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

• Published in: Plants
• Main Authors: Semerikov, V. L., Semerikova, S. A., Khrunyk, Y. Y., Putintseva, Y. A.
• Format: Article in Journal/Newspaper
• Language: English
• Published: MDPI 2022
• Subjects: INTERCONTINENTAL MIGRATIONS; MITOCHONDRIAL DNA; MOLECULAR DATING; PHYLOGENY; TARGET ENRICHMENT; Sakhalin
• Online Access: http://elar.urfu.ru/handle/10995/111108; https://doi.org/10.3390/plants11060762

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. © 2022 by the authors. Licensee MDPI, Basel, Switzerland. Funding: This research was funded by the Russian Foundation for Basic Research, grant no. 19-04-00795 and by the State Contract of the Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, no. 122021000090-5.