Complete Chloroplast Genomes of Fagus sylvatica L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs.

Bartosz Ulaszewski,Marco Thines,Joanna Meger,Bagdevi Mishra,Jarosław Burczyk

doi:10.3390/genes12091357

Abstract

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.

Highlights

Chloroplasts play a key role in photosynthesis and other metabolic processes of green plants [1]
Chloroplast genome structure was stable throughout the studied sequences, and assembly sizes varied from 158,391 bp to 158,464 bp, with highest length variance observed in the large single copy region (LSC) (87,634–87,706 bp)
To the previously published F. sylvatica chloroplast assemblies [26,39] each of the 16 new genomes had an identical set of 131 annotated elements: 83 protein coding genes, 8 rRNAs and 40 tRNAs

Summary

Introduction

Chloroplasts play a key role in photosynthesis and other metabolic processes of green plants [1]. With an increased availability of whole chloroplast sequences, numerous studies demonstrated the presence of variation among individuals within species, which includes SNPs, indels, inversions, translocations, copy number variations and IR expansion, gene loss and intron retention [14]. The level of this variability is usually considered low, both in terms of composition, as well as in terms of the degree of variation within the different regions [14,15,16,17]. While chloroplast genomes can be a good tool for phylogeographic analyses, such studies are currently limited to only few conifers [16,17]

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