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 pu… Show more
“…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.…”
Section: Resultsmentioning
confidence: 96%
“…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.…”
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
“…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.…”
Section: Resultsmentioning
confidence: 96%
“…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.…”
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
“…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.…”
Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (He) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a min–max scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also supports the hypothesis that different lineages met and admixed north of the European mountain ranges. As a result, we present a map of genetic diversity across the range of European beech which could help to identify seed source populations harboring greater diversity and guide sampling strategies for future genome-wide and functional investigations of genetic variation. Our approach illustrates how to combine information from several nuclear microsatellite data sets to describe patterns of genetic diversity extending beyond the geographic scale or mean number of loci used in each individual study, and thus is a proof-of-concept for synthesizing knowledge from existing studies also in other species.
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