Abstract
Chloroplasts are difficult to assemble because of the presence of large inverted repeats. At the same time, correct assemblies are important, as chloroplast loci are frequently used for biogeography and population genetics studies. In an attempt to elucidate the orientation of the single-copy regions and to find suitable loci for chloroplast single nucleotide polymorphism (SNP)-based studies, circular chloroplast sequences for the ultra-centenary reference individual of European Beech (Fagus sylvatica), Bhaga, and an additional Polish individual (named Jamy) was obtained based on hybrid assemblies. The chloroplast genome of Bhaga was 158,458 bp, and that of Jamy was 158,462 bp long. Using long-read mapping on the configuration inferred in this study and the one suggested in a previous study, we found an inverted orientation of the small single-copy region. The chloroplast genome of Bhaga and of the individual from Poland both have only two mismatches as well as three and two indels as compared to the previously published genome, respectively. The low divergence suggests low seed dispersal but high pollen dispersal. However, once chloroplast genomes become available from Pleistocene refugia, where a high degree of variation has been reported, they might prove useful for tracing the migration history of Fagus sylvatica in the Holocene.
Highlights
The European Beech is a dominant species in Germany and other parts of CentralEurope [1]
As one of the most important forest trees of central Europe, the European beech has been intensely studied throughout the past decades with respect to its ecology [33,34,35], phenology [36,37], and population genetics [11,38]
For maternal inheritance, which can inform about seed dispersal rates, phylogeography, migration, and tracking of historic and current humanmediated seed transfer, chloroplast-based analyses are useful
Summary
The European Beech is a dominant species in Germany and other parts of CentralEurope [1]. The European Beech is a dominant species in Germany and other parts of Central. The European beech has recently experienced drought stress in several areas [3,4], which probably marks a transition to oak (Quercus robur s.l.) in drier regions of Germany [5]. There are several population genetics studies for European Beech available [7,8,9,10,11,12], and some of them are focused on chloroplast-based genetic diversity [9,13,14,15,16]. Analyses considering SNPs in the complete chloroplast genome are so far lacking, even though such a dataset might help understanding maternal gene flow within local stands and understanding population dynamics and phylogeography in conjunction with past and present climate change [17,18]
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