochondrial Genome with PCR-Generated Baits Provides New Insights into the Biogeography of the Genus Abies Mill.

Semerikov, Vladimir L.; Semerikova, Svetlana A.; Khrunyk, Yuliya Y.; Putintseva, Yuliya A.

doi:10.3390/plants11060762

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Sequence Capture of Mitochondrial Genome with PCR-Generated Baits Provides New Insights into the Biogeography of the Genus Abies Mill.

Vladimir L. Semerikov

^1,*,

Svetlana A. Semerikova

¹,

Yuliya Y. Khrunyk

and

Yuliya A. Putintseva

Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 620144 Ekaterinburg, Russia

Department of Heat Treatment and Physics of Metal, Ural Federal University Named after the First President of Russia B.N. Yeltsin, 620002 Ekaterinburg, Russia

Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia

Author to whom correspondence should be addressed.

Academic Editor: Alex Troitsky

Plants 2022, 11(6), 762; https://doi.org/10.3390/plants11060762

Received: 23 November 2021 / Revised: 10 March 2022 / Accepted: 11 March 2022 / Published: 13 March 2022

(This article belongs to the Special Issue New Systematics)

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Abstract

Mitochondrial DNA (mtDNA), being maternally inherited in plants of the family Pinaceae, is an important source of phylogeographic information. However, its use is hindered by a low mutation rate and frequent structure rearrangements. In the present study, we tested the method of genomic libraries enrichment with mtDNA via the sequence capture method yielding mtDNA data which were further used to reconstruct the phylogenetic tree of the genus Abies. The baits for hybrid capture were obtained by long-range PCR using primers designed on the basis of the assembly of Abies sibirica Ledeb. mitochondrial genome. Mitochondrial genomes of Picea sitchensis (Bong.) Carr., Larix sibirica Ledeb., and Keteleeria davidiana (Bertrand) Beissn. were used as an outgroup. The resulting phylogenetic tree consists of two sister branches, including the Eurasian and American species, respectively, with some exceptions. The subclade of A. sachalinensis (F. Schmidt) Mast. and A. veitchii Lindl. (Japan and Sakhalin islands) occupies a basal position in the branch of American firs, probably due to the complex history of fir migrations from North America to Eurasia. The tree has high support for majority of clades. For species represented by more than one sample an intraspecific variability was found which is suitable to design mtDNA markers for phylogeographic and population studies. View Full-Text

Keywords: intercontinental migrations; mitochondrial DNA; target enrichment; phylogeny; molecular dating

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MDPI and ACS Style

Semerikov, V.L.; Semerikova, S.A.; Khrunyk, Y.Y.; Putintseva, Y.A. Sequence Capture of Mitochondrial Genome with PCR-Generated Baits Provides New Insights into the Biogeography of the Genus Abies Mill. Plants 2022, 11, 762. https://doi.org/10.3390/plants11060762

AMA Style

Semerikov VL, Semerikova SA, Khrunyk YY, Putintseva YA. Sequence Capture of Mitochondrial Genome with PCR-Generated Baits Provides New Insights into the Biogeography of the Genus Abies Mill. Plants. 2022; 11(6):762. https://doi.org/10.3390/plants11060762

Chicago/Turabian Style

Semerikov, Vladimir L., Svetlana A. Semerikova, Yuliya Y. Khrunyk, and Yuliya A. Putintseva. 2022. "Sequence Capture of Mitochondrial Genome with PCR-Generated Baits Provides New Insights into the Biogeography of the Genus Abies Mill." Plants 11, no. 6: 762. https://doi.org/10.3390/plants11060762

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Sequence Capture of Mitochondrial Genome with PCR-Generated Baits Provides New Insights into the Biogeography of the Genus Abies Mill.

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