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

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.

Niche conservatism and strong phylogenetic signals in climate, soil, and morphological variation of Neotropical firs (Abies, Pinaceae)

“…We inferred that Mesoamerican fir divergence began in northern Mexico during the Pliocene (~4.8 Ma), coinciding with the earliest pollen remains in Mexico (Graham, 1976, 1999) and consistent with previous inferences for this clade (Semerikova et al, 2018, 2022). These estimated ages are, however, younger than those previously inferred based on plastid and nuclear DNA evidence (Aguirre‐Planter et al, 2012; Xiang et al, 2015).…”

Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data

“…4 and 5 ) represent the most extensive sets of genes from the three plant genomes for Abies phylogenetics. Our analyses were largely consistent with previous studies based on the nuclear ITS region 3 , five plastid genes, and a single nuclear locus 4 ; and a combined analysis of six mitochondrial, plastid, and nuclear ITS regions 2 ; and large portion of the mitochondrial genes 9 . Collectively, these studies demonstrate that Abies is monophyletic and sister to the genus Keteleeria .…”

“…Genomic resources can provide the opportunity for a comprehensive understanding of the origin and evolution of this hierarchical complexity. Recent research has examined the genome-scale biogeography of the genus Abies ; however, only the mitogenome has been used 9 .…”

Common methods in mitochondrial research (Review)

“…PcR, as a molecular biology technology that emerged in the 1980s, is a method for enzymatically synthesizing and amplifying specific nucleic acid fragments in vitro based on the semi-conservative replication mechanism of dNA. This can purposefully amplify target regions and is especially suitable for enriching small-scale genomes such as mtdNA (349)(350)(351)(352)(353). However, mtdNA is present in primer-binding regions, but accuracy is not sufficient due to heterogeneity.…”

“…However, mtdNA is present in primer-binding regions, but accuracy is not sufficient due to heterogeneity. Over time, reverse transcription-quantitative (RT-q) PCR is able to monitor the number of amplified DNA molecules in real time, facilitating the determination of mtdNA in individual cells, along with the copy number and other impairments (deletions) (350)(351)(352). As a contemporaneous product of PCR, FISH is also a classic specific detection method.…”