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

Abstract

Similar to chloroplast loci, mitochondrial markers are frequently used for genotyping, phylogenetic studies, and population genetics, as they are easily amplified due to their multiple copies per cell. In a recent study, it was revealed that the chloroplast offers little variation for this purpose in central European populations of beech. Thus, it was the aim of this study to elucidate, if mitochondrial sequences might offer an alternative, or whether they are similarly conserved in central Europe. For this purpose, a circular mitochondrial genome sequence from the more than 300-year-old beech reference individual Bhaga from the German National Park Kellerwald-Edersee was assembled using long and short reads and compared to an individual from the Jamy Nature Reserve in Poland and a recently published mitochondrial genome from eastern Germany. The mitochondrial genome of Bhaga was 504,730 bp, while the mitochondrial genomes of the other two individuals were 15 bases shorter, due to seven indel locations, with four having more bases in Bhaga and three locations having one base less in Bhaga. In addition, 19 SNP locations were found, none of which were inside genes. In these SNP locations, 17 bases were different in Bhaga, as compared to the other two genomes, while 2 SNP locations had the same base in Bhaga and the Polish individual. While these figures are slightly higher than for the chloroplast genome, the comparison confirms the low degree of genetic divergence in organelle DNA of beech in central Europe, suggesting the colonisation from a common gene pool after the Weichsel Glaciation. The mitochondrial genome might have limited use for population studies in central Europe, but once mitochondrial genomes from glacial refugia become available, it might be suitable to pinpoint the origin of migration for the re-colonising beech population.

A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

“…As it has previously been shown that organelle DNA insertions can be uneven across the genome and associated with chromatin structure ( Wang and Timmis 2013 ), their distribution in the genome of Bhaga was analysed. For both chloroplast ( Mishra et al, 2021a ) and mitochondria ( Mishra et al, 2021b ), multiple integrations of fragments of variable length were observed in all chromosomes (Figures 3 , 4 ). These fragments varied in length from the minimum size threshold (100 bp) to 54,784 bp for the chloroplast and to 26,510 bp for the mitochondrial DNA.…”

“…Separately assembled chloroplast ( Mishra et al, 2021a ) and mitochondrial ( Mishra et al, 2021b ) genomes were aligned to the genomic assembly using blastn with an e-value cut-off of 10e-10 and 100 bp word size. Information for different match lengths and different identity cut-offs were tabulated and analysed.…”

A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia

“…An important solution to the problem of different marker systems, as well as the need to select a priori to study either neutral or functional genetic diversity, is on the horizon in the form of cost-effective whole-genome sequencing and sequence analysis to identify single-nucleotide polymorphisms (SNPs) and other genomic markers. Reference nuclear (Mishra et al 2022), plastid (Mader et al 2019;Mishra et al 2021b), and mitochondrial (Mishra et al 2021a) genomes of F. sylvatica have recently been published. Yet, the currently employed methods for cost-effective SNP identification, such as restriction-site-associated DNA (RAD) sequencing (Peterson et al 2012), tend to bias results toward neutral loci and have high missing data rates.…”