The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

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1 Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan
2 Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, China
3 Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan, Japan
DOI
10.7287/peerj.preprints.27473v1
Published
Accepted
Subject Areas
Biodiversity, Evolutionary Studies, Genetics, Plant Science
Keywords
beech, chloroplast SSRs, Fagaceae phylogeny, Fagus crenata, whole chloroplast genome
Copyright
© 2019 Worth et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Worth J, Liu L, Tomaru N. 2019. The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana) PeerJ Preprints 7:e27473v1

Abstract

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed between them and differing by 311 single nucleotide polymorphisms. The six most variable regions between the two genomes were the psbK-psbI, trnG-psbfM, trnV, rpl32, ndhD-psaC and ndhI-ndh regions. These highly variable chloroplast regions and the identification of 42 variable chloroplast SSRs found to be shared between the two species will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Details of all the 104 chloroplast SSRs identified in Fagus crenata and F. engleriana including their position in the alignment of the two genomes, length and repeat motif type

DOI: 10.7287/peerj.preprints.27473v1/supp-1

Genbank file of the whole chloroplast genome of Fagus crenata

DOI: 10.7287/peerj.preprints.27473v1/supp-2