A Circular Chloroplast Genome of Fagus sylvatica Reveals High Conservation between Two Individuals from Germany and One Individual from Poland and an Alternate Direction of the Small Single-Copy Region

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.

A Comparison of Three Circular Mitochondrial Genomes of Fagus sylvatica from Germany and Poland Reveals Low Variation and Complete Identity of the Gene Space

“…The same three individuals had previously been used for assessing chloroplast genome diversity in northern central Europe [23]. In line with the low diversity found among the three chloroplast genomes [18,23], also the mitochondrial genome showed little variation when comparing the three individuals. Apart from seven indel positions, 19 SNP positions were found, but none was located within a gene.…”

“…Thus, it was the aim of this study to provide additional complete mitochondrial sequences from the two other individuals from which chloroplast sequences had been obtained previously [23]. These were the more than 300-year-old reference individual Bhaga from the National Park Kellerwald-Edersee in Germany [24], which corresponds to the centre of the current distribution range, and a younger individual, Jamy, sampled from the Jamy Nature Reserve in Poland, corresponding to the north-eastern area of the distribution range.…”

“…The PacBio reads were double corrected by first performing a correction with Illumina reads using proovread [25], which was followed by self-correction using Canu [26]. Double-corrected PacBio reads were aligned with five different plant mitochondrial genomes using BLAST, as described previously [23]. All PacBio reads with a match over more than 50% of their length to any of the targets were used for the construction of an assembly using Canu.…”

“…The sequence of the mitochondrial genome was annotated as described previously for the chloroplast genome of Bhaga [23], using GeSeq ChloroBox [31] but with the sequence MT446430.1 [22] as reference for CDS + rRNA prediction and manual corrections performed using Unipro UGENE [32] assisted by bwa-mem [33]. Duplicate annotations were removed from the GenBank file manually, and the resulting file was used to obtain a graphical representation using OGDraw of the GeSeq Chlorobox package.…”

“…The mitochondrial genome of the reference individual Bhaga from the National Park Kellerwald-Edersee in central Germany and the individual Jamy from the Jamy Nature Reserve in northern Poland were assembled and compared with the mitochondrial genome previously published for an individual from eastern Germany [22]. The same three individuals had previously been used for assessing chloroplast genome diversity in northern central Europe [23]. In line with the low diversity found among the three chloroplast genomes [18,23], also the mitochondrial genome showed little variation when comparing the three individuals.…”