TY  - JOUR
A1  - Ulaszewski, Bartosz
A1  - Meger, Joanna
A1  - Mishra, Bagdevi
A1  - Thines, Marco
A1  - Burczyk, Jarosław
T1  - Complete chloroplast genomes of Fagus sylvatica L. reveal sequence conservation in the inverted repeat and the presence of allelic variation in NUPTs
T2  - Genes
N2  - Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of Fagus sylvatica, an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution. Our results confirm the hypothesis of a low cpDNA diversity in European beech. The chloroplast genome size was remarkably stable (158,428 ± 37 bp). The polymorphic markers, 12 microsatellites (SSR), four SNPs and one indel, were found only in the single copy regions, while inverted repeat regions were monomorphic both in terms of length and sequence, suggesting highly efficient suppression of mutation. The within-individual analysis of polymorphisms showed >9k of markers which were proportionally present in gene and non-gene areas. However, an investigation of the frequency of alternate alleles revealed that the source of this diversity originated likely from nuclear-encoded plastome remnants (NUPTs). Phylogeographic and Mantel correlation analysis based on the complete chloroplast genomes exhibited clustering of individuals according to geographic distance in the first distance class, suggesting that the novel markers and in particular the cpSSRs could provide a more detailed picture of beech population structure in Central Europe.
KW  - complete chloroplast genome
KW  - microsatellite
KW  - SNP
KW  - indel
KW  - heteroplasmy
KW  - population genomics
KW  - European beech
Y1  - 2021
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/62184
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-621843
SN  - 2073-4425
N1  - The study was supported by the National Science Center, Poland (2012/04/A/NZ9/00500), the Polish Ministry of Science and Higher Education under the program “Regional Initiative of Excellence” in 2019–2022 (Grant No. 008/RID/2018/19), and the German Science Foundation (Grant No. Thi1362/18-1). Additional support by the LOEWE initiative in the framework of the Centre for Translational Biodiversity Genomics (TBG) is gratefully acknowledged.
VL  - 12
IS  - 9, art. 1357
SP  - 1
EP  - 11
PB  - MDPI
CY  - Basel
ER  -